diff --git a/CHANGELOG.md b/CHANGELOG.md
index 717ee40c..5821ece2 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,9 @@
+# biobox 0.3.1
+
+## NEW FUNCTIONALITY
+
+* `bcl_convert`: add `force` argument (PR #171).
+
 # biobox 0.3.0
 
 ## NEW FUNCTIONALITY
@@ -49,6 +55,8 @@
 
 * `umi_tools/umi_tools_extract`: Remove `umi_discard_reads` option and change `log2stderr` to input argument (PR #162).
 
+* `star/star_genome_generate`: Fix passing of optional sjdb parameters (PR #170).
+
 ## MINOR CHANGES
 
 * `agat_convert_bed2gff`: change type of argument `inflate_off` from `boolean_false` to `boolean_true` (PR #160).
diff --git a/_viash.yaml b/_viash.yaml
index d08f2fb2..2fec1f37 100644
--- a/_viash.yaml
+++ b/_viash.yaml
@@ -7,7 +7,7 @@ links:
   issue_tracker: https://github.com/viash-hub/biobox/issues
   repository: https://github.com/viash-hub/biobox
 
-viash_version: 0.9.0
+viash_version: 0.9.2
 
 config_mods: |
   .requirements.commands := ['ps']
diff --git a/src/agat/agat_convert_bed2gff/config.vsh.yaml b/src/agat/agat_convert_bed2gff/config.vsh.yaml
index 4466b5f1..e091d78f 100644
--- a/src/agat/agat_convert_bed2gff/config.vsh.yaml
+++ b/src/agat/agat_convert_bed2gff/config.vsh.yaml
@@ -11,6 +11,8 @@ links:
 references: 
   doi: 10.5281/zenodo.3552717
 license: GPL-3.0
+requirements:
+  commands: ["agat_convert_bed2gff.pl"]
 authors:
   - __merge__: /src/_authors/leila_paquay.yaml
     roles: [ author, maintainer ]
diff --git a/src/agat/agat_convert_embl2gff/config.vsh.yaml b/src/agat/agat_convert_embl2gff/config.vsh.yaml
index 99ceec46..19d8c194 100644
--- a/src/agat/agat_convert_embl2gff/config.vsh.yaml
+++ b/src/agat/agat_convert_embl2gff/config.vsh.yaml
@@ -11,10 +11,11 @@ links:
 references: 
   doi: 10.5281/zenodo.3552717
 license: GPL-3.0
+requirements:
+  commands: ["agat_convert_embl2gff.pl"]
 authors:
   - __merge__: /src/_authors/leila_paquay.yaml
     roles: [ author, maintainer ]
-
 argument_groups:
   - name: Inputs
     arguments:
diff --git a/src/agat/agat_convert_genscan2gff/config.vsh.yaml b/src/agat/agat_convert_genscan2gff/config.vsh.yaml
index 2adce1da..7f54536a 100644
--- a/src/agat/agat_convert_genscan2gff/config.vsh.yaml
+++ b/src/agat/agat_convert_genscan2gff/config.vsh.yaml
@@ -22,11 +22,10 @@ references:
   doi: 10.5281/zenodo.3552717
 license: GPL-3.0
 requirements:
-  - commands: [agat]
+  commands: ["agat_convert_genscan2gff.pl"]
 authors:
   - __merge__: /src/_authors/leila_paquay.yaml
     roles: [ author, maintainer ]
-
 argument_groups:
   - name: Inputs
     arguments:
diff --git a/src/agat/agat_convert_mfannot2gff/config.vsh.yaml b/src/agat/agat_convert_mfannot2gff/config.vsh.yaml
index 625c4613..b34c942a 100644
--- a/src/agat/agat_convert_mfannot2gff/config.vsh.yaml
+++ b/src/agat/agat_convert_mfannot2gff/config.vsh.yaml
@@ -12,9 +12,9 @@ links:
   repository: https://github.com/NBISweden/AGAT
 references: 
   doi: 10.5281/zenodo.3552717
-license: GPL-3.
+license: GPL-3.0
 requirements:
-  - command: [agat]
+  commands: ["agat_convert_mfannot2gff.pl"]
 authors:
   - __merge__: /src/_authors/leila_paquay.yaml
     roles: [ author, maintainer ]
diff --git a/src/agat/agat_convert_sp_gff2gtf/config.vsh.yaml b/src/agat/agat_convert_sp_gff2gtf/config.vsh.yaml
index 757cbd85..7a3c5be5 100644
--- a/src/agat/agat_convert_sp_gff2gtf/config.vsh.yaml
+++ b/src/agat/agat_convert_sp_gff2gtf/config.vsh.yaml
@@ -27,10 +27,11 @@ links:
 references: 
   doi: 10.5281/zenodo.3552717
 license: GPL-3.0
+requirements:
+  commands: ["agat_convert_sp_gff2gtf.pl"]
 authors:
   - __merge__: /src/_authors/leila_paquay.yaml
     roles: [ author, maintainer ]
-
 argument_groups:
   - name: Inputs
     arguments:
diff --git a/src/agat/agat_convert_sp_gff2tsv/config.vsh.yaml b/src/agat/agat_convert_sp_gff2tsv/config.vsh.yaml
index f1c78590..cffdea3a 100644
--- a/src/agat/agat_convert_sp_gff2tsv/config.vsh.yaml
+++ b/src/agat/agat_convert_sp_gff2tsv/config.vsh.yaml
@@ -12,10 +12,11 @@ links:
 references: 
   doi: 10.5281/zenodo.3552717
 license: GPL-3.0
+requirements:
+  commands: ["agat_convert_sp_gff2tsv.pl"]
 authors:
   - __merge__: /src/_authors/leila_paquay.yaml
     roles: [ author, maintainer ]
-
 argument_groups:
   - name: Inputs
     arguments:
diff --git a/src/agat/agat_convert_sp_gxf2gxf/config.vsh.yaml b/src/agat/agat_convert_sp_gxf2gxf/config.vsh.yaml
index 9e77b09d..4ad05673 100644
--- a/src/agat/agat_convert_sp_gxf2gxf/config.vsh.yaml
+++ b/src/agat/agat_convert_sp_gxf2gxf/config.vsh.yaml
@@ -21,10 +21,11 @@ links:
 references: 
   doi: 10.5281/zenodo.3552717
 license: GPL-3.0
+requirements:
+  commands: ["agat_convert_sp_gxf2gxf.pl"]
 authors:
   - __merge__: /src/_authors/leila_paquay.yaml
     roles: [ author, maintainer ]
-
 argument_groups:
   - name: Inputs
     arguments:
diff --git a/src/agat/agat_sp_add_introns/config.vsh.yaml b/src/agat/agat_sp_add_introns/config.vsh.yaml
index 06ec8474..3916c350 100644
--- a/src/agat/agat_sp_add_introns/config.vsh.yaml
+++ b/src/agat/agat_sp_add_introns/config.vsh.yaml
@@ -12,11 +12,10 @@ references:
   doi: 10.5281/zenodo.3552717
 license: GPL-3.0
 requirements:
-  commands: [agat]
+  commands: ["agat_sp_add_introns.pl"]
 authors:
   - __merge__: /src/_authors/leila_paquay.yaml
     roles: [ author, maintainer ]
-
 argument_groups:
   - name: Inputs
     arguments:
diff --git a/src/agat/agat_sp_filter_feature_from_kill_list/config.vsh.yaml b/src/agat/agat_sp_filter_feature_from_kill_list/config.vsh.yaml
index 0608ad4d..80857e23 100644
--- a/src/agat/agat_sp_filter_feature_from_kill_list/config.vsh.yaml
+++ b/src/agat/agat_sp_filter_feature_from_kill_list/config.vsh.yaml
@@ -15,11 +15,10 @@ references:
   doi: 10.5281/zenodo.3552717
 license: GPL-3.0
 requirements:
-  - commands: [agat]
+  commands: ["agat_sp_filter_feature_from_kill_list.pl"]
 authors:
   - __merge__: /src/_authors/leila_paquay.yaml
     roles: [ author, maintainer ]
-
 argument_groups:
   - name: Inputs
     arguments:
diff --git a/src/agat/agat_sp_merge_annotations/config.vsh.yaml b/src/agat/agat_sp_merge_annotations/config.vsh.yaml
index bc47921a..ba87f446 100644
--- a/src/agat/agat_sp_merge_annotations/config.vsh.yaml
+++ b/src/agat/agat_sp_merge_annotations/config.vsh.yaml
@@ -13,7 +13,7 @@ references:
   doi: 10.5281/zenodo.3552717
 license: GPL-3.0
 requirements:
-  commands: [agat]
+  commands: ["agat_sp_merge_annotations.pl"]
 authors:
   - __merge__: /src/_authors/leila_paquay.yaml
     roles: [ author, maintainer ]
diff --git a/src/agat/agat_sp_statistics/config.vsh.yaml b/src/agat/agat_sp_statistics/config.vsh.yaml
index 6890bb84..930ff156 100644
--- a/src/agat/agat_sp_statistics/config.vsh.yaml
+++ b/src/agat/agat_sp_statistics/config.vsh.yaml
@@ -19,11 +19,10 @@ references:
   doi: 10.5281/zenodo.3552717
 license: GPL-3.0
 requirements:
- - commands: [agat]
+  commands: ["agat_sp_statistics.pl"]
 authors:
   - __merge__: /src/_authors/leila_paquay.yaml
     roles: [ author, maintainer ]
-
 argument_groups:
   - name: Inputs
     arguments:
diff --git a/src/agat/agat_sq_stat_basic/config.vsh.yaml b/src/agat/agat_sq_stat_basic/config.vsh.yaml
index 64958991..a0f05830 100644
--- a/src/agat/agat_sq_stat_basic/config.vsh.yaml
+++ b/src/agat/agat_sq_stat_basic/config.vsh.yaml
@@ -12,7 +12,7 @@ references:
   doi: 10.5281/zenodo.3552717
 license: GPL-3.0
 requirements:
- - commands: [agat]
+  commands: ["agat_sq_stat_basic.pl"]
 authors:
   - __merge__: /src/_authors/leila_paquay.yaml
     roles: [ author, maintainer ]
diff --git a/src/bcl_convert/config.vsh.yaml b/src/bcl_convert/config.vsh.yaml
index 81103776..a2c584d7 100644
--- a/src/bcl_convert/config.vsh.yaml
+++ b/src/bcl_convert/config.vsh.yaml
@@ -134,6 +134,13 @@ argument_groups:
         required: false
         description: Reports directory
         example: logs_dir
+      - name: "--force"
+        description: |
+          Allow destination directory to already exist and overwrite files.
+        type: boolean
+        required: false
+        example: true
+
 
 # bcl-convert arguments not taken into account
 #   --force
diff --git a/src/bcl_convert/script.sh b/src/bcl_convert/script.sh
index 6a59acd5..09873062 100644
--- a/src/bcl_convert/script.sh
+++ b/src/bcl_convert/script.sh
@@ -2,9 +2,13 @@
 
 set -eo pipefail
 
+[[ "$par_force" == "false" ]] && unset par_force
+
+
 $(which bcl-convert) \
  --bcl-input-directory "$par_bcl_input_directory" \
  --output-directory "$par_output_directory" \
+  ${par_force:+--force} \
   ${par_sample_sheet:+ --sample-sheet "$par_sample_sheet"} \
   ${par_run_info:+ --run-info "$par_run_info"} \
   ${par_bcl_only_lane:+ --bcl-only-lane "$par_bcl_only_lane"} \
diff --git a/src/star/star_genome_generate/script.sh b/src/star/star_genome_generate/script.sh
index fc232672..02f5e9bb 100644
--- a/src/star/star_genome_generate/script.sh
+++ b/src/star/star_genome_generate/script.sh
@@ -17,10 +17,10 @@ STAR \
     ${par_genome_sa_index_nbases:+--genomeSAindexNbases "${par_genome_sa_index_nbases}"} \
     ${par_sjdb_gtf_chr_prefix:+--sjdbGTFchrPrefix "${par_sjdb_gtf_chr_prefix}"} \
     ${par_sjdb_gtf_feature_exon:+--sjdbGTFfeatureExon "${par_sjdb_gtf_feature_exon}"} \
-    ${par_sjdb_gtf_tag_exon_parent_transcript:+--sjdbGTFtag_exon_parent_transcript "${par_sjdb_gtf_tag_exon_parent_transcript}"} \
-    ${par_sjdb_gtf_tag_exon_parent_gene:+--sjdbGTFtag_exon_parent_gene "${par_sjdb_gtf_tag_exon_parent_gene}"} \
-    ${par_sjdb_gtf_tag_exon_parent_geneName:+--sjdbGTFtag_exon_parent_geneName "${par_sjdb_gtf_tag_exon_parent_geneName}"} \
-    ${par_sjdb_gtf_tag_exon_parent_geneType:+--sjdbGTFtag_exon_parent_geneType "${sjdbGTFtag_exon_parent_geneType}"} \
+    ${par_sjdb_gtf_tag_exon_parent_transcript:+--sjdbGTFtagExonParentTranscript "${par_sjdb_gtf_tag_exon_parent_transcript}"} \
+    ${par_sjdb_gtf_tag_exon_parent_gene:+--sjdbGTFtagExonParentGene "${par_sjdb_gtf_tag_exon_parent_gene}"} \
+    ${sjdb_gtf_tag_exon_parent_gene_name:+--sjdbGTFtagExonParentGeneName "${sjdb_gtf_tag_exon_parent_gene_name}"} \
+    ${sjdb_gtf_tag_exon_parent_gene_type:+--sjdbGTFtagExonParentGeneType "${sjdb_gtf_tag_exon_parent_gene_type}"} \
     ${par_limit_genome_generate_ram:+--limitGenomeGenerateRAM "${par_limit_genome_generate_ram}"} \
     ${par_genome_chr_bin_nbits:+--genomeChrBinNbits "${par_genome_chr_bin_nbits}"} \
     ${par_genome_sa_sparse_d:+--genomeSAsparseD "${par_genome_sa_sparse_d}"} \
diff --git a/src/star/star_genome_generate/test.sh b/src/star/star_genome_generate/test.sh
index 681f3494..efec575b 100644
--- a/src/star/star_genome_generate/test.sh
+++ b/src/star/star_genome_generate/test.sh
@@ -44,5 +44,28 @@ grep -q "200" "star_index/chrLength.txt" || (echo "Chromosome length in file 'ch
 grep -q "chr1" "star_index/chrName.txt" || (echo "Chromosome name in file 'chrName.txt' is incorrect! " && exit 1)
 grep -q "chr1	200" "star_index/chrNameLength.txt" || (echo "Chromosome name in file 'chrNameLength.txt' is incorrect! " && exit 1)
 
+echo "> Test optional parameters"
+"$meta_executable" \
+  ${meta_cpus:+---cpus $meta_cpus} \
+  --index "star_index/" \
+  --genome_fasta_files "genome.fasta" \
+  --sjdb_gtf_file "genes.gtf" \
+  --sjdb_overhang 100 \
+  --genome_sa_index_nbases 4 \
+  --sjdb_gtf_tag_exon_parent_transcript "transcript_id" \
+  --sjdb_gtf_tag_exon_parent_gene "gene_id" \
+  --sjdb_gtf_tag_exon_parent_gene_name "gene_name" \
+  --sjdb_gtf_tag_exon_parent_gene_type "gene_type" \
+  --genome_chr_bin_nbits 10 \
+  --sjdb_gtf_feature_exon "exon"
+
+files=("Genome" "Log.out" "SA" "SAindex" "chrLength.txt" "chrName.txt" "chrNameLength.txt" "chrStart.txt" "exonGeTrInfo.tab" "exonInfo.tab" "geneInfo.tab" "genomeParameters.txt" "sjdbInfo.txt" "sjdbList.fromGTF.out.tab" "sjdbList.out.tab" "transcriptInfo.tab")
+
+echo ">> Check if output exists"
+[ ! -d "star_index" ] && echo "Directory 'star_index' does not exist!" && exit 1
+for file in "${files[@]}"; do
+    [ ! -f "star_index/$file" ] && echo "File '$file' does not exist in 'star_index'." && exit 1
+done
+
 echo ">>> Test finished successfully"
 exit 0
diff --git a/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml b/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml
index dc5fffeb..0e5072fd 100644
--- a/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml
@@ -133,6 +133,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -234,16 +237,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/agat/agat_convert_bed2gff"
   executable: "target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff b/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff
index 21a9a3d6..a04c9e6a 100755
--- a/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff
+++ b/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff
@@ -2,7 +2,7 @@
 
 # agat_convert_bed2gff main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,69 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "agat_convert_bed2gff main"
-  echo ""
-  echo "The script takes a bed file as input, and will translate it in gff format. The"
-  echo "BED format is described here The script converts 0-based, half-open [start-1,"
-  echo "end) bed file to 1-based, closed [start, end] General Feature Format v3 (GFF3)."
-  echo ""
-  echo "Inputs:"
-  echo "    --bed"
-  echo "        type: file, required parameter, file must exist"
-  echo "        example: input.bed"
-  echo "        Input bed file that will be converted."
-  echo ""
-  echo "Outputs:"
-  echo "    -o, --out, --outfile, --gff, --output"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        example: output.gff"
-  echo "        Output GFF file. If no output file is specified, the output will be"
-  echo "        written to STDOUT."
-  echo ""
-  echo "Arguments:"
-  echo "    --source"
-  echo "        type: string"
-  echo "        example: Stringtie"
-  echo "        The source informs about the tool used to produce the data and is stored"
-  echo "        in 2nd field of a gff file. Example: Stringtie, Maker, Augustus, etc."
-  echo "        [default: data]"
-  echo ""
-  echo "    --primary_tag"
-  echo "        type: string"
-  echo "        example: gene"
-  echo "        The primary_tag corresponds to the data type and is stored in 3rd field"
-  echo "        of a gff file. Example: gene, mRNA, CDS, etc. [default: gene]"
-  echo ""
-  echo "    --inflate_off"
-  echo "        type: boolean_true"
-  echo "        By default we inflate the block fields (blockCount, blockSizes,"
-  echo "        blockStarts) to create subfeatures of the main feature (primary_tag)."
-  echo "        The type of subfeature created is based on the inflate_type parameter."
-  echo "        If you do not want this inflating behaviour you can deactivate it by"
-  echo "        using the --inflate_off option."
-  echo ""
-  echo "    --inflate_type"
-  echo "        type: string"
-  echo "        example: exon"
-  echo "        Feature type (3rd column in gff) created when inflate parameter"
-  echo "        activated [default: exon]."
-  echo ""
-  echo "    --verbose"
-  echo "        type: boolean_true"
-  echo "        add verbosity"
-  echo ""
-  echo "    -c, --config"
-  echo "        type: file, file must exist"
-  echo "        example: custom_agat_config.yaml"
-  echo "        Input agat config file. By default AGAT takes as input agat_config.yaml"
-  echo "        file from the working directory if any, otherwise it takes the orignal"
-  echo "        agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally"
-  echo "        type: \"agat config --expose\". The --config option gives you the"
-  echo "        possibility to use your own AGAT config file (located elsewhere or named"
-  echo "        differently)."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -515,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t
 
 LABEL org.opencontainers.image.authors="Leïla Paquay"
 LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_bed2gff"
-LABEL org.opencontainers.image.created="2024-12-03T10:33:51Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:38Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -632,6 +569,95 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "agat_convert_bed2gff main"
+  echo ""
+  echo "The script takes a bed file as input, and will translate it in gff format. The"
+  echo "BED format is described here The script converts 0-based, half-open [start-1,"
+  echo "end) bed file to 1-based, closed [start, end] General Feature Format v3 (GFF3)."
+  echo ""
+  echo "Inputs:"
+  echo "    --bed"
+  echo "        type: file, required parameter, file must exist"
+  echo "        example: input.bed"
+  echo "        Input bed file that will be converted."
+  echo ""
+  echo "Outputs:"
+  echo "    -o, --out, --outfile, --gff, --output"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        example: output.gff"
+  echo "        Output GFF file. If no output file is specified, the output will be"
+  echo "        written to STDOUT."
+  echo ""
+  echo "Arguments:"
+  echo "    --source"
+  echo "        type: string"
+  echo "        example: Stringtie"
+  echo "        The source informs about the tool used to produce the data and is stored"
+  echo "        in 2nd field of a gff file. Example: Stringtie, Maker, Augustus, etc."
+  echo "        [default: data]"
+  echo ""
+  echo "    --primary_tag"
+  echo "        type: string"
+  echo "        example: gene"
+  echo "        The primary_tag corresponds to the data type and is stored in 3rd field"
+  echo "        of a gff file. Example: gene, mRNA, CDS, etc. [default: gene]"
+  echo ""
+  echo "    --inflate_off"
+  echo "        type: boolean_true"
+  echo "        By default we inflate the block fields (blockCount, blockSizes,"
+  echo "        blockStarts) to create subfeatures of the main feature (primary_tag)."
+  echo "        The type of subfeature created is based on the inflate_type parameter."
+  echo "        If you do not want this inflating behaviour you can deactivate it by"
+  echo "        using the --inflate_off option."
+  echo ""
+  echo "    --inflate_type"
+  echo "        type: string"
+  echo "        example: exon"
+  echo "        Feature type (3rd column in gff) created when inflate parameter"
+  echo "        activated [default: exon]."
+  echo ""
+  echo "    --verbose"
+  echo "        type: boolean_true"
+  echo "        add verbosity"
+  echo ""
+  echo "    -c, --config"
+  echo "        type: file, file must exist"
+  echo "        example: custom_agat_config.yaml"
+  echo "        Input agat config file. By default AGAT takes as input agat_config.yaml"
+  echo "        file from the working directory if any, otherwise it takes the orignal"
+  echo "        agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally"
+  echo "        type: \"agat config --expose\". The --config option gives you the"
+  echo "        possibility to use your own AGAT config file (located elsewhere or named"
+  echo "        differently)."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml b/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml
index c503b95a..2ecc8e80 100644
--- a/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml
@@ -123,6 +123,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -224,16 +227,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/agat/agat_convert_embl2gff"
   executable: "target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff b/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff
index 034dd7dd..a4e89183 100755
--- a/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff
+++ b/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff
@@ -2,7 +2,7 @@
 
 # agat_convert_embl2gff main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,59 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "agat_convert_embl2gff main"
-  echo ""
-  echo "The script takes an EMBL file as input, and will translate it in gff format."
-  echo ""
-  echo "Inputs:"
-  echo "    --embl"
-  echo "        type: file, required parameter, file must exist"
-  echo "        example: input.embl"
-  echo "        Input EMBL file that will be read."
-  echo ""
-  echo "Outputs:"
-  echo "    -o, --out, --outfile, --gff, --output"
-  echo "        type: file, output, file must exist"
-  echo "        example: output.gff"
-  echo "        Output GFF file. If no output file is specified, the output will be"
-  echo "        written to STDOUT."
-  echo ""
-  echo "Arguments:"
-  echo "    --emblmygff3"
-  echo "        type: boolean_true"
-  echo "        Means that the EMBL flat file comes from the EMBLmyGFF3 software. This"
-  echo "        is an EMBL format dedicated for submission and contains particularity to"
-  echo "        deal with. This parameter is needed to get a proper sequence id in the"
-  echo "        GFF3 from an embl made with EMBLmyGFF3."
-  echo ""
-  echo "    --pt, -t, --primary_tag"
-  echo "        type: string, multiple values allowed"
-  echo "        example: tag1;tag2"
-  echo "        List of \"primary tag\". Useful to discard or keep specific features."
-  echo "        Multiple tags must be comma-separated."
-  echo ""
-  echo "    -d, --discard"
-  echo "        type: boolean_true"
-  echo "        Means that primary tags provided by the option \"primary_tag\" will be"
-  echo "        discarded."
-  echo ""
-  echo "    -k, --keep"
-  echo "        type: boolean_true"
-  echo "        Means that only primary tags provided by the option \"primary_tag\" will"
-  echo "        be kept."
-  echo ""
-  echo "    -c, --config"
-  echo "        type: file, file must exist"
-  echo "        example: custom_agat_config.yaml"
-  echo "        Input agat config file. By default AGAT takes as input agat_config.yaml"
-  echo "        file from the working directory if any, otherwise it takes the original"
-  echo "        agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally"
-  echo "        type: \"agat config --expose\". The --config option gives you the"
-  echo "        possibility to use your own AGAT config file (located elsewhere or named"
-  echo "        differently)."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -505,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t
 
 LABEL org.opencontainers.image.authors="Leïla Paquay"
 LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_embl2gff"
-LABEL org.opencontainers.image.created="2024-12-03T10:33:53Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:37Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -622,6 +569,85 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "agat_convert_embl2gff main"
+  echo ""
+  echo "The script takes an EMBL file as input, and will translate it in gff format."
+  echo ""
+  echo "Inputs:"
+  echo "    --embl"
+  echo "        type: file, required parameter, file must exist"
+  echo "        example: input.embl"
+  echo "        Input EMBL file that will be read."
+  echo ""
+  echo "Outputs:"
+  echo "    -o, --out, --outfile, --gff, --output"
+  echo "        type: file, output, file must exist"
+  echo "        example: output.gff"
+  echo "        Output GFF file. If no output file is specified, the output will be"
+  echo "        written to STDOUT."
+  echo ""
+  echo "Arguments:"
+  echo "    --emblmygff3"
+  echo "        type: boolean_true"
+  echo "        Means that the EMBL flat file comes from the EMBLmyGFF3 software. This"
+  echo "        is an EMBL format dedicated for submission and contains particularity to"
+  echo "        deal with. This parameter is needed to get a proper sequence id in the"
+  echo "        GFF3 from an embl made with EMBLmyGFF3."
+  echo ""
+  echo "    --pt, -t, --primary_tag"
+  echo "        type: string, multiple values allowed"
+  echo "        example: tag1;tag2"
+  echo "        List of \"primary tag\". Useful to discard or keep specific features."
+  echo "        Multiple tags must be comma-separated."
+  echo ""
+  echo "    -d, --discard"
+  echo "        type: boolean_true"
+  echo "        Means that primary tags provided by the option \"primary_tag\" will be"
+  echo "        discarded."
+  echo ""
+  echo "    -k, --keep"
+  echo "        type: boolean_true"
+  echo "        Means that only primary tags provided by the option \"primary_tag\" will"
+  echo "        be kept."
+  echo ""
+  echo "    -c, --config"
+  echo "        type: file, file must exist"
+  echo "        example: custom_agat_config.yaml"
+  echo "        Input agat config file. By default AGAT takes as input agat_config.yaml"
+  echo "        file from the working directory if any, otherwise it takes the original"
+  echo "        agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally"
+  echo "        type: \"agat config --expose\". The --config option gives you the"
+  echo "        possibility to use your own AGAT config file (located elsewhere or named"
+  echo "        differently)."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/agat/agat_convert_genscan2gff/.config.vsh.yaml b/target/executable/agat/agat_convert_genscan2gff/.config.vsh.yaml
index 6620ba0c..ebc23a02 100644
--- a/target/executable/agat/agat_convert_genscan2gff/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_genscan2gff/.config.vsh.yaml
@@ -127,6 +127,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -229,16 +232,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/agat/agat_convert_genscan2gff"
   executable: "target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff b/target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff
index af5b1266..1d16e2e2 100755
--- a/target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff
+++ b/target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff
@@ -2,7 +2,7 @@
 
 # agat_convert_genscan2gff main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,68 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "agat_convert_genscan2gff main"
-  echo ""
-  echo "The script takes a GENSCAN file as input, and will translate it in gff"
-  echo "format. The GENSCAN format is described"
-  echo "[here](http://genome.crg.es/courses/Bioinformatics2003_genefinding/results/genscan.html)."
-  echo ""
-  echo "**Known problem**"
-  echo ""
-  echo "You must have submited only DNA sequence, without any header!! Indeed the tool"
-  echo "expects only DNA"
-  echo "sequences and does not crash/warn if an header is submited along the"
-  echo "sequence. e.g If you have an header \">seq\" s-e-q are seen as the 3 first"
-  echo "nucleotides of the sequence. Then all prediction location are shifted"
-  echo "accordingly. (checked only on the [online"
-  echo "version](http://argonaute.mit.edu/GENSCAN.html)."
-  echo "I don't know if there is the same problem elsewhere.)"
-  echo ""
-  echo "Inputs:"
-  echo "    -g, --genscan"
-  echo "        type: file, required parameter, file must exist"
-  echo "        Input genscan bed file that will be converted."
-  echo ""
-  echo "Outputs:"
-  echo "    -o, --out, --outfile, --gff, --output"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        example: output.gff"
-  echo "        Output GFF file. If no output file is specified, the output will be"
-  echo "        written to STDOUT."
-  echo ""
-  echo "Arguments:"
-  echo "    --source"
-  echo "        type: string"
-  echo "        example: Stringtie"
-  echo "        The source informs about the tool used to produce the data and is stored"
-  echo "        in 2nd field of a gff file. Example: Stringtie, Maker, Augustus, etc."
-  echo "        [default: data]"
-  echo ""
-  echo "    --primary_tag"
-  echo "        type: string"
-  echo "        example: gene"
-  echo "        The primary_tag corresponds to the data type and is stored in 3rd field"
-  echo "        of a gff file. Example: gene, mRNA, CDS, etc. [default: gene]"
-  echo ""
-  echo "    --inflate_type"
-  echo "        type: string"
-  echo "        example: exon"
-  echo "        Feature type (3rd column in gff) created when inflate parameter"
-  echo "        activated [default: exon]."
-  echo ""
-  echo "    --verbose"
-  echo "        type: boolean_true"
-  echo "        add verbosity"
-  echo ""
-  echo "    -c, --config"
-  echo "        type: file, file must exist"
-  echo "        example: custom_agat_config.yaml"
-  echo "        AGAT config file. By default AGAT takes the original agat_config.yaml"
-  echo "        shipped with AGAT. The \`--config\` option gives you the possibility to"
-  echo "        use your own AGAT config file (located elsewhere or named differently)."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -514,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t
 
 LABEL org.opencontainers.image.authors="Leïla Paquay"
 LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_genscan2gff"
-LABEL org.opencontainers.image.created="2024-12-03T10:33:54Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:37Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -631,6 +569,94 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "agat_convert_genscan2gff main"
+  echo ""
+  echo "The script takes a GENSCAN file as input, and will translate it in gff"
+  echo "format. The GENSCAN format is described"
+  echo "[here](http://genome.crg.es/courses/Bioinformatics2003_genefinding/results/genscan.html)."
+  echo ""
+  echo "**Known problem**"
+  echo ""
+  echo "You must have submited only DNA sequence, without any header!! Indeed the tool"
+  echo "expects only DNA"
+  echo "sequences and does not crash/warn if an header is submited along the"
+  echo "sequence. e.g If you have an header \">seq\" s-e-q are seen as the 3 first"
+  echo "nucleotides of the sequence. Then all prediction location are shifted"
+  echo "accordingly. (checked only on the [online"
+  echo "version](http://argonaute.mit.edu/GENSCAN.html)."
+  echo "I don't know if there is the same problem elsewhere.)"
+  echo ""
+  echo "Inputs:"
+  echo "    -g, --genscan"
+  echo "        type: file, required parameter, file must exist"
+  echo "        Input genscan bed file that will be converted."
+  echo ""
+  echo "Outputs:"
+  echo "    -o, --out, --outfile, --gff, --output"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        example: output.gff"
+  echo "        Output GFF file. If no output file is specified, the output will be"
+  echo "        written to STDOUT."
+  echo ""
+  echo "Arguments:"
+  echo "    --source"
+  echo "        type: string"
+  echo "        example: Stringtie"
+  echo "        The source informs about the tool used to produce the data and is stored"
+  echo "        in 2nd field of a gff file. Example: Stringtie, Maker, Augustus, etc."
+  echo "        [default: data]"
+  echo ""
+  echo "    --primary_tag"
+  echo "        type: string"
+  echo "        example: gene"
+  echo "        The primary_tag corresponds to the data type and is stored in 3rd field"
+  echo "        of a gff file. Example: gene, mRNA, CDS, etc. [default: gene]"
+  echo ""
+  echo "    --inflate_type"
+  echo "        type: string"
+  echo "        example: exon"
+  echo "        Feature type (3rd column in gff) created when inflate parameter"
+  echo "        activated [default: exon]."
+  echo ""
+  echo "    --verbose"
+  echo "        type: boolean_true"
+  echo "        add verbosity"
+  echo ""
+  echo "    -c, --config"
+  echo "        type: file, file must exist"
+  echo "        example: custom_agat_config.yaml"
+  echo "        AGAT config file. By default AGAT takes the original agat_config.yaml"
+  echo "        shipped with AGAT. The \`--config\` option gives you the possibility to"
+  echo "        use your own AGAT config file (located elsewhere or named differently)."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/agat/agat_convert_mfannot2gff/.config.vsh.yaml b/target/executable/agat/agat_convert_mfannot2gff/.config.vsh.yaml
index e04e9331..75a84f3d 100644
--- a/target/executable/agat/agat_convert_mfannot2gff/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_mfannot2gff/.config.vsh.yaml
@@ -83,6 +83,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -90,7 +93,7 @@ keywords:
 - "gene annotations"
 - "GFF"
 - "Mfannot"
-license: "GPL-3."
+license: "GPL-3.0"
 references:
   doi:
   - "10.5281/zenodo.3552717"
@@ -185,16 +188,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/agat/agat_convert_mfannot2gff"
   executable: "target/executable/agat/agat_convert_mfannot2gff/agat_convert_mfannot2gff"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/agat/agat_convert_mfannot2gff/agat_convert_mfannot2gff b/target/executable/agat/agat_convert_mfannot2gff/agat_convert_mfannot2gff
index e25f3622..d451fd0c 100755
--- a/target/executable/agat/agat_convert_mfannot2gff/agat_convert_mfannot2gff
+++ b/target/executable/agat/agat_convert_mfannot2gff/agat_convert_mfannot2gff
@@ -2,7 +2,7 @@
 
 # agat_convert_mfannot2gff main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,34 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "agat_convert_mfannot2gff main"
-  echo ""
-  echo "Conversion utility for MFannot \"masterfile\" annotation produced by the"
-  echo "[MFannot pipeline](http://megasun.bch.umontreal.ca/RNAweasel/). Reports"
-  echo "GFF3 format."
-  echo ""
-  echo "Inputs:"
-  echo "    -m, -i, --mfannot"
-  echo "        type: file, required parameter, file must exist"
-  echo "        example: input.mfannot"
-  echo "        The mfannot input file."
-  echo ""
-  echo "Outputs:"
-  echo "    -g, -o, --gff"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        example: output.gff"
-  echo "        The GFF output file."
-  echo ""
-  echo "Arguments:"
-  echo "    -c, --config"
-  echo "        type: file, file must exist"
-  echo "        example: custom_agat_config.yaml"
-  echo "        AGAT config file. By default AGAT takes the original agat_config.yaml"
-  echo "        shipped with AGAT. The \`--config\` option gives you the possibility to"
-  echo "        use your own AGAT config file (located elsewhere or named differently)."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -480,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t
 
 LABEL org.opencontainers.image.authors="Leïla Paquay"
 LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_mfannot2gff"
-LABEL org.opencontainers.image.created="2024-12-03T10:34:05Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:39Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -597,6 +569,60 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "agat_convert_mfannot2gff main"
+  echo ""
+  echo "Conversion utility for MFannot \"masterfile\" annotation produced by the"
+  echo "[MFannot pipeline](http://megasun.bch.umontreal.ca/RNAweasel/). Reports"
+  echo "GFF3 format."
+  echo ""
+  echo "Inputs:"
+  echo "    -m, -i, --mfannot"
+  echo "        type: file, required parameter, file must exist"
+  echo "        example: input.mfannot"
+  echo "        The mfannot input file."
+  echo ""
+  echo "Outputs:"
+  echo "    -g, -o, --gff"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        example: output.gff"
+  echo "        The GFF output file."
+  echo ""
+  echo "Arguments:"
+  echo "    -c, --config"
+  echo "        type: file, file must exist"
+  echo "        example: custom_agat_config.yaml"
+  echo "        AGAT config file. By default AGAT takes the original agat_config.yaml"
+  echo "        shipped with AGAT. The \`--config\` option gives you the possibility to"
+  echo "        use your own AGAT config file (located elsewhere or named differently)."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml b/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml
index adc17a57..46b7793a 100644
--- a/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml
@@ -126,6 +126,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -227,16 +230,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/agat/agat_convert_sp_gff2gtf"
   executable: "target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf b/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf
index 69c8d41a..81c39676 100755
--- a/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf
+++ b/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf
@@ -2,7 +2,7 @@
 
 # agat_convert_sp_gff2gtf main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,73 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "agat_convert_sp_gff2gtf main"
-  echo ""
-  echo "The script aims to convert any GTF/GFF file into a proper GTF file. Full"
-  echo "information about the format can be found here:"
-  echo "https://agat.readthedocs.io/en/latest/gxf.html You can choose among 7"
-  echo "different GTF types (1, 2, 2.1, 2.2, 2.5, 3 or relax). Depending the"
-  echo "version selected the script will filter out the features that are not"
-  echo "accepted. For GTF2.5 and 3, every level1 feature (e.g nc_gene"
-  echo "pseudogene) will be converted into gene feature and every level2 feature"
-  echo "(e.g mRNA ncRNA) will be converted into transcript feature. Using the"
-  echo "\"relax\" option you will produce a GTF-like output keeping all original"
-  echo "feature types (3rd column). No modification will occur e.g. mRNA to"
-  echo "transcript."
-  echo ""
-  echo "To be fully GTF compliant all feature have a gene_id and a transcript_id"
-  echo "attribute. The gene_id is unique identifier for the genomic source of"
-  echo "the transcript, which is used to group transcripts into genes. The"
-  echo "transcript_id is a unique identifier for the predicted transcript, which"
-  echo "is used to group features into transcripts."
-  echo ""
-  echo "Inputs:"
-  echo "    -i, --gff"
-  echo "        type: file, required parameter, file must exist"
-  echo "        example: input.gff"
-  echo "        Input GFF/GTF file that will be read"
-  echo ""
-  echo "Outputs:"
-  echo "    -o, --out, --outfile, --gtf, --output"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        example: output.gtf"
-  echo "        Output GTF file. If no output file is specified, the output will be"
-  echo "        written to STDOUT."
-  echo ""
-  echo "Arguments:"
-  echo "    --gtf_version"
-  echo "        type: string"
-  echo "        example: 3"
-  echo "        choices: [ relax, 1, 2, 2.1, 2.2, 2.5, 3 ]"
-  echo "        Version of the GTF output (1,2,2.1,2.2,2.5,3 or relax). Default value"
-  echo "        from AGAT config file (relax for the default config). The script option"
-  echo "        has the higher priority."
-  echo "          * relax: all feature types are accepted."
-  echo "          * GTF3 (9 feature types accepted): gene, transcript, exon, CDS,"
-  echo "        Selenocysteine, start_codon, stop_codon, three_prime_utr and"
-  echo "        five_prime_utr."
-  echo "          * GTF2.5 (8 feature types accepted): gene, transcript, exon, CDS, UTR,"
-  echo "        start_codon, stop_codon, Selenocysteine."
-  echo "          * GTF2.2 (9 feature types accepted): CDS, start_codon, stop_codon,"
-  echo "        5UTR, 3UTR, inter, inter_CNS, intron_CNS and exon."
-  echo "          * GTF2.1 (6 feature types accepted): CDS, start_codon, stop_codon,"
-  echo "        exon, 5UTR, 3UTR."
-  echo "          * GTF2 (4 feature types accepted): CDS, start_codon, stop_codon, exon."
-  echo "          * GTF1 (5 feature types accepted): CDS, start_codon, stop_codon, exon,"
-  echo "        intron."
-  echo ""
-  echo "    -c, --config"
-  echo "        type: file, file must exist"
-  echo "        example: custom_agat_config.yaml"
-  echo "        Input agat config file. By default AGAT takes as input agat_config.yaml"
-  echo "        file from the working directory if any, otherwise it takes the orignal"
-  echo "        agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally"
-  echo "        type: \"agat config --expose\". The --config option gives you the"
-  echo "        possibility to use your own AGAT config file (located elsewhere or named"
-  echo "        differently)."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -519,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t
 
 LABEL org.opencontainers.image.authors="Leïla Paquay"
 LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_sp_gff2gtf"
-LABEL org.opencontainers.image.created="2024-12-03T10:33:52Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:37Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -636,6 +569,99 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "agat_convert_sp_gff2gtf main"
+  echo ""
+  echo "The script aims to convert any GTF/GFF file into a proper GTF file. Full"
+  echo "information about the format can be found here:"
+  echo "https://agat.readthedocs.io/en/latest/gxf.html You can choose among 7"
+  echo "different GTF types (1, 2, 2.1, 2.2, 2.5, 3 or relax). Depending the"
+  echo "version selected the script will filter out the features that are not"
+  echo "accepted. For GTF2.5 and 3, every level1 feature (e.g nc_gene"
+  echo "pseudogene) will be converted into gene feature and every level2 feature"
+  echo "(e.g mRNA ncRNA) will be converted into transcript feature. Using the"
+  echo "\"relax\" option you will produce a GTF-like output keeping all original"
+  echo "feature types (3rd column). No modification will occur e.g. mRNA to"
+  echo "transcript."
+  echo ""
+  echo "To be fully GTF compliant all feature have a gene_id and a transcript_id"
+  echo "attribute. The gene_id is unique identifier for the genomic source of"
+  echo "the transcript, which is used to group transcripts into genes. The"
+  echo "transcript_id is a unique identifier for the predicted transcript, which"
+  echo "is used to group features into transcripts."
+  echo ""
+  echo "Inputs:"
+  echo "    -i, --gff"
+  echo "        type: file, required parameter, file must exist"
+  echo "        example: input.gff"
+  echo "        Input GFF/GTF file that will be read"
+  echo ""
+  echo "Outputs:"
+  echo "    -o, --out, --outfile, --gtf, --output"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        example: output.gtf"
+  echo "        Output GTF file. If no output file is specified, the output will be"
+  echo "        written to STDOUT."
+  echo ""
+  echo "Arguments:"
+  echo "    --gtf_version"
+  echo "        type: string"
+  echo "        example: 3"
+  echo "        choices: [ relax, 1, 2, 2.1, 2.2, 2.5, 3 ]"
+  echo "        Version of the GTF output (1,2,2.1,2.2,2.5,3 or relax). Default value"
+  echo "        from AGAT config file (relax for the default config). The script option"
+  echo "        has the higher priority."
+  echo "          * relax: all feature types are accepted."
+  echo "          * GTF3 (9 feature types accepted): gene, transcript, exon, CDS,"
+  echo "        Selenocysteine, start_codon, stop_codon, three_prime_utr and"
+  echo "        five_prime_utr."
+  echo "          * GTF2.5 (8 feature types accepted): gene, transcript, exon, CDS, UTR,"
+  echo "        start_codon, stop_codon, Selenocysteine."
+  echo "          * GTF2.2 (9 feature types accepted): CDS, start_codon, stop_codon,"
+  echo "        5UTR, 3UTR, inter, inter_CNS, intron_CNS and exon."
+  echo "          * GTF2.1 (6 feature types accepted): CDS, start_codon, stop_codon,"
+  echo "        exon, 5UTR, 3UTR."
+  echo "          * GTF2 (4 feature types accepted): CDS, start_codon, stop_codon, exon."
+  echo "          * GTF1 (5 feature types accepted): CDS, start_codon, stop_codon, exon,"
+  echo "        intron."
+  echo ""
+  echo "    -c, --config"
+  echo "        type: file, file must exist"
+  echo "        example: custom_agat_config.yaml"
+  echo "        Input agat config file. By default AGAT takes as input agat_config.yaml"
+  echo "        file from the working directory if any, otherwise it takes the orignal"
+  echo "        agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally"
+  echo "        type: \"agat config --expose\". The --config option gives you the"
+  echo "        possibility to use your own AGAT config file (located elsewhere or named"
+  echo "        differently)."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml b/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml
index 57b300b1..727d00b6 100644
--- a/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml
@@ -86,6 +86,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -187,16 +190,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/agat/agat_convert_sp_gff2tsv"
   executable: "target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv b/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv
index bab0c23f..bf09bfe4 100755
--- a/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv
+++ b/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv
@@ -2,7 +2,7 @@
 
 # agat_convert_sp_gff2tsv main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,38 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "agat_convert_sp_gff2tsv main"
-  echo ""
-  echo "The script aims to convert gtf/gff file into tabulated file. Attribute's"
-  echo "tags from the 9th column become column titles."
-  echo ""
-  echo "Inputs:"
-  echo "    -f, --gff"
-  echo "        type: file, required parameter, file must exist"
-  echo "        example: input.gff"
-  echo "        Input GTF/GFF file."
-  echo ""
-  echo "Outputs:"
-  echo "    -o, --out, --outfile, --output"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        example: output.gff"
-  echo "        Output GFF file. If no output file is specified, the output will be"
-  echo "        written to STDOUT."
-  echo ""
-  echo "Arguments:"
-  echo "    -c, --config"
-  echo "        type: file, file must exist"
-  echo "        example: custom_agat_config.yaml"
-  echo "        String - Input agat config file. By default AGAT takes as input"
-  echo "        agat_config.yaml file from the working directory if any,"
-  echo "        otherwise it takes the orignal agat_config.yaml shipped with"
-  echo "        AGAT. To get the agat_config.yaml locally type: \"agat config"
-  echo "        --expose\". The --config option gives you the possibility to use"
-  echo "        your own AGAT config file (located elsewhere or named"
-  echo "        differently)."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -484,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t
 
 LABEL org.opencontainers.image.authors="Leïla Paquay"
 LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_sp_gff2tsv"
-LABEL org.opencontainers.image.created="2024-12-03T10:33:52Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:38Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -601,6 +569,64 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "agat_convert_sp_gff2tsv main"
+  echo ""
+  echo "The script aims to convert gtf/gff file into tabulated file. Attribute's"
+  echo "tags from the 9th column become column titles."
+  echo ""
+  echo "Inputs:"
+  echo "    -f, --gff"
+  echo "        type: file, required parameter, file must exist"
+  echo "        example: input.gff"
+  echo "        Input GTF/GFF file."
+  echo ""
+  echo "Outputs:"
+  echo "    -o, --out, --outfile, --output"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        example: output.gff"
+  echo "        Output GFF file. If no output file is specified, the output will be"
+  echo "        written to STDOUT."
+  echo ""
+  echo "Arguments:"
+  echo "    -c, --config"
+  echo "        type: file, file must exist"
+  echo "        example: custom_agat_config.yaml"
+  echo "        String - Input agat config file. By default AGAT takes as input"
+  echo "        agat_config.yaml file from the working directory if any,"
+  echo "        otherwise it takes the orignal agat_config.yaml shipped with"
+  echo "        AGAT. To get the agat_config.yaml locally type: \"agat config"
+  echo "        --expose\". The --config option gives you the possibility to use"
+  echo "        your own AGAT config file (located elsewhere or named"
+  echo "        differently)."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml b/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml
index 35c372fb..7af73d04 100644
--- a/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml
@@ -93,6 +93,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -194,16 +197,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/agat/agat_convert_sp_gxf2gxf"
   executable: "target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf b/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf
index 524ab4a6..2a6e8d10 100755
--- a/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf
+++ b/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf
@@ -2,7 +2,7 @@
 
 # agat_convert_sp_gxf2gxf main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,47 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "agat_convert_sp_gxf2gxf main"
-  echo ""
-  echo "This script fixes and/or standardizes any GTF/GFF file into full sorted"
-  echo "GTF/GFF file. It AGAT parser removes duplicate features, fixes"
-  echo "duplicated IDs, adds missing ID and/or Parent attributes, deflates"
-  echo "factorized attributes (attributes with several parents are duplicated"
-  echo "with uniq ID), add missing features when possible (e.g. add exon if only"
-  echo "CDS described, add UTR if CDS and exon described), fix feature locations"
-  echo "(e.g. check exon is embedded in the parent features mRNA, gene), etc..."
-  echo ""
-  echo "All AGAT's scripts with the _sp_ prefix use the AGAT parser, before to"
-  echo "perform any supplementary task. So, it is not necessary to run this"
-  echo "script prior the use of any other _sp_ script."
-  echo ""
-  echo "Inputs:"
-  echo "    -g, --gtf, --gff, --gxf"
-  echo "        type: file, required parameter, file must exist"
-  echo "        example: input.gff"
-  echo "        String - Input GTF/GFF file. Compressed file with .gz extension is"
-  echo "        accepted."
-  echo ""
-  echo "Outputs:"
-  echo "    -o, --output"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        example: output.gff"
-  echo "        String - Output GFF file. If no output file is specified, the output"
-  echo "        will be written to STDOUT."
-  echo ""
-  echo "Arguments:"
-  echo "    -c, --config"
-  echo "        type: file, file must exist"
-  echo "        example: custom_agat_config.yaml"
-  echo "        String - Input agat config file. By default AGAT takes as input"
-  echo "        agat_config.yaml file from the working directory if any, otherwise it"
-  echo "        takes the original agat_config.yaml shipped with AGAT. To get the"
-  echo "        agat_config.yaml locally type: \"agat config --expose\". The --config"
-  echo "        option gives you the possibility to use your own AGAT config file"
-  echo "        (located elsewhere or named differently)."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -493,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t
 
 LABEL org.opencontainers.image.authors="Leïla Paquay"
 LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_sp_gxf2gxf"
-LABEL org.opencontainers.image.created="2024-12-03T10:34:05Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:39Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -610,6 +569,73 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "agat_convert_sp_gxf2gxf main"
+  echo ""
+  echo "This script fixes and/or standardizes any GTF/GFF file into full sorted"
+  echo "GTF/GFF file. It AGAT parser removes duplicate features, fixes"
+  echo "duplicated IDs, adds missing ID and/or Parent attributes, deflates"
+  echo "factorized attributes (attributes with several parents are duplicated"
+  echo "with uniq ID), add missing features when possible (e.g. add exon if only"
+  echo "CDS described, add UTR if CDS and exon described), fix feature locations"
+  echo "(e.g. check exon is embedded in the parent features mRNA, gene), etc..."
+  echo ""
+  echo "All AGAT's scripts with the _sp_ prefix use the AGAT parser, before to"
+  echo "perform any supplementary task. So, it is not necessary to run this"
+  echo "script prior the use of any other _sp_ script."
+  echo ""
+  echo "Inputs:"
+  echo "    -g, --gtf, --gff, --gxf"
+  echo "        type: file, required parameter, file must exist"
+  echo "        example: input.gff"
+  echo "        String - Input GTF/GFF file. Compressed file with .gz extension is"
+  echo "        accepted."
+  echo ""
+  echo "Outputs:"
+  echo "    -o, --output"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        example: output.gff"
+  echo "        String - Output GFF file. If no output file is specified, the output"
+  echo "        will be written to STDOUT."
+  echo ""
+  echo "Arguments:"
+  echo "    -c, --config"
+  echo "        type: file, file must exist"
+  echo "        example: custom_agat_config.yaml"
+  echo "        String - Input agat config file. By default AGAT takes as input"
+  echo "        agat_config.yaml file from the working directory if any, otherwise it"
+  echo "        takes the original agat_config.yaml shipped with AGAT. To get the"
+  echo "        agat_config.yaml locally type: \"agat config --expose\". The --config"
+  echo "        option gives you the possibility to use your own AGAT config file"
+  echo "        (located elsewhere or named differently)."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/agat/agat_sp_add_introns/.config.vsh.yaml b/target/executable/agat/agat_sp_add_introns/.config.vsh.yaml
index 096aa701..a6fe77a7 100644
--- a/target/executable/agat/agat_sp_add_introns/.config.vsh.yaml
+++ b/target/executable/agat/agat_sp_add_introns/.config.vsh.yaml
@@ -84,6 +84,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -185,16 +188,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/agat/agat_sp_add_introns"
   executable: "target/executable/agat/agat_sp_add_introns/agat_sp_add_introns"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/agat/agat_sp_add_introns/agat_sp_add_introns b/target/executable/agat/agat_sp_add_introns/agat_sp_add_introns
index 17894379..4d6be9e8 100755
--- a/target/executable/agat/agat_sp_add_introns/agat_sp_add_introns
+++ b/target/executable/agat/agat_sp_add_introns/agat_sp_add_introns
@@ -2,7 +2,7 @@
 
 # agat_sp_add_introns main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,33 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "agat_sp_add_introns main"
-  echo ""
-  echo "Add intronic elements to a gtf/gff file without intron features."
-  echo ""
-  echo "Inputs:"
-  echo "    -f, --ref, --reffile, --gff"
-  echo "        type: file, required parameter, file must exist"
-  echo "        example: input.gff"
-  echo "        Input GTF/GFF file."
-  echo ""
-  echo "Outputs:"
-  echo "    -o, --out, --outfile, --gtf, --output"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        example: output.gff"
-  echo "        Output GFF3 file."
-  echo ""
-  echo "Arguments:"
-  echo "    -c, --config"
-  echo "        type: file, file must exist"
-  echo "        example: custom_agat_config.yaml"
-  echo "        AGAT config file. By default AGAT takes the original agat_config.yaml"
-  echo "        shipped with AGAT. The \`--config\` option"
-  echo "        gives you the possibility to use your own AGAT config file (located"
-  echo "        elsewhere or named differently)."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -479,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t
 
 LABEL org.opencontainers.image.authors="Leïla Paquay"
 LABEL org.opencontainers.image.description="Companion container for running component agat agat_sp_add_introns"
-LABEL org.opencontainers.image.created="2024-12-03T10:33:52Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:38Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -596,6 +569,59 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "agat_sp_add_introns main"
+  echo ""
+  echo "Add intronic elements to a gtf/gff file without intron features."
+  echo ""
+  echo "Inputs:"
+  echo "    -f, --ref, --reffile, --gff"
+  echo "        type: file, required parameter, file must exist"
+  echo "        example: input.gff"
+  echo "        Input GTF/GFF file."
+  echo ""
+  echo "Outputs:"
+  echo "    -o, --out, --outfile, --gtf, --output"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        example: output.gff"
+  echo "        Output GFF3 file."
+  echo ""
+  echo "Arguments:"
+  echo "    -c, --config"
+  echo "        type: file, file must exist"
+  echo "        example: custom_agat_config.yaml"
+  echo "        AGAT config file. By default AGAT takes the original agat_config.yaml"
+  echo "        shipped with AGAT. The \`--config\` option"
+  echo "        gives you the possibility to use your own AGAT config file (located"
+  echo "        elsewhere or named differently)."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/agat/agat_sp_filter_feature_from_kill_list/.config.vsh.yaml b/target/executable/agat/agat_sp_filter_feature_from_kill_list/.config.vsh.yaml
index 2b8e664b..b9ba57ae 100644
--- a/target/executable/agat/agat_sp_filter_feature_from_kill_list/.config.vsh.yaml
+++ b/target/executable/agat/agat_sp_filter_feature_from_kill_list/.config.vsh.yaml
@@ -133,6 +133,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -235,16 +238,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/agat/agat_sp_filter_feature_from_kill_list"
   executable: "target/executable/agat/agat_sp_filter_feature_from_kill_list/agat_sp_filter_feature_from_kill_list"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/agat/agat_sp_filter_feature_from_kill_list/agat_sp_filter_feature_from_kill_list b/target/executable/agat/agat_sp_filter_feature_from_kill_list/agat_sp_filter_feature_from_kill_list
index 9ca9bdd9..efd68e17 100755
--- a/target/executable/agat/agat_sp_filter_feature_from_kill_list/agat_sp_filter_feature_from_kill_list
+++ b/target/executable/agat/agat_sp_filter_feature_from_kill_list/agat_sp_filter_feature_from_kill_list
@@ -2,7 +2,7 @@
 
 # agat_sp_filter_feature_from_kill_list main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,71 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "agat_sp_filter_feature_from_kill_list main"
-  echo ""
-  echo "Remove features based on a kill list. The default behaviour is to look at the"
-  echo "features's ID."
-  echo "If the feature has an ID (case insensitive) listed among the kill list it will"
-  echo "be removed."
-  echo "Removing a level1 or level2 feature will automatically remove all linked"
-  echo "subfeatures, and"
-  echo "removing all children of a feature will automatically remove this feature too."
-  echo ""
-  echo "Inputs:"
-  echo "    -f, --ref, --reffile, --gff"
-  echo "        type: file, required parameter, file must exist"
-  echo "        Input GFF3 file that will be read."
-  echo ""
-  echo "    --kl, --kill_list"
-  echo "        type: file, required parameter, file must exist"
-  echo "        example: kill_list.txt"
-  echo "        Text file containing the kill list. One value per line."
-  echo ""
-  echo "Outputs:"
-  echo "    -o, --out, --output"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        Path to the output GFF file that contains filtered features."
-  echo ""
-  echo "Arguments:"
-  echo "    -p, -l, --type"
-  echo "        type: string, multiple values allowed"
-  echo "        Primary tag option, case insensitive, list. Allow to specify the feature"
-  echo "        types that"
-  echo "        will be handled."
-  echo "        You can specify a specific feature by giving its primary tag name"
-  echo "        (column 3) as:"
-  echo "          * cds"
-  echo "          * Gene"
-  echo "          * mRNA"
-  echo "        You can specify directly all the feature of a particular"
-  echo "        level:"
-  echo "          * level2=mRNA,ncRNA,tRNA,etc"
-  echo "          * level3=CDS,exon,UTR,etc."
-  echo "        By default all features are taken into account. Fill the option with the"
-  echo "        value \"all\" will"
-  echo "        have the same behaviour."
-  echo ""
-  echo "    -a, --attribute"
-  echo "        type: string"
-  echo "        example: ID"
-  echo "        Attribute tag to specify the attribute to analyse. Case sensitive."
-  echo "        Default: ID"
-  echo ""
-  echo "    -c, --config"
-  echo "        type: file, file must exist"
-  echo "        example: custom_agat_config.yaml"
-  echo "        AGAT config file. By default AGAT takes the original agat_config.yaml"
-  echo "        shipped with AGAT."
-  echo "        The \`--config\` option gives you the possibility to use your own AGAT"
-  echo "        config file (located"
-  echo "        elsewhere or named differently)."
-  echo ""
-  echo "    -v, --verbose"
-  echo "        type: boolean_true"
-  echo "        Verbose option for debugging purpose."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -517,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t
 
 LABEL org.opencontainers.image.authors="Leïla Paquay"
 LABEL org.opencontainers.image.description="Companion container for running component agat agat_sp_filter_feature_from_kill_list"
-LABEL org.opencontainers.image.created="2024-12-03T10:33:53Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:39Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -634,6 +569,97 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "agat_sp_filter_feature_from_kill_list main"
+  echo ""
+  echo "Remove features based on a kill list. The default behaviour is to look at the"
+  echo "features's ID."
+  echo "If the feature has an ID (case insensitive) listed among the kill list it will"
+  echo "be removed."
+  echo "Removing a level1 or level2 feature will automatically remove all linked"
+  echo "subfeatures, and"
+  echo "removing all children of a feature will automatically remove this feature too."
+  echo ""
+  echo "Inputs:"
+  echo "    -f, --ref, --reffile, --gff"
+  echo "        type: file, required parameter, file must exist"
+  echo "        Input GFF3 file that will be read."
+  echo ""
+  echo "    --kl, --kill_list"
+  echo "        type: file, required parameter, file must exist"
+  echo "        example: kill_list.txt"
+  echo "        Text file containing the kill list. One value per line."
+  echo ""
+  echo "Outputs:"
+  echo "    -o, --out, --output"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        Path to the output GFF file that contains filtered features."
+  echo ""
+  echo "Arguments:"
+  echo "    -p, -l, --type"
+  echo "        type: string, multiple values allowed"
+  echo "        Primary tag option, case insensitive, list. Allow to specify the feature"
+  echo "        types that"
+  echo "        will be handled."
+  echo "        You can specify a specific feature by giving its primary tag name"
+  echo "        (column 3) as:"
+  echo "          * cds"
+  echo "          * Gene"
+  echo "          * mRNA"
+  echo "        You can specify directly all the feature of a particular"
+  echo "        level:"
+  echo "          * level2=mRNA,ncRNA,tRNA,etc"
+  echo "          * level3=CDS,exon,UTR,etc."
+  echo "        By default all features are taken into account. Fill the option with the"
+  echo "        value \"all\" will"
+  echo "        have the same behaviour."
+  echo ""
+  echo "    -a, --attribute"
+  echo "        type: string"
+  echo "        example: ID"
+  echo "        Attribute tag to specify the attribute to analyse. Case sensitive."
+  echo "        Default: ID"
+  echo ""
+  echo "    -c, --config"
+  echo "        type: file, file must exist"
+  echo "        example: custom_agat_config.yaml"
+  echo "        AGAT config file. By default AGAT takes the original agat_config.yaml"
+  echo "        shipped with AGAT."
+  echo "        The \`--config\` option gives you the possibility to use your own AGAT"
+  echo "        config file (located"
+  echo "        elsewhere or named differently)."
+  echo ""
+  echo "    -v, --verbose"
+  echo "        type: boolean_true"
+  echo "        Verbose option for debugging purpose."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/agat/agat_sp_merge_annotations/.config.vsh.yaml b/target/executable/agat/agat_sp_merge_annotations/.config.vsh.yaml
index 5b8a8348..ca364083 100644
--- a/target/executable/agat/agat_sp_merge_annotations/.config.vsh.yaml
+++ b/target/executable/agat/agat_sp_merge_annotations/.config.vsh.yaml
@@ -81,6 +81,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -183,16 +186,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/agat/agat_sp_merge_annotations"
   executable: "target/executable/agat/agat_sp_merge_annotations/agat_sp_merge_annotations"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/agat/agat_sp_merge_annotations/agat_sp_merge_annotations b/target/executable/agat/agat_sp_merge_annotations/agat_sp_merge_annotations
index 66313326..6cff0377 100755
--- a/target/executable/agat/agat_sp_merge_annotations/agat_sp_merge_annotations
+++ b/target/executable/agat/agat_sp_merge_annotations/agat_sp_merge_annotations
@@ -2,7 +2,7 @@
 
 # agat_sp_merge_annotations main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,36 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "agat_sp_merge_annotations main"
-  echo ""
-  echo "Merge different gff annotation files into one. It uses the AGAT parser that"
-  echo "takes care of"
-  echo "duplicated names and fixes other oddities met in those files."
-  echo ""
-  echo "Inputs:"
-  echo "    -f, --gff"
-  echo "        type: file, required parameter, multiple values allowed, file must exist"
-  echo "        example: input1.gff;input2.gff"
-  echo "        Input GTF/GFF file(s)."
-  echo ""
-  echo "Outputs:"
-  echo "    -o, --out, --output"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        example: output.gff"
-  echo "        Output gff3 file where the gene incriminated will be writen."
-  echo ""
-  echo "Arguments:"
-  echo "    -c, --config"
-  echo "        type: file, file must exist"
-  echo "        example: custom_agat_config.yaml"
-  echo "        AGAT config file. By default AGAT takes the original agat_config.yaml"
-  echo "        shipped with AGAT."
-  echo "        The \`--config\` option gives you the possibility to use your own AGAT"
-  echo "        config file (located"
-  echo "        elsewhere or named differently)."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -482,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t
 
 LABEL org.opencontainers.image.authors="Leïla Paquay"
 LABEL org.opencontainers.image.description="Companion container for running component agat agat_sp_merge_annotations"
-LABEL org.opencontainers.image.created="2024-12-03T10:33:53Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:37Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -599,6 +569,62 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "agat_sp_merge_annotations main"
+  echo ""
+  echo "Merge different gff annotation files into one. It uses the AGAT parser that"
+  echo "takes care of"
+  echo "duplicated names and fixes other oddities met in those files."
+  echo ""
+  echo "Inputs:"
+  echo "    -f, --gff"
+  echo "        type: file, required parameter, multiple values allowed, file must exist"
+  echo "        example: input1.gff;input2.gff"
+  echo "        Input GTF/GFF file(s)."
+  echo ""
+  echo "Outputs:"
+  echo "    -o, --out, --output"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        example: output.gff"
+  echo "        Output gff3 file where the gene incriminated will be writen."
+  echo ""
+  echo "Arguments:"
+  echo "    -c, --config"
+  echo "        type: file, file must exist"
+  echo "        example: custom_agat_config.yaml"
+  echo "        AGAT config file. By default AGAT takes the original agat_config.yaml"
+  echo "        shipped with AGAT."
+  echo "        The \`--config\` option gives you the possibility to use your own AGAT"
+  echo "        config file (located"
+  echo "        elsewhere or named differently)."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/agat/agat_sp_statistics/.config.vsh.yaml b/target/executable/agat/agat_sp_statistics/.config.vsh.yaml
index 6edc7774..eace4c83 100644
--- a/target/executable/agat/agat_sp_statistics/.config.vsh.yaml
+++ b/target/executable/agat/agat_sp_statistics/.config.vsh.yaml
@@ -128,6 +128,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -230,16 +233,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/agat/agat_sp_statistics"
   executable: "target/executable/agat/agat_sp_statistics/agat_sp_statistics"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/agat/agat_sp_statistics/agat_sp_statistics b/target/executable/agat/agat_sp_statistics/agat_sp_statistics
index 7158b4c1..c9c3bea6 100755
--- a/target/executable/agat/agat_sp_statistics/agat_sp_statistics
+++ b/target/executable/agat/agat_sp_statistics/agat_sp_statistics
@@ -2,7 +2,7 @@
 
 # agat_sp_statistics main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,61 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "agat_sp_statistics main"
-  echo ""
-  echo "The script provides exhaustive statistics of a gft/gff file."
-  echo ""
-  echo "If you have isoforms in your file, even if correct, some values calculated"
-  echo "might sounds incoherent: e.g. total length mRNA can be superior than the"
-  echo "genome size. Because all isoforms length is added... It is why by"
-  echo "default we always compute the statistics twice when there are isoforms,"
-  echo "once with the isoforms, once without (In that case we keep the longest"
-  echo "isoform per locus)."
-  echo ""
-  echo "Inputs:"
-  echo "    -i, --gff"
-  echo "        type: file, required parameter, file must exist"
-  echo "        example: input.gff"
-  echo "        Input GTF/GFF file."
-  echo ""
-  echo "    --gs_fasta"
-  echo "        type: file, file must exist"
-  echo "        example: genome.fasta"
-  echo "        Genome size directly from a fasta file to compute more statistics."
-  echo ""
-  echo "Outputs:"
-  echo "    -o, --output"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        example: output.txt"
-  echo "        The file where the results will be written."
-  echo ""
-  echo "Options:"
-  echo "    -p, -d, --plot"
-  echo "        type: boolean_true"
-  echo "        When this option is used, an histogram of distribution of the features"
-  echo "        will be printed in pdf files."
-  echo ""
-  echo "    --gs_size"
-  echo "        type: integer"
-  echo "        example: 1000000"
-  echo "        Genome size in nucleotides to compute more statistics."
-  echo ""
-  echo "    -v, --verbose"
-  echo "        type: integer"
-  echo "        example: 1"
-  echo "        Verbose option. To modify verbosity. Default is 1. 0 is quiet, 2 and 3"
-  echo "        are increasing verbosity."
-  echo ""
-  echo "    -c, --config"
-  echo "        type: file, file must exist"
-  echo "        example: custom_agat_config.yaml"
-  echo "        AGAT config file. By default AGAT takes the original agat_config.yaml"
-  echo "        shipped with AGAT. The \`--config\`"
-  echo "        option gives you the possibility to use your own AGAT config file"
-  echo "        (located elsewhere or named differently)."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -507,9 +452,9 @@ RUN agat --version | sed 's/.*v\.//; s/\s.*//' | sed 's/^/AGAT: /' > /var/softwa
 
 LABEL org.opencontainers.image.authors="Leïla Paquay"
 LABEL org.opencontainers.image.description="Companion container for running component agat agat_sp_statistics"
-LABEL org.opencontainers.image.created="2024-12-03T10:33:52Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:38Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -624,6 +569,87 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "agat_sp_statistics main"
+  echo ""
+  echo "The script provides exhaustive statistics of a gft/gff file."
+  echo ""
+  echo "If you have isoforms in your file, even if correct, some values calculated"
+  echo "might sounds incoherent: e.g. total length mRNA can be superior than the"
+  echo "genome size. Because all isoforms length is added... It is why by"
+  echo "default we always compute the statistics twice when there are isoforms,"
+  echo "once with the isoforms, once without (In that case we keep the longest"
+  echo "isoform per locus)."
+  echo ""
+  echo "Inputs:"
+  echo "    -i, --gff"
+  echo "        type: file, required parameter, file must exist"
+  echo "        example: input.gff"
+  echo "        Input GTF/GFF file."
+  echo ""
+  echo "    --gs_fasta"
+  echo "        type: file, file must exist"
+  echo "        example: genome.fasta"
+  echo "        Genome size directly from a fasta file to compute more statistics."
+  echo ""
+  echo "Outputs:"
+  echo "    -o, --output"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        example: output.txt"
+  echo "        The file where the results will be written."
+  echo ""
+  echo "Options:"
+  echo "    -p, -d, --plot"
+  echo "        type: boolean_true"
+  echo "        When this option is used, an histogram of distribution of the features"
+  echo "        will be printed in pdf files."
+  echo ""
+  echo "    --gs_size"
+  echo "        type: integer"
+  echo "        example: 1000000"
+  echo "        Genome size in nucleotides to compute more statistics."
+  echo ""
+  echo "    -v, --verbose"
+  echo "        type: integer"
+  echo "        example: 1"
+  echo "        Verbose option. To modify verbosity. Default is 1. 0 is quiet, 2 and 3"
+  echo "        are increasing verbosity."
+  echo ""
+  echo "    -c, --config"
+  echo "        type: file, file must exist"
+  echo "        example: custom_agat_config.yaml"
+  echo "        AGAT config file. By default AGAT takes the original agat_config.yaml"
+  echo "        shipped with AGAT. The \`--config\`"
+  echo "        option gives you the possibility to use your own AGAT config file"
+  echo "        (located elsewhere or named differently)."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/agat/agat_sq_stat_basic/.config.vsh.yaml b/target/executable/agat/agat_sq_stat_basic/.config.vsh.yaml
index 9027e832..23df60d5 100644
--- a/target/executable/agat/agat_sq_stat_basic/.config.vsh.yaml
+++ b/target/executable/agat/agat_sq_stat_basic/.config.vsh.yaml
@@ -124,6 +124,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -226,16 +229,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/agat/agat_sq_stat_basic"
   executable: "target/executable/agat/agat_sq_stat_basic/agat_sq_stat_basic"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/agat/agat_sq_stat_basic/agat_sq_stat_basic b/target/executable/agat/agat_sq_stat_basic/agat_sq_stat_basic
index aab33380..12b33fc9 100755
--- a/target/executable/agat/agat_sq_stat_basic/agat_sq_stat_basic
+++ b/target/executable/agat/agat_sq_stat_basic/agat_sq_stat_basic
@@ -2,7 +2,7 @@
 
 # agat_sq_stat_basic main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,61 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "agat_sq_stat_basic main"
-  echo ""
-  echo "The script aims to provide basic statistics of a gtf/gff file."
-  echo ""
-  echo "Inputs:"
-  echo "    -i, --file, --input, --gff"
-  echo "        type: file, required parameter, multiple values allowed, file must exist"
-  echo "        example: input.gff"
-  echo "        Input GTF/GFF file."
-  echo ""
-  echo "    -g, --genome_size"
-  echo "        type: integer"
-  echo "        example: 10000"
-  echo "        That input is designed to know the genome size in order to calculate the"
-  echo "        percentage of the genome represented by each kind of feature type. You"
-  echo "        can provide an INTEGER. Or you can also pass a fasta file using the"
-  echo "        argument --genome_size_fasta. If both are provided, only the value of"
-  echo "        --genome_size will be considered."
-  echo ""
-  echo "    --genome_size_fasta"
-  echo "        type: file, file must exist"
-  echo "        example: genome.fasta"
-  echo "        That input is designed to know the genome size in order to calculate the"
-  echo "        percentage of the genome represented by each kind of feature type. You"
-  echo "        can provide the genome in fasta format. Or you can also pass the size"
-  echo "        directly as an integer using the argument --genome_size. If you provide"
-  echo "        the fasta, the genome size will be calculated on the fly. If both are"
-  echo "        provided, only the value of --genome_size will be considered."
-  echo ""
-  echo "Outputs:"
-  echo "    -o, --output"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        example: output.txt"
-  echo "        Output file. The result is in tabulate format."
-  echo ""
-  echo "Arguments:"
-  echo "    --inflate"
-  echo "        type: boolean_true"
-  echo "        Inflate the statistics taking into account feature with"
-  echo "        multi-parents. Indeed to avoid redundant information, some gff"
-  echo "        factorize identical features. e.g: one exon used in two"
-  echo "        different isoform will be defined only once, and will have"
-  echo "        multiple parent. By default the script count such feature only"
-  echo "        once. Using the inflate option allows to count the feature and"
-  echo "        its size as many time there are parents."
-  echo ""
-  echo "    -c, --config"
-  echo "        type: file, file must exist"
-  echo "        example: custom_agat_config.yaml"
-  echo "        AGAT config file. By default AGAT takes the original agat_config.yaml"
-  echo "        shipped with AGAT. The \`--config\` option gives you the possibility to"
-  echo "        use your own AGAT config file (located elsewhere or named differently)."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -507,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t
 
 LABEL org.opencontainers.image.authors="Leïla Paquay"
 LABEL org.opencontainers.image.description="Companion container for running component agat agat_sq_stat_basic"
-LABEL org.opencontainers.image.created="2024-12-03T10:34:05Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:39Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -624,6 +569,87 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "agat_sq_stat_basic main"
+  echo ""
+  echo "The script aims to provide basic statistics of a gtf/gff file."
+  echo ""
+  echo "Inputs:"
+  echo "    -i, --file, --input, --gff"
+  echo "        type: file, required parameter, multiple values allowed, file must exist"
+  echo "        example: input.gff"
+  echo "        Input GTF/GFF file."
+  echo ""
+  echo "    -g, --genome_size"
+  echo "        type: integer"
+  echo "        example: 10000"
+  echo "        That input is designed to know the genome size in order to calculate the"
+  echo "        percentage of the genome represented by each kind of feature type. You"
+  echo "        can provide an INTEGER. Or you can also pass a fasta file using the"
+  echo "        argument --genome_size_fasta. If both are provided, only the value of"
+  echo "        --genome_size will be considered."
+  echo ""
+  echo "    --genome_size_fasta"
+  echo "        type: file, file must exist"
+  echo "        example: genome.fasta"
+  echo "        That input is designed to know the genome size in order to calculate the"
+  echo "        percentage of the genome represented by each kind of feature type. You"
+  echo "        can provide the genome in fasta format. Or you can also pass the size"
+  echo "        directly as an integer using the argument --genome_size. If you provide"
+  echo "        the fasta, the genome size will be calculated on the fly. If both are"
+  echo "        provided, only the value of --genome_size will be considered."
+  echo ""
+  echo "Outputs:"
+  echo "    -o, --output"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        example: output.txt"
+  echo "        Output file. The result is in tabulate format."
+  echo ""
+  echo "Arguments:"
+  echo "    --inflate"
+  echo "        type: boolean_true"
+  echo "        Inflate the statistics taking into account feature with"
+  echo "        multi-parents. Indeed to avoid redundant information, some gff"
+  echo "        factorize identical features. e.g: one exon used in two"
+  echo "        different isoform will be defined only once, and will have"
+  echo "        multiple parent. By default the script count such feature only"
+  echo "        once. Using the inflate option allows to count the feature and"
+  echo "        its size as many time there are parents."
+  echo ""
+  echo "    -c, --config"
+  echo "        type: file, file must exist"
+  echo "        example: custom_agat_config.yaml"
+  echo "        AGAT config file. By default AGAT takes the original agat_config.yaml"
+  echo "        shipped with AGAT. The \`--config\` option gives you the possibility to"
+  echo "        use your own AGAT config file (located elsewhere or named differently)."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/arriba/.config.vsh.yaml b/target/executable/arriba/.config.vsh.yaml
index 5b9cba5e..3d4e2c8e 100644
--- a/target/executable/arriba/.config.vsh.yaml
+++ b/target/executable/arriba/.config.vsh.yaml
@@ -603,6 +603,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   cpus: 1
   commands:
@@ -705,16 +708,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/arriba"
   executable: "target/executable/arriba/arriba"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/arriba/arriba b/target/executable/arriba/arriba
index 61780ae3..533e7052 100755
--- a/target/executable/arriba/arriba
+++ b/target/executable/arriba/arriba
@@ -2,7 +2,7 @@
 
 # arriba main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,6 +172,404 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
+
+# initialise variables
+VIASH_MODE='run'
+VIASH_ENGINE_ID='docker'
+
+######## Helper functions for setting up Docker images for viash ########
+# expects: ViashDockerBuild
+
+# ViashDockerInstallationCheck: check whether Docker is installed correctly
+#
+# examples:
+#   ViashDockerInstallationCheck
+function ViashDockerInstallationCheck {
+  ViashDebug "Checking whether Docker is installed"
+  if [ ! command -v docker &> /dev/null ]; then
+    ViashCritical "Docker doesn't seem to be installed. See 'https://docs.docker.com/get-docker/' for instructions."
+    exit 1
+  fi
+
+  ViashDebug "Checking whether the Docker daemon is running"
+  local save=$-; set +e
+  local docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
+  local out=$?
+  [[ $save =~ e ]] && set -e
+  if [ $out -ne 0 ]; then
+    ViashCritical "Docker daemon does not seem to be running. Try one of the following:"
+    ViashCritical "- Try running 'dockerd' in the command line"
+    ViashCritical "- See https://docs.docker.com/config/daemon/"
+    exit 1
+  fi
+}
+
+# ViashDockerRemoteTagCheck: check whether a Docker image is available 
+# on a remote. Assumes `docker login` has been performed, if relevant.
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   ViashDockerRemoteTagCheck python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerRemoteTagCheck sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerRemoteTagCheck {
+  docker manifest inspect $1 > /dev/null 2> /dev/null
+}
+
+# ViashDockerLocalTagCheck: check whether a Docker image is available locally
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   docker pull python:latest
+#   ViashDockerLocalTagCheck python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerLocalTagCheck sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerLocalTagCheck {
+  [ -n "$(docker images -q $1)" ]
+}
+
+# ViashDockerPull: pull a Docker image
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   ViashDockerPull python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerPull sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerPull {
+  ViashNotice "Checking if Docker image is available at '$1'"
+  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
+    docker pull $1 && return 0 || return 1
+  else
+    local save=$-; set +e
+    docker pull $1 2> /dev/null > /dev/null
+    local out=$?
+    [[ $save =~ e ]] && set -e
+    if [ $out -ne 0 ]; then
+      ViashWarning "Could not pull from '$1'. Docker image doesn't exist or is not accessible."
+    fi
+    return $out
+  fi
+}
+
+# ViashDockerPush: push a Docker image
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   ViashDockerPush python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerPush sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerPush {
+  ViashNotice "Pushing image to '$1'"
+  local save=$-; set +e
+  local out
+  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
+    docker push $1
+    out=$?
+  else
+    docker push $1 2> /dev/null > /dev/null
+    out=$?
+  fi
+  [[ $save =~ e ]] && set -e
+  if [ $out -eq 0 ]; then
+    ViashNotice "Container '$1' push succeeded."
+  else
+    ViashError "Container '$1' push errored. You might not be logged in or have the necessary permissions."
+  fi
+  return $out
+}
+
+# ViashDockerPullElseBuild: pull a Docker image, else build it
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# ViashDockerBuild    : a Bash function which builds a docker image, takes image identifier as argument.
+# examples:
+#   ViashDockerPullElseBuild mynewcomponent
+function ViashDockerPullElseBuild {
+  local save=$-; set +e
+  ViashDockerPull $1
+  local out=$?
+  [[ $save =~ e ]] && set -e
+  if [ $out -ne 0 ]; then
+    ViashDockerBuild $@
+  fi
+}
+
+# ViashDockerSetup: create a Docker image, according to specified docker setup strategy
+#
+# $1          : image identifier with format `[registry/]image[:tag]`
+# $2          : docker setup strategy, see DockerSetupStrategy.scala
+# examples:
+#   ViashDockerSetup mynewcomponent alwaysbuild
+function ViashDockerSetup {
+  local image_id="$1"
+  local setup_strategy="$2"
+  if [ "$setup_strategy" == "alwaysbuild" -o "$setup_strategy" == "build" -o "$setup_strategy" == "b" ]; then
+    ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+  elif [ "$setup_strategy" == "alwayspull" -o "$setup_strategy" == "pull" -o "$setup_strategy" == "p" ]; then
+    ViashDockerPull $image_id
+  elif [ "$setup_strategy" == "alwayspullelsebuild" -o "$setup_strategy" == "pullelsebuild" ]; then
+    ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+  elif [ "$setup_strategy" == "alwayspullelsecachedbuild" -o "$setup_strategy" == "pullelsecachedbuild" ]; then
+    ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+  elif [ "$setup_strategy" == "alwayscachedbuild" -o "$setup_strategy" == "cachedbuild" -o "$setup_strategy" == "cb" ]; then
+    ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+  elif [[ "$setup_strategy" =~ ^ifneedbe ]]; then
+    local save=$-; set +e
+    ViashDockerLocalTagCheck $image_id
+    local outCheck=$?
+    [[ $save =~ e ]] && set -e
+    if [ $outCheck -eq 0 ]; then
+      ViashInfo "Image $image_id already exists"
+    elif [ "$setup_strategy" == "ifneedbebuild" ]; then
+      ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+    elif [ "$setup_strategy" == "ifneedbecachedbuild" ]; then
+      ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+    elif [ "$setup_strategy" == "ifneedbepull" ]; then
+      ViashDockerPull $image_id
+    elif [ "$setup_strategy" == "ifneedbepullelsebuild" ]; then
+      ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+    elif [ "$setup_strategy" == "ifneedbepullelsecachedbuild" ]; then
+      ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+    else
+      ViashError "Unrecognised Docker strategy: $setup_strategy"
+      exit 1
+    fi
+  elif [ "$setup_strategy" == "push" -o "$setup_strategy" == "forcepush" -o "$setup_strategy" == "alwayspush" ]; then
+    ViashDockerPush "$image_id"
+  elif [ "$setup_strategy" == "pushifnotpresent" -o "$setup_strategy" == "gentlepush" -o "$setup_strategy" == "maybepush" ]; then
+    local save=$-; set +e
+    ViashDockerRemoteTagCheck $image_id
+    local outCheck=$?
+    [[ $save =~ e ]] && set -e
+    if [ $outCheck -eq 0 ]; then
+      ViashNotice "Container '$image_id' exists, doing nothing."
+    else
+      ViashNotice "Container '$image_id' does not yet exist."
+      ViashDockerPush "$image_id"
+    fi
+  elif [ "$setup_strategy" == "donothing" -o "$setup_strategy" == "meh" ]; then
+    ViashNotice "Skipping setup."
+  else
+    ViashError "Unrecognised Docker strategy: $setup_strategy"
+    exit 1
+  fi
+}
+
+# ViashDockerCheckCommands: Check whether a docker container has the required commands
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# $@                  : commands to verify being present
+# examples:
+#   ViashDockerCheckCommands bash:4.0 bash ps foo
+function ViashDockerCheckCommands {
+  local image_id="$1"
+  shift 1
+  local commands="$@"
+  local save=$-; set +e
+  local missing # mark 'missing' as local in advance, otherwise the exit code of the command will be missing and always be '0'
+  missing=$(docker run --rm --entrypoint=sh "$image_id" -c "for command in $commands; do command -v \$command >/dev/null 2>&1; if [ \$? -ne 0 ]; then echo \$command; exit 1; fi; done")
+  local outCheck=$?
+  [[ $save =~ e ]] && set -e
+  if [ $outCheck -ne 0 ]; then
+  	ViashError "Docker container '$image_id' does not contain command '$missing'."
+  	exit 1
+  fi
+}
+
+# ViashDockerBuild: build a docker image
+# $1                               : image identifier with format `[registry/]image[:tag]`
+# $...                             : additional arguments to pass to docker build
+# $VIASH_META_TEMP_DIR             : temporary directory to store dockerfile & optional resources in
+# $VIASH_META_NAME                 : name of the component
+# $VIASH_META_RESOURCES_DIR        : directory containing the resources
+# $VIASH_VERBOSITY                 : verbosity level
+# exit code $?                     : whether or not the image was built successfully
+function ViashDockerBuild {
+  local image_id="$1"
+  shift 1
+
+  # create temporary directory to store dockerfile & optional resources in
+  local tmpdir=$(mktemp -d "$VIASH_META_TEMP_DIR/dockerbuild-$VIASH_META_NAME-XXXXXX")
+  local dockerfile="$tmpdir/Dockerfile"
+  function clean_up {
+    rm -rf "$tmpdir"
+  }
+  trap clean_up EXIT
+
+  # store dockerfile and resources
+  ViashDockerfile "$VIASH_ENGINE_ID" > "$dockerfile"
+
+  # generate the build command
+  local docker_build_cmd="docker build -t '$image_id' $@ '$VIASH_META_RESOURCES_DIR' -f '$dockerfile'"
+
+  # build the container
+  ViashNotice "Building container '$image_id' with Dockerfile"
+  ViashInfo "$docker_build_cmd"
+  local save=$-; set +e
+  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
+    eval $docker_build_cmd
+  else
+    eval $docker_build_cmd &> "$tmpdir/docker_build.log"
+  fi
+
+  # check exit code
+  local out=$?
+  [[ $save =~ e ]] && set -e
+  if [ $out -ne 0 ]; then
+    ViashError "Error occurred while building container '$image_id'"
+    if [ $VIASH_VERBOSITY -lt $VIASH_LOGCODE_INFO ]; then
+      ViashError "Transcript: --------------------------------"
+      cat "$tmpdir/docker_build.log"
+      ViashError "End of transcript --------------------------"
+    fi
+    exit 1
+  fi
+}
+
+######## End of helper functions for setting up Docker images for viash ########
+
+# ViashDockerFile: print the dockerfile to stdout
+# $1    : engine identifier
+# return : dockerfile required to run this component
+# examples:
+#   ViashDockerFile
+function ViashDockerfile {
+  local engine_id="$1"
+
+  if [[ "$engine_id" == "docker" ]]; then
+    cat << 'VIASHDOCKER'
+FROM quay.io/biocontainers/arriba:2.4.0--h0033a41_2
+ENTRYPOINT []
+RUN arriba -h | grep 'Version:' 2>&1 |  sed 's/Version:\s\(.*\)/arriba: "\1"/' > /var/software_versions.txt
+
+LABEL org.opencontainers.image.authors="Robrecht Cannoodt"
+LABEL org.opencontainers.image.description="Companion container for running component arriba"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:44Z"
+LABEL org.opencontainers.image.source="https://github.com/suhrig/arriba"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+LABEL org.opencontainers.image.version="main"
+
+VIASHDOCKER
+  fi
+}
+
+# ViashDockerBuildArgs: return the arguments to pass to docker build
+# $1    : engine identifier
+# return : arguments to pass to docker build
+function ViashDockerBuildArgs {
+  local engine_id="$1"
+
+  if [[ "$engine_id" == "docker" ]]; then
+    echo ""
+  fi
+}
+
+# ViashAbsolutePath: generate absolute path from relative path
+# borrowed from https://stackoverflow.com/a/21951256
+# $1     : relative filename
+# return : absolute path
+# examples:
+#   ViashAbsolutePath some_file.txt   # returns /path/to/some_file.txt
+#   ViashAbsolutePath /foo/bar/..     # returns /foo
+function ViashAbsolutePath {
+  local thePath
+  local parr
+  local outp
+  local len
+  if [[ ! "$1" =~ ^/ ]]; then
+    thePath="$PWD/$1"
+  else
+    thePath="$1"
+  fi
+  echo "$thePath" | (
+    IFS=/
+    read -a parr
+    declare -a outp
+    for i in "${parr[@]}"; do
+      case "$i" in
+      ''|.) continue ;;
+      ..)
+        len=${#outp[@]}
+        if ((len==0)); then
+          continue
+        else
+          unset outp[$((len-1))]
+        fi
+        ;;
+      *)
+        len=${#outp[@]}
+        outp[$len]="$i"
+      ;;
+      esac
+    done
+    echo /"${outp[*]}"
+  )
+}
+# ViashDockerAutodetectMount: auto configuring docker mounts from parameters
+# $1                             : The parameter value
+# returns                        : New parameter
+# $VIASH_DIRECTORY_MOUNTS        : Added another parameter to be passed to docker
+# $VIASH_DOCKER_AUTOMOUNT_PREFIX : The prefix to be used for the automounts
+# examples:
+#   ViashDockerAutodetectMount /path/to/bar      # returns '/viash_automount/path/to/bar'
+#   ViashDockerAutodetectMountArg /path/to/bar   # returns '--volume="/path/to:/viash_automount/path/to"'
+function ViashDockerAutodetectMount {
+  local abs_path=$(ViashAbsolutePath "$1")
+  local mount_source
+  local base_name
+  if [ -d "$abs_path" ]; then
+    mount_source="$abs_path"
+    base_name=""
+  else
+    mount_source=`dirname "$abs_path"`
+    base_name=`basename "$abs_path"`
+  fi
+  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
+  if [ -z "$base_name" ]; then
+    echo "$mount_target"
+  else
+    echo "$mount_target/$base_name"
+  fi
+}
+function ViashDockerAutodetectMountArg {
+  local abs_path=$(ViashAbsolutePath "$1")
+  local mount_source
+  local base_name
+  if [ -d "$abs_path" ]; then
+    mount_source="$abs_path"
+    base_name=""
+  else
+    mount_source=`dirname "$abs_path"`
+    base_name=`basename "$abs_path"`
+  fi
+  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
+  ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target"
+  echo "--volume=\"$mount_source:$mount_target\""
+}
+function ViashDockerStripAutomount {
+  local abs_path=$(ViashAbsolutePath "$1")
+  echo "${abs_path#$VIASH_DOCKER_AUTOMOUNT_PREFIX}"
+}
+# initialise variables
+VIASH_DIRECTORY_MOUNTS=()
+
+# configure default docker automount prefix if it is unset
+if [ -z "${VIASH_DOCKER_AUTOMOUNT_PREFIX+x}" ]; then
+  VIASH_DOCKER_AUTOMOUNT_PREFIX="/viash_automount"
+fi
+
+# initialise docker variables
+VIASH_DOCKER_RUN_ARGS=(-i --rm)
+
+
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
   echo "arriba main"
@@ -473,404 +871,32 @@ function ViashHelp {
   echo "        is incomplete"
   echo "        (denoted as '...'), fill the gaps using the assembly sequence wherever"
   echo "        possible."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
 }
 
-# initialise variables
-VIASH_MODE='run'
-VIASH_ENGINE_ID='docker'
-
-######## Helper functions for setting up Docker images for viash ########
-# expects: ViashDockerBuild
-
-# ViashDockerInstallationCheck: check whether Docker is installed correctly
-#
-# examples:
-#   ViashDockerInstallationCheck
-function ViashDockerInstallationCheck {
-  ViashDebug "Checking whether Docker is installed"
-  if [ ! command -v docker &> /dev/null ]; then
-    ViashCritical "Docker doesn't seem to be installed. See 'https://docs.docker.com/get-docker/' for instructions."
-    exit 1
-  fi
-
-  ViashDebug "Checking whether the Docker daemon is running"
-  local save=$-; set +e
-  local docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
-  local out=$?
-  [[ $save =~ e ]] && set -e
-  if [ $out -ne 0 ]; then
-    ViashCritical "Docker daemon does not seem to be running. Try one of the following:"
-    ViashCritical "- Try running 'dockerd' in the command line"
-    ViashCritical "- See https://docs.docker.com/config/daemon/"
-    exit 1
-  fi
-}
-
-# ViashDockerRemoteTagCheck: check whether a Docker image is available 
-# on a remote. Assumes `docker login` has been performed, if relevant.
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   ViashDockerRemoteTagCheck python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerRemoteTagCheck sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerRemoteTagCheck {
-  docker manifest inspect $1 > /dev/null 2> /dev/null
-}
-
-# ViashDockerLocalTagCheck: check whether a Docker image is available locally
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   docker pull python:latest
-#   ViashDockerLocalTagCheck python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerLocalTagCheck sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerLocalTagCheck {
-  [ -n "$(docker images -q $1)" ]
-}
-
-# ViashDockerPull: pull a Docker image
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   ViashDockerPull python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerPull sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerPull {
-  ViashNotice "Checking if Docker image is available at '$1'"
-  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
-    docker pull $1 && return 0 || return 1
-  else
-    local save=$-; set +e
-    docker pull $1 2> /dev/null > /dev/null
-    local out=$?
-    [[ $save =~ e ]] && set -e
-    if [ $out -ne 0 ]; then
-      ViashWarning "Could not pull from '$1'. Docker image doesn't exist or is not accessible."
-    fi
-    return $out
-  fi
-}
-
-# ViashDockerPush: push a Docker image
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   ViashDockerPush python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerPush sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerPush {
-  ViashNotice "Pushing image to '$1'"
-  local save=$-; set +e
-  local out
-  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
-    docker push $1
-    out=$?
-  else
-    docker push $1 2> /dev/null > /dev/null
-    out=$?
-  fi
-  [[ $save =~ e ]] && set -e
-  if [ $out -eq 0 ]; then
-    ViashNotice "Container '$1' push succeeded."
-  else
-    ViashError "Container '$1' push errored. You might not be logged in or have the necessary permissions."
-  fi
-  return $out
-}
-
-# ViashDockerPullElseBuild: pull a Docker image, else build it
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# ViashDockerBuild    : a Bash function which builds a docker image, takes image identifier as argument.
-# examples:
-#   ViashDockerPullElseBuild mynewcomponent
-function ViashDockerPullElseBuild {
-  local save=$-; set +e
-  ViashDockerPull $1
-  local out=$?
-  [[ $save =~ e ]] && set -e
-  if [ $out -ne 0 ]; then
-    ViashDockerBuild $@
-  fi
-}
-
-# ViashDockerSetup: create a Docker image, according to specified docker setup strategy
-#
-# $1          : image identifier with format `[registry/]image[:tag]`
-# $2          : docker setup strategy, see DockerSetupStrategy.scala
-# examples:
-#   ViashDockerSetup mynewcomponent alwaysbuild
-function ViashDockerSetup {
-  local image_id="$1"
-  local setup_strategy="$2"
-  if [ "$setup_strategy" == "alwaysbuild" -o "$setup_strategy" == "build" -o "$setup_strategy" == "b" ]; then
-    ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-  elif [ "$setup_strategy" == "alwayspull" -o "$setup_strategy" == "pull" -o "$setup_strategy" == "p" ]; then
-    ViashDockerPull $image_id
-  elif [ "$setup_strategy" == "alwayspullelsebuild" -o "$setup_strategy" == "pullelsebuild" ]; then
-    ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-  elif [ "$setup_strategy" == "alwayspullelsecachedbuild" -o "$setup_strategy" == "pullelsecachedbuild" ]; then
-    ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-  elif [ "$setup_strategy" == "alwayscachedbuild" -o "$setup_strategy" == "cachedbuild" -o "$setup_strategy" == "cb" ]; then
-    ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-  elif [[ "$setup_strategy" =~ ^ifneedbe ]]; then
-    local save=$-; set +e
-    ViashDockerLocalTagCheck $image_id
-    local outCheck=$?
-    [[ $save =~ e ]] && set -e
-    if [ $outCheck -eq 0 ]; then
-      ViashInfo "Image $image_id already exists"
-    elif [ "$setup_strategy" == "ifneedbebuild" ]; then
-      ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-    elif [ "$setup_strategy" == "ifneedbecachedbuild" ]; then
-      ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-    elif [ "$setup_strategy" == "ifneedbepull" ]; then
-      ViashDockerPull $image_id
-    elif [ "$setup_strategy" == "ifneedbepullelsebuild" ]; then
-      ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-    elif [ "$setup_strategy" == "ifneedbepullelsecachedbuild" ]; then
-      ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-    else
-      ViashError "Unrecognised Docker strategy: $setup_strategy"
-      exit 1
-    fi
-  elif [ "$setup_strategy" == "push" -o "$setup_strategy" == "forcepush" -o "$setup_strategy" == "alwayspush" ]; then
-    ViashDockerPush "$image_id"
-  elif [ "$setup_strategy" == "pushifnotpresent" -o "$setup_strategy" == "gentlepush" -o "$setup_strategy" == "maybepush" ]; then
-    local save=$-; set +e
-    ViashDockerRemoteTagCheck $image_id
-    local outCheck=$?
-    [[ $save =~ e ]] && set -e
-    if [ $outCheck -eq 0 ]; then
-      ViashNotice "Container '$image_id' exists, doing nothing."
-    else
-      ViashNotice "Container '$image_id' does not yet exist."
-      ViashDockerPush "$image_id"
-    fi
-  elif [ "$setup_strategy" == "donothing" -o "$setup_strategy" == "meh" ]; then
-    ViashNotice "Skipping setup."
-  else
-    ViashError "Unrecognised Docker strategy: $setup_strategy"
-    exit 1
-  fi
-}
-
-# ViashDockerCheckCommands: Check whether a docker container has the required commands
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# $@                  : commands to verify being present
-# examples:
-#   ViashDockerCheckCommands bash:4.0 bash ps foo
-function ViashDockerCheckCommands {
-  local image_id="$1"
-  shift 1
-  local commands="$@"
-  local save=$-; set +e
-  local missing # mark 'missing' as local in advance, otherwise the exit code of the command will be missing and always be '0'
-  missing=$(docker run --rm --entrypoint=sh "$image_id" -c "for command in $commands; do command -v \$command >/dev/null 2>&1; if [ \$? -ne 0 ]; then echo \$command; exit 1; fi; done")
-  local outCheck=$?
-  [[ $save =~ e ]] && set -e
-  if [ $outCheck -ne 0 ]; then
-  	ViashError "Docker container '$image_id' does not contain command '$missing'."
-  	exit 1
-  fi
-}
-
-# ViashDockerBuild: build a docker image
-# $1                               : image identifier with format `[registry/]image[:tag]`
-# $...                             : additional arguments to pass to docker build
-# $VIASH_META_TEMP_DIR             : temporary directory to store dockerfile & optional resources in
-# $VIASH_META_NAME                 : name of the component
-# $VIASH_META_RESOURCES_DIR        : directory containing the resources
-# $VIASH_VERBOSITY                 : verbosity level
-# exit code $?                     : whether or not the image was built successfully
-function ViashDockerBuild {
-  local image_id="$1"
-  shift 1
-
-  # create temporary directory to store dockerfile & optional resources in
-  local tmpdir=$(mktemp -d "$VIASH_META_TEMP_DIR/dockerbuild-$VIASH_META_NAME-XXXXXX")
-  local dockerfile="$tmpdir/Dockerfile"
-  function clean_up {
-    rm -rf "$tmpdir"
-  }
-  trap clean_up EXIT
-
-  # store dockerfile and resources
-  ViashDockerfile "$VIASH_ENGINE_ID" > "$dockerfile"
-
-  # generate the build command
-  local docker_build_cmd="docker build -t '$image_id' $@ '$VIASH_META_RESOURCES_DIR' -f '$dockerfile'"
-
-  # build the container
-  ViashNotice "Building container '$image_id' with Dockerfile"
-  ViashInfo "$docker_build_cmd"
-  local save=$-; set +e
-  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
-    eval $docker_build_cmd
-  else
-    eval $docker_build_cmd &> "$tmpdir/docker_build.log"
-  fi
-
-  # check exit code
-  local out=$?
-  [[ $save =~ e ]] && set -e
-  if [ $out -ne 0 ]; then
-    ViashError "Error occurred while building container '$image_id'"
-    if [ $VIASH_VERBOSITY -lt $VIASH_LOGCODE_INFO ]; then
-      ViashError "Transcript: --------------------------------"
-      cat "$tmpdir/docker_build.log"
-      ViashError "End of transcript --------------------------"
-    fi
-    exit 1
-  fi
-}
-
-######## End of helper functions for setting up Docker images for viash ########
-
-# ViashDockerFile: print the dockerfile to stdout
-# $1    : engine identifier
-# return : dockerfile required to run this component
-# examples:
-#   ViashDockerFile
-function ViashDockerfile {
-  local engine_id="$1"
-
-  if [[ "$engine_id" == "docker" ]]; then
-    cat << 'VIASHDOCKER'
-FROM quay.io/biocontainers/arriba:2.4.0--h0033a41_2
-ENTRYPOINT []
-RUN arriba -h | grep 'Version:' 2>&1 |  sed 's/Version:\s\(.*\)/arriba: "\1"/' > /var/software_versions.txt
-
-LABEL org.opencontainers.image.authors="Robrecht Cannoodt"
-LABEL org.opencontainers.image.description="Companion container for running component arriba"
-LABEL org.opencontainers.image.created="2024-12-03T10:33:55Z"
-LABEL org.opencontainers.image.source="https://github.com/suhrig/arriba"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-LABEL org.opencontainers.image.version="main"
-
-VIASHDOCKER
-  fi
-}
-
-# ViashDockerBuildArgs: return the arguments to pass to docker build
-# $1    : engine identifier
-# return : arguments to pass to docker build
-function ViashDockerBuildArgs {
-  local engine_id="$1"
-
-  if [[ "$engine_id" == "docker" ]]; then
-    echo ""
-  fi
-}
-
-# ViashAbsolutePath: generate absolute path from relative path
-# borrowed from https://stackoverflow.com/a/21951256
-# $1     : relative filename
-# return : absolute path
-# examples:
-#   ViashAbsolutePath some_file.txt   # returns /path/to/some_file.txt
-#   ViashAbsolutePath /foo/bar/..     # returns /foo
-function ViashAbsolutePath {
-  local thePath
-  local parr
-  local outp
-  local len
-  if [[ ! "$1" =~ ^/ ]]; then
-    thePath="$PWD/$1"
-  else
-    thePath="$1"
-  fi
-  echo "$thePath" | (
-    IFS=/
-    read -a parr
-    declare -a outp
-    for i in "${parr[@]}"; do
-      case "$i" in
-      ''|.) continue ;;
-      ..)
-        len=${#outp[@]}
-        if ((len==0)); then
-          continue
-        else
-          unset outp[$((len-1))]
-        fi
-        ;;
-      *)
-        len=${#outp[@]}
-        outp[$len]="$i"
-      ;;
-      esac
-    done
-    echo /"${outp[*]}"
-  )
-}
-# ViashDockerAutodetectMount: auto configuring docker mounts from parameters
-# $1                             : The parameter value
-# returns                        : New parameter
-# $VIASH_DIRECTORY_MOUNTS        : Added another parameter to be passed to docker
-# $VIASH_DOCKER_AUTOMOUNT_PREFIX : The prefix to be used for the automounts
-# examples:
-#   ViashDockerAutodetectMount /path/to/bar      # returns '/viash_automount/path/to/bar'
-#   ViashDockerAutodetectMountArg /path/to/bar   # returns '--volume="/path/to:/viash_automount/path/to"'
-function ViashDockerAutodetectMount {
-  local abs_path=$(ViashAbsolutePath "$1")
-  local mount_source
-  local base_name
-  if [ -d "$abs_path" ]; then
-    mount_source="$abs_path"
-    base_name=""
-  else
-    mount_source=`dirname "$abs_path"`
-    base_name=`basename "$abs_path"`
-  fi
-  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
-  if [ -z "$base_name" ]; then
-    echo "$mount_target"
-  else
-    echo "$mount_target/$base_name"
-  fi
-}
-function ViashDockerAutodetectMountArg {
-  local abs_path=$(ViashAbsolutePath "$1")
-  local mount_source
-  local base_name
-  if [ -d "$abs_path" ]; then
-    mount_source="$abs_path"
-    base_name=""
-  else
-    mount_source=`dirname "$abs_path"`
-    base_name=`basename "$abs_path"`
-  fi
-  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
-  ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target"
-  echo "--volume=\"$mount_source:$mount_target\""
-}
-function ViashDockerStripAutomount {
-  local abs_path=$(ViashAbsolutePath "$1")
-  echo "${abs_path#$VIASH_DOCKER_AUTOMOUNT_PREFIX}"
-}
-# initialise variables
-VIASH_DIRECTORY_MOUNTS=()
-
-# configure default docker automount prefix if it is unset
-if [ -z "${VIASH_DOCKER_AUTOMOUNT_PREFIX+x}" ]; then
-  VIASH_DOCKER_AUTOMOUNT_PREFIX="/viash_automount"
-fi
-
-# initialise docker variables
-VIASH_DOCKER_RUN_ARGS=(-i --rm)
-
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/bases2fastq/.config.vsh.yaml b/target/executable/bases2fastq/.config.vsh.yaml
index 1c5f7e08..14c3d4bb 100644
--- a/target/executable/bases2fastq/.config.vsh.yaml
+++ b/target/executable/bases2fastq/.config.vsh.yaml
@@ -285,6 +285,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -393,16 +396,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/bases2fastq"
   executable: "target/executable/bases2fastq/bases2fastq"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/bases2fastq/bases2fastq b/target/executable/bases2fastq/bases2fastq
index d1fcc9c2..59b5e102 100755
--- a/target/executable/bases2fastq/bases2fastq
+++ b/target/executable/bases2fastq/bases2fastq
@@ -2,7 +2,7 @@
 
 # bases2fastq main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,154 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "bases2fastq main"
-  echo ""
-  echo "Bases2Fastq demultiplexes sequencing data generated by Element Biosciences"
-  echo "instruments and converts base calls into FASTQ files."
-  echo ""
-  echo "Input:"
-  echo "    --analysis_directory"
-  echo "        type: file, required parameter, file must exist"
-  echo "        example: input"
-  echo "        Location of analysis directory"
-  echo ""
-  echo "    -r, --run_manifest"
-  echo "        type: file, file must exist"
-  echo "        Location of run manifest to use instead of default RunManifest.csv found"
-  echo "        in analysis directory"
-  echo ""
-  echo "Output:"
-  echo "    -o, --output_directory"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        example: fastq_dir"
-  echo "        Location to save output fastqs"
-  echo ""
-  echo "    --report"
-  echo "        type: file, output, file must exist"
-  echo "        Output location for the HTML report"
-  echo ""
-  echo "    --logs"
-  echo "        type: file, output, file must exist"
-  echo "        example: logs_dir"
-  echo "        Directory containing log files"
-  echo ""
-  echo "Arguments:"
-  echo "    --chemistry_version"
-  echo "        type: string"
-  echo "        Run parameters override, chemistry version."
-  echo ""
-  echo "    -d, --demux_only"
-  echo "        type: boolean_true"
-  echo "        Generate demux files and indexing stats without generating FASTQ"
-  echo ""
-  echo "    --detect_adapters"
-  echo "        type: boolean_true"
-  echo "        Detect adapters sequences, overriding any sequences present in run"
-  echo "        manifest."
-  echo ""
-  echo "    --error_on_missing"
-  echo "        type: boolean_true"
-  echo "        Terminate execution for a missing file (by default, missing files are"
-  echo "        skipped and execution continues). Also set by --strict."
-  echo ""
-  echo "    -e, --exclude_tile"
-  echo "        type: string, multiple values allowed"
-  echo "        Regex matching tile names to exclude. This flag can be specified"
-  echo "        multiple times. (e.g. L1.*C0[23]S.)"
-  echo ""
-  echo "    --filter_mask"
-  echo "        type: string"
-  echo "        Run parameters override, custom pass filter mask."
-  echo ""
-  echo "    --flowcell_id"
-  echo "        type: string"
-  echo "        Run parameters override, flowcell ID."
-  echo ""
-  echo "    --force_index_orientation"
-  echo "        type: boolean_true"
-  echo "        Do not attempt to find orientation for I1/I2 reads (reverse complement)."
-  echo "        Use orientation given in run manifest."
-  echo ""
-  echo "    --group_fastq"
-  echo "        type: boolean_true"
-  echo "        Group all FASTQ/stats/metrics for a project are in the project folder."
-  echo ""
-  echo "    --i1_cycles"
-  echo "        type: integer"
-  echo "        min: 1"
-  echo "        Run parameters override, I1 cycles."
-  echo ""
-  echo "    --i2_cycles"
-  echo "        type: integer"
-  echo "        min: 1"
-  echo "        Run parameters override, I2 cycles"
-  echo ""
-  echo "    -i, --include_tile"
-  echo "        type: string, multiple values allowed"
-  echo "        Regex matching tile names to include. This flag"
-  echo "        can be specified multiple times. (e.g. L1.*C0[23]S.)"
-  echo ""
-  echo "    --kit_configuration"
-  echo "        type: string"
-  echo "        Run parameters override, kit configuration."
-  echo ""
-  echo "    --legacy_fastq"
-  echo "        type: boolean_true"
-  echo "        Legacy naming for FASTQ files (e.g. SampleName_S1_L001_R1_001.fastq.gz)"
-  echo ""
-  echo "    -l, --log_level"
-  echo "        type: string"
-  echo "        example: INFO"
-  echo "        choices: [ DEBUG, INFO, WARNING, ERROR ]"
-  echo "        Severity level for logging."
-  echo ""
-  echo "    --no_error_on_invalid"
-  echo "        type: boolean_true"
-  echo "        Skip invalid files and continue execution. Overridden by --strict"
-  echo "        options"
-  echo ""
-  echo "    --no_projects"
-  echo "        type: boolean_true"
-  echo "        Disable project directories"
-  echo ""
-  echo "    --num_unassigned"
-  echo "        type: integer"
-  echo "        example: 30"
-  echo "        min: 0"
-  echo "        max: 1000"
-  echo "        Max Number of unassigned sequences to report."
-  echo ""
-  echo "    --preparation_workflow"
-  echo "        type: string"
-  echo "        Run parameters override, preparation workflow."
-  echo ""
-  echo "    --qc_only"
-  echo "        type: boolean_true"
-  echo "        Quickly generate run stats for single tile without generating FASTQ."
-  echo "        Use --include_tile/--exclude_tile to define custom tile set."
-  echo ""
-  echo "    --r1_cycles"
-  echo "        type: integer"
-  echo "        min: 1"
-  echo "        Run parameters override, R1 cycles."
-  echo ""
-  echo "    --r2_cycles"
-  echo "        type: integer"
-  echo "        min: 1"
-  echo "        Run parameters override, R2 cycles."
-  echo ""
-  echo "    --split_lanes"
-  echo "        type: boolean_true"
-  echo "        Split FASTQ files by lane."
-  echo ""
-  echo "    --strict"
-  echo "        type: boolean_true"
-  echo "        In strict mode any invalid or missing input file will terminate"
-  echo "        execution"
-  echo "        (overrides no_error_on_invalid and sets --error_on_missing)"
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -604,9 +456,9 @@ RUN echo "bases2fastq: $(bases2fastq --version | cut -d' ' -f3)" > /var/software
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component bases2fastq"
-LABEL org.opencontainers.image.created="2024-12-03T10:34:06Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:42Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -721,6 +573,180 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "bases2fastq main"
+  echo ""
+  echo "Bases2Fastq demultiplexes sequencing data generated by Element Biosciences"
+  echo "instruments and converts base calls into FASTQ files."
+  echo ""
+  echo "Input:"
+  echo "    --analysis_directory"
+  echo "        type: file, required parameter, file must exist"
+  echo "        example: input"
+  echo "        Location of analysis directory"
+  echo ""
+  echo "    -r, --run_manifest"
+  echo "        type: file, file must exist"
+  echo "        Location of run manifest to use instead of default RunManifest.csv found"
+  echo "        in analysis directory"
+  echo ""
+  echo "Output:"
+  echo "    -o, --output_directory"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        example: fastq_dir"
+  echo "        Location to save output fastqs"
+  echo ""
+  echo "    --report"
+  echo "        type: file, output, file must exist"
+  echo "        Output location for the HTML report"
+  echo ""
+  echo "    --logs"
+  echo "        type: file, output, file must exist"
+  echo "        example: logs_dir"
+  echo "        Directory containing log files"
+  echo ""
+  echo "Arguments:"
+  echo "    --chemistry_version"
+  echo "        type: string"
+  echo "        Run parameters override, chemistry version."
+  echo ""
+  echo "    -d, --demux_only"
+  echo "        type: boolean_true"
+  echo "        Generate demux files and indexing stats without generating FASTQ"
+  echo ""
+  echo "    --detect_adapters"
+  echo "        type: boolean_true"
+  echo "        Detect adapters sequences, overriding any sequences present in run"
+  echo "        manifest."
+  echo ""
+  echo "    --error_on_missing"
+  echo "        type: boolean_true"
+  echo "        Terminate execution for a missing file (by default, missing files are"
+  echo "        skipped and execution continues). Also set by --strict."
+  echo ""
+  echo "    -e, --exclude_tile"
+  echo "        type: string, multiple values allowed"
+  echo "        Regex matching tile names to exclude. This flag can be specified"
+  echo "        multiple times. (e.g. L1.*C0[23]S.)"
+  echo ""
+  echo "    --filter_mask"
+  echo "        type: string"
+  echo "        Run parameters override, custom pass filter mask."
+  echo ""
+  echo "    --flowcell_id"
+  echo "        type: string"
+  echo "        Run parameters override, flowcell ID."
+  echo ""
+  echo "    --force_index_orientation"
+  echo "        type: boolean_true"
+  echo "        Do not attempt to find orientation for I1/I2 reads (reverse complement)."
+  echo "        Use orientation given in run manifest."
+  echo ""
+  echo "    --group_fastq"
+  echo "        type: boolean_true"
+  echo "        Group all FASTQ/stats/metrics for a project are in the project folder."
+  echo ""
+  echo "    --i1_cycles"
+  echo "        type: integer"
+  echo "        min: 1"
+  echo "        Run parameters override, I1 cycles."
+  echo ""
+  echo "    --i2_cycles"
+  echo "        type: integer"
+  echo "        min: 1"
+  echo "        Run parameters override, I2 cycles"
+  echo ""
+  echo "    -i, --include_tile"
+  echo "        type: string, multiple values allowed"
+  echo "        Regex matching tile names to include. This flag"
+  echo "        can be specified multiple times. (e.g. L1.*C0[23]S.)"
+  echo ""
+  echo "    --kit_configuration"
+  echo "        type: string"
+  echo "        Run parameters override, kit configuration."
+  echo ""
+  echo "    --legacy_fastq"
+  echo "        type: boolean_true"
+  echo "        Legacy naming for FASTQ files (e.g. SampleName_S1_L001_R1_001.fastq.gz)"
+  echo ""
+  echo "    -l, --log_level"
+  echo "        type: string"
+  echo "        example: INFO"
+  echo "        choices: [ DEBUG, INFO, WARNING, ERROR ]"
+  echo "        Severity level for logging."
+  echo ""
+  echo "    --no_error_on_invalid"
+  echo "        type: boolean_true"
+  echo "        Skip invalid files and continue execution. Overridden by --strict"
+  echo "        options"
+  echo ""
+  echo "    --no_projects"
+  echo "        type: boolean_true"
+  echo "        Disable project directories"
+  echo ""
+  echo "    --num_unassigned"
+  echo "        type: integer"
+  echo "        example: 30"
+  echo "        min: 0"
+  echo "        max: 1000"
+  echo "        Max Number of unassigned sequences to report."
+  echo ""
+  echo "    --preparation_workflow"
+  echo "        type: string"
+  echo "        Run parameters override, preparation workflow."
+  echo ""
+  echo "    --qc_only"
+  echo "        type: boolean_true"
+  echo "        Quickly generate run stats for single tile without generating FASTQ."
+  echo "        Use --include_tile/--exclude_tile to define custom tile set."
+  echo ""
+  echo "    --r1_cycles"
+  echo "        type: integer"
+  echo "        min: 1"
+  echo "        Run parameters override, R1 cycles."
+  echo ""
+  echo "    --r2_cycles"
+  echo "        type: integer"
+  echo "        min: 1"
+  echo "        Run parameters override, R2 cycles."
+  echo ""
+  echo "    --split_lanes"
+  echo "        type: boolean_true"
+  echo "        Split FASTQ files by lane."
+  echo ""
+  echo "    --strict"
+  echo "        type: boolean_true"
+  echo "        In strict mode any invalid or missing input file will terminate"
+  echo "        execution"
+  echo "        (overrides no_error_on_invalid and sets --error_on_missing)"
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/bbmap/bbmap_bbsplit/.config.vsh.yaml b/target/executable/bbmap/bbmap_bbsplit/.config.vsh.yaml
index 541818f4..d73c1076 100644
--- a/target/executable/bbmap/bbmap_bbsplit/.config.vsh.yaml
+++ b/target/executable/bbmap/bbmap_bbsplit/.config.vsh.yaml
@@ -267,6 +267,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -367,16 +370,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/bbmap/bbmap_bbsplit"
   executable: "target/executable/bbmap/bbmap_bbsplit/bbmap_bbsplit"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/bbmap/bbmap_bbsplit/bbmap_bbsplit b/target/executable/bbmap/bbmap_bbsplit/bbmap_bbsplit
index 5e631179..34429cf2 100755
--- a/target/executable/bbmap/bbmap_bbsplit/bbmap_bbsplit
+++ b/target/executable/bbmap/bbmap_bbsplit/bbmap_bbsplit
@@ -2,7 +2,7 @@
 
 # bbmap_bbsplit main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -169,152 +169,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "bbmap_bbsplit main"
-  echo ""
-  echo "Split sequencing reads by mapping them to multiple references simultaneously."
-  echo ""
-  echo "Input:"
-  echo "    --id"
-  echo "        type: string"
-  echo "        Sample ID"
-  echo ""
-  echo "    --paired"
-  echo "        type: boolean_true"
-  echo "        Paired fastq files or not?"
-  echo ""
-  echo "    --input"
-  echo "        type: file, multiple values allowed, file must exist"
-  echo "        example: reads.fastq"
-  echo "        Input fastq files, either one or two (paired), separated by \";\"."
-  echo ""
-  echo "    --ref"
-  echo "        type: file, multiple values allowed, file must exist"
-  echo "        Reference FASTA files, separated by \";\". The primary reference should be"
-  echo "        specified first."
-  echo ""
-  echo "    --only_build_index"
-  echo "        type: boolean_true"
-  echo "        If set, only builds the index. Otherwise, mapping is performed."
-  echo ""
-  echo "    --build"
-  echo "        type: file, file must exist"
-  echo "        Index to be used for mapping."
-  echo ""
-  echo "    --qin"
-  echo "        type: string"
-  echo "        Set to 33 or 64 to specify input quality value ASCII offset."
-  echo "        Automatically detected if"
-  echo "        not specified."
-  echo ""
-  echo "    --interleaved"
-  echo "        type: boolean_true"
-  echo "        True forces paired/interleaved input; false forces single-ended mapping."
-  echo "        If not specified, interleaved status will be autodetected from read"
-  echo "        names."
-  echo ""
-  echo "    --maxindel"
-  echo "        type: integer"
-  echo "        example: 20"
-  echo "        Don't look for indels longer than this. Lower is faster. Set to >=100k"
-  echo "        for RNA-seq."
-  echo ""
-  echo "    --minratio"
-  echo "        type: double"
-  echo "        example: 0.56"
-  echo "        Fraction of max alignment score required to keep a site. Higher is"
-  echo "        faster."
-  echo ""
-  echo "    --minhits"
-  echo "        type: integer"
-  echo "        example: 1"
-  echo "        Minimum number of seed hits required for candidate sites. Higher is"
-  echo "        faster."
-  echo ""
-  echo "    --ambiguous"
-  echo "        type: string"
-  echo "        example: best"
-  echo "        choices: [ best, toss, random, all ]"
-  echo "        Set behavior on ambiguously-mapped reads (with multiple top-scoring"
-  echo "        mapping locations)."
-  echo "          * best    Use the first best site (Default)"
-  echo "          * toss    Consider unmapped"
-  echo "          * random  Select one top-scoring site randomly"
-  echo "          * all     Retain all top-scoring sites.  Does not work yet with SAM"
-  echo "        output"
-  echo ""
-  echo "    --ambiguous2"
-  echo "        type: string"
-  echo "        example: best"
-  echo "        choices: [ best, toss, all, split ]"
-  echo "        Set behavior only for reads that map ambiguously to multiple different"
-  echo "        references."
-  echo "        Normal 'ambiguous=' controls behavior on all ambiguous reads;"
-  echo "        Ambiguous2 excludes reads that map ambiguously within a single"
-  echo "        reference."
-  echo "          * best    Use the first best site (Default)"
-  echo "          * toss    Consider unmapped"
-  echo "          * all     Write a copy to the output for each reference to which it"
-  echo "        maps"
-  echo "          * split   Write a copy to the AMBIGUOUS_ output for each reference to"
-  echo "        which it maps"
-  echo ""
-  echo "    --qtrim"
-  echo "        type: string"
-  echo "        choices: [ l, r, lr ]"
-  echo "        Quality-trim ends to Q5 before mapping. Options are 'l' (left), 'r'"
-  echo "        (right), and 'lr' (both)."
-  echo ""
-  echo "    --untrim"
-  echo "        type: boolean_true"
-  echo "        Undo trimming after mapping. Untrimmed bases will be soft-clipped in"
-  echo "        cigar strings."
-  echo ""
-  echo "Output:"
-  echo "    --index"
-  echo "        type: file, output, file must exist"
-  echo "        example: BBSplit_index"
-  echo "        Location to write the index."
-  echo ""
-  echo "    --fastq_1"
-  echo "        type: file, output, file must exist"
-  echo "        example: read_out1.fastq"
-  echo "        Output file for read 1."
-  echo ""
-  echo "    --fastq_2"
-  echo "        type: file, output, file must exist"
-  echo "        example: read_out2.fastq"
-  echo "        Output file for read 2."
-  echo ""
-  echo "    --bs, --sam2bam"
-  echo "        type: file, output, file must exist"
-  echo "        example: script.sh"
-  echo "        Write a shell script to 'file' that will turn the sam output into a"
-  echo "        sorted, indexed bam file."
-  echo ""
-  echo "    --scafstats"
-  echo "        type: file, output, file must exist"
-  echo "        example: scaffold_stats.txt"
-  echo "        Write statistics on how many reads mapped to which scaffold to this"
-  echo "        file."
-  echo ""
-  echo "    --refstats"
-  echo "        type: file, output, file must exist"
-  echo "        example: reference_stats.txt"
-  echo "        Write statistics on how many reads were assigned to which reference to"
-  echo "        this file."
-  echo "        Unmapped reads whose mate mapped to a reference are considered assigned"
-  echo "        and will be counted."
-  echo ""
-  echo "    --nzo"
-  echo "        type: boolean_true"
-  echo "        Only print lines with nonzero coverage."
-  echo ""
-  echo "    --bbmap_args"
-  echo "        type: string"
-  echo "        Additional arguments from BBMap to pass to BBSplit."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -600,9 +454,9 @@ cp -r bbmap/* /usr/local/bin
 RUN bbsplit.sh --version 2>&1 | awk '/BBMap version/{print "BBMAP:", $NF}' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.description="Companion container for running component bbmap bbmap_bbsplit"
-LABEL org.opencontainers.image.created="2024-12-03T10:33:54Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:45Z"
 LABEL org.opencontainers.image.source="https://github.com/BioInfoTools/BBMap/blob/master/sh/bbsplit.sh"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -717,6 +571,178 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "bbmap_bbsplit main"
+  echo ""
+  echo "Split sequencing reads by mapping them to multiple references simultaneously."
+  echo ""
+  echo "Input:"
+  echo "    --id"
+  echo "        type: string"
+  echo "        Sample ID"
+  echo ""
+  echo "    --paired"
+  echo "        type: boolean_true"
+  echo "        Paired fastq files or not?"
+  echo ""
+  echo "    --input"
+  echo "        type: file, multiple values allowed, file must exist"
+  echo "        example: reads.fastq"
+  echo "        Input fastq files, either one or two (paired), separated by \";\"."
+  echo ""
+  echo "    --ref"
+  echo "        type: file, multiple values allowed, file must exist"
+  echo "        Reference FASTA files, separated by \";\". The primary reference should be"
+  echo "        specified first."
+  echo ""
+  echo "    --only_build_index"
+  echo "        type: boolean_true"
+  echo "        If set, only builds the index. Otherwise, mapping is performed."
+  echo ""
+  echo "    --build"
+  echo "        type: file, file must exist"
+  echo "        Index to be used for mapping."
+  echo ""
+  echo "    --qin"
+  echo "        type: string"
+  echo "        Set to 33 or 64 to specify input quality value ASCII offset."
+  echo "        Automatically detected if"
+  echo "        not specified."
+  echo ""
+  echo "    --interleaved"
+  echo "        type: boolean_true"
+  echo "        True forces paired/interleaved input; false forces single-ended mapping."
+  echo "        If not specified, interleaved status will be autodetected from read"
+  echo "        names."
+  echo ""
+  echo "    --maxindel"
+  echo "        type: integer"
+  echo "        example: 20"
+  echo "        Don't look for indels longer than this. Lower is faster. Set to >=100k"
+  echo "        for RNA-seq."
+  echo ""
+  echo "    --minratio"
+  echo "        type: double"
+  echo "        example: 0.56"
+  echo "        Fraction of max alignment score required to keep a site. Higher is"
+  echo "        faster."
+  echo ""
+  echo "    --minhits"
+  echo "        type: integer"
+  echo "        example: 1"
+  echo "        Minimum number of seed hits required for candidate sites. Higher is"
+  echo "        faster."
+  echo ""
+  echo "    --ambiguous"
+  echo "        type: string"
+  echo "        example: best"
+  echo "        choices: [ best, toss, random, all ]"
+  echo "        Set behavior on ambiguously-mapped reads (with multiple top-scoring"
+  echo "        mapping locations)."
+  echo "          * best    Use the first best site (Default)"
+  echo "          * toss    Consider unmapped"
+  echo "          * random  Select one top-scoring site randomly"
+  echo "          * all     Retain all top-scoring sites.  Does not work yet with SAM"
+  echo "        output"
+  echo ""
+  echo "    --ambiguous2"
+  echo "        type: string"
+  echo "        example: best"
+  echo "        choices: [ best, toss, all, split ]"
+  echo "        Set behavior only for reads that map ambiguously to multiple different"
+  echo "        references."
+  echo "        Normal 'ambiguous=' controls behavior on all ambiguous reads;"
+  echo "        Ambiguous2 excludes reads that map ambiguously within a single"
+  echo "        reference."
+  echo "          * best    Use the first best site (Default)"
+  echo "          * toss    Consider unmapped"
+  echo "          * all     Write a copy to the output for each reference to which it"
+  echo "        maps"
+  echo "          * split   Write a copy to the AMBIGUOUS_ output for each reference to"
+  echo "        which it maps"
+  echo ""
+  echo "    --qtrim"
+  echo "        type: string"
+  echo "        choices: [ l, r, lr ]"
+  echo "        Quality-trim ends to Q5 before mapping. Options are 'l' (left), 'r'"
+  echo "        (right), and 'lr' (both)."
+  echo ""
+  echo "    --untrim"
+  echo "        type: boolean_true"
+  echo "        Undo trimming after mapping. Untrimmed bases will be soft-clipped in"
+  echo "        cigar strings."
+  echo ""
+  echo "Output:"
+  echo "    --index"
+  echo "        type: file, output, file must exist"
+  echo "        example: BBSplit_index"
+  echo "        Location to write the index."
+  echo ""
+  echo "    --fastq_1"
+  echo "        type: file, output, file must exist"
+  echo "        example: read_out1.fastq"
+  echo "        Output file for read 1."
+  echo ""
+  echo "    --fastq_2"
+  echo "        type: file, output, file must exist"
+  echo "        example: read_out2.fastq"
+  echo "        Output file for read 2."
+  echo ""
+  echo "    --bs, --sam2bam"
+  echo "        type: file, output, file must exist"
+  echo "        example: script.sh"
+  echo "        Write a shell script to 'file' that will turn the sam output into a"
+  echo "        sorted, indexed bam file."
+  echo ""
+  echo "    --scafstats"
+  echo "        type: file, output, file must exist"
+  echo "        example: scaffold_stats.txt"
+  echo "        Write statistics on how many reads mapped to which scaffold to this"
+  echo "        file."
+  echo ""
+  echo "    --refstats"
+  echo "        type: file, output, file must exist"
+  echo "        example: reference_stats.txt"
+  echo "        Write statistics on how many reads were assigned to which reference to"
+  echo "        this file."
+  echo "        Unmapped reads whose mate mapped to a reference are considered assigned"
+  echo "        and will be counted."
+  echo ""
+  echo "    --nzo"
+  echo "        type: boolean_true"
+  echo "        Only print lines with nonzero coverage."
+  echo ""
+  echo "    --bbmap_args"
+  echo "        type: string"
+  echo "        Additional arguments from BBMap to pass to BBSplit."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/bcftools/bcftools_annotate/.config.vsh.yaml b/target/executable/bcftools/bcftools_annotate/.config.vsh.yaml
index 4cfbe259..95410503 100644
--- a/target/executable/bcftools/bcftools_annotate/.config.vsh.yaml
+++ b/target/executable/bcftools/bcftools_annotate/.config.vsh.yaml
@@ -355,6 +355,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -468,16 +471,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/bcftools/bcftools_annotate"
   executable: "target/executable/bcftools/bcftools_annotate/bcftools_annotate"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/bcftools/bcftools_annotate/bcftools_annotate b/target/executable/bcftools/bcftools_annotate/bcftools_annotate
index 09cdffc7..22fff05b 100755
--- a/target/executable/bcftools/bcftools_annotate/bcftools_annotate
+++ b/target/executable/bcftools/bcftools_annotate/bcftools_annotate
@@ -2,7 +2,7 @@
 
 # bcftools_annotate main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,200 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "bcftools_annotate main"
-  echo ""
-  echo "Add or remove annotations from a VCF/BCF file."
-  echo ""
-  echo "Inputs:"
-  echo "    -i, --input"
-  echo "        type: file, required parameter, multiple values allowed, file must exist"
-  echo "        Input VCF/BCF file."
-  echo ""
-  echo "Outputs:"
-  echo "    -o, --output"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        Output annotated file."
-  echo ""
-  echo "Options:"
-  echo "    For examples on how to use use bcftools annotate see"
-  echo "    http://samtools.github.io/bcftools/howtos/annotate.html."
-  echo "    For more details on the options see"
-  echo "    https://samtools.github.io/bcftools/bcftools.html#annotate."
-  echo ""
-  echo "    --a, --annotations"
-  echo "        type: file, file must exist"
-  echo "        VCF file or tabix-indexed FILE with annotations: CHR\\tPOS[\\tVALUE]+ ."
-  echo ""
-  echo "    --c, --columns"
-  echo "        type: string"
-  echo "        List of columns in the annotation file, e.g."
-  echo "        CHROM,POS,REF,ALT,-,INFO/TAG."
-  echo "        See man page for details."
-  echo ""
-  echo "    --C, --columns_file"
-  echo "        type: file, file must exist"
-  echo "        Read -c columns from FILE, one name per row, with optional --merge_logic"
-  echo "        TYPE: NAME[ TYPE]."
-  echo ""
-  echo "    --e, --exclude"
-  echo "        type: string"
-  echo "        example: QUAL >= 30 && DP >= 10"
-  echo "        Exclude sites for which the expression is true."
-  echo "        See https://samtools.github.io/bcftools/bcftools.html#expressions for"
-  echo "        details."
-  echo ""
-  echo "    --force"
-  echo "        type: boolean_true"
-  echo "        continue even when parsing errors, such as undefined tags, are"
-  echo "        encountered."
-  echo "        Note this can be an unsafe operation and can result in corrupted BCF"
-  echo "        files."
-  echo "        If this option is used, make sure to sanity check the result thoroughly."
-  echo ""
-  echo "    --H, --header_line"
-  echo "        type: string"
-  echo "        Header line which should be appended to the VCF header, can be given"
-  echo "        multiple times."
-  echo ""
-  echo "    --h, --header_lines"
-  echo "        type: file, file must exist"
-  echo "        File with header lines to append to the VCF header."
-  echo "        For example:"
-  echo "          ##INFO=<ID=NUMERIC_TAG,Number=1,Type=Integer,Description=\"Example"
-  echo "        header line\">"
-  echo "          ##INFO=<ID=STRING_TAG,Number=1,Type=String,Description=\"Yet another"
-  echo "        header line\">"
-  echo ""
-  echo "    --I, --set_id"
-  echo "        type: string"
-  echo "        Set ID column using a \`bcftools query\`-like expression, see man page for"
-  echo "        details."
-  echo ""
-  echo "    --include"
-  echo "        type: string"
-  echo "        example: QUAL >= 30 && DP >= 10"
-  echo "        Select sites for which the expression is true."
-  echo "        See https://samtools.github.io/bcftools/bcftools.html#expressions for"
-  echo "        details."
-  echo ""
-  echo "    --k, --keep_sites"
-  echo "        type: boolean_true"
-  echo "        Leave --include/--exclude sites unchanged instead of discarding them."
-  echo ""
-  echo "    --l, --merge_logic"
-  echo "        type: string"
-  echo "        When multiple regions overlap a single record, this option defines how"
-  echo "        to treat multiple annotation values."
-  echo "        See man page for more details."
-  echo ""
-  echo "    --m, --mark_sites"
-  echo "        type: string"
-  echo "        Annotate sites which are present (\"+\") or absent (\"-\") in the -a file"
-  echo "        with a new INFO/TAG flag."
-  echo ""
-  echo "    --min_overlap"
-  echo "        type: string"
-  echo "        Minimum overlap required as a fraction of the variant in the annotation"
-  echo "        -a file (ANN),"
-  echo "        in the target VCF file (:VCF), or both for reciprocal overlap (ANN:VCF)."
-  echo "        By default overlaps of arbitrary length are sufficient."
-  echo "        The option can be used only with the tab-delimited annotation -a file"
-  echo "        and with BEG and END columns present."
-  echo ""
-  echo "    --no_version"
-  echo "        type: boolean_true"
-  echo "        Do not append version and command line information to the output VCF"
-  echo "        header."
-  echo ""
-  echo "    --O, --output_type"
-  echo "        type: string"
-  echo "        choices: [ u, z, b, v ]"
-  echo "        Output type:"
-  echo "          u: uncompressed BCF"
-  echo "          z: compressed VCF"
-  echo "          b: compressed BCF"
-  echo "          v: uncompressed VCF"
-  echo ""
-  echo "    --pair_logic"
-  echo "        type: string"
-  echo "        choices: [ snps, indels, both, all, some, exact ]"
-  echo "        Controls how to match records from the annotation file to the target"
-  echo "        VCF."
-  echo "        Effective only when -a is a VCF or BCF file."
-  echo "        The option replaces the former uninuitive --collapse."
-  echo "        See Common Options for more."
-  echo ""
-  echo "    --r, --regions"
-  echo "        type: string"
-  echo "        example: 20:1000000-2000000"
-  echo "        Restrict to comma-separated list of regions."
-  echo "        Following formats are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​]."
-  echo ""
-  echo "    --R, --regions_file"
-  echo "        type: file, file must exist"
-  echo "        Restrict to regions listed in a file."
-  echo "        Regions can be specified either on a VCF, BED, or tab-delimited file"
-  echo "        (the default)."
-  echo "        For more information check manual."
-  echo ""
-  echo "    --regions_overlap"
-  echo "        type: string"
-  echo "        choices: [ pos, record, variant, 0, 1, 2 ]"
-  echo "        This option controls how overlapping records are determined:"
-  echo "        set to 'pos' or '0' if the VCF record has to have POS inside a region"
-  echo "        (this corresponds to the default behavior of -t/-T);"
-  echo "        set to 'record' or '1' if also overlapping records with POS outside a"
-  echo "        region should be included (this is the default behavior of -r/-R,"
-  echo "        and includes indels with POS at the end of a region, which are"
-  echo "        technically outside the region);"
-  echo "        or set to 'variant' or '2' to include only true overlapping variation"
-  echo "        (compare the full VCF representation \"TA>T-\" vs the true sequence"
-  echo "        variation \"A>-\")."
-  echo ""
-  echo "    --rename_annotations"
-  echo "        type: file, file must exist"
-  echo "        Rename annotations: TYPE/old\\tnew, where TYPE is one of"
-  echo "        FILTER,INFO,FORMAT."
-  echo ""
-  echo "    --rename_chromosomes"
-  echo "        type: file, file must exist"
-  echo "        Rename chromosomes according to the map in file, with \"old_name"
-  echo "        new_name\\n\" pairs"
-  echo "        separated by whitespaces, each on a separate line."
-  echo ""
-  echo "    --samples"
-  echo "        type: string"
-  echo "        Subset of samples to annotate."
-  echo "        See also"
-  echo "        https://samtools.github.io/bcftools/bcftools.html#common_options."
-  echo ""
-  echo "    --samples_file"
-  echo "        type: file, file must exist"
-  echo "        Subset of samples to annotate in file format."
-  echo "        See also"
-  echo "        https://samtools.github.io/bcftools/bcftools.html#common_options."
-  echo ""
-  echo "    --single_overlaps"
-  echo "        type: boolean_true"
-  echo "        Use this option to keep memory requirements low with very large"
-  echo "        annotation files."
-  echo "        Note, however, that this comes at a cost, only single overlapping"
-  echo "        intervals are considered in this mode."
-  echo "        This was the default mode until the commit af6f0c9 (Feb 24 2019)."
-  echo ""
-  echo "    --x, --remove"
-  echo "        type: string"
-  echo "        List of annotations to remove."
-  echo "        Use \"FILTER\" to remove all filters or \"FILTER/SomeFilter\" to remove a"
-  echo "        specific filter."
-  echo "        Similarly, \"INFO\" can be used to remove all INFO tags and \"FORMAT\" to"
-  echo "        remove all FORMAT tags except GT."
-  echo "        To remove all INFO tags except \"FOO\" and \"BAR\", use \"^INFO/FOO,INFO/BAR\""
-  echo "        (and similarly for FORMAT and FILTER)."
-  echo "        \"INFO\" can be abbreviated to \"INF\" and \"FORMAT\" to \"FMT\"."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -650,9 +456,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo
 
 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_annotate"
-LABEL org.opencontainers.image.created="2024-12-03T10:34:03Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:35Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -767,6 +573,226 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "bcftools_annotate main"
+  echo ""
+  echo "Add or remove annotations from a VCF/BCF file."
+  echo ""
+  echo "Inputs:"
+  echo "    -i, --input"
+  echo "        type: file, required parameter, multiple values allowed, file must exist"
+  echo "        Input VCF/BCF file."
+  echo ""
+  echo "Outputs:"
+  echo "    -o, --output"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        Output annotated file."
+  echo ""
+  echo "Options:"
+  echo "    For examples on how to use use bcftools annotate see"
+  echo "    http://samtools.github.io/bcftools/howtos/annotate.html."
+  echo "    For more details on the options see"
+  echo "    https://samtools.github.io/bcftools/bcftools.html#annotate."
+  echo ""
+  echo "    --a, --annotations"
+  echo "        type: file, file must exist"
+  echo "        VCF file or tabix-indexed FILE with annotations: CHR\\tPOS[\\tVALUE]+ ."
+  echo ""
+  echo "    --c, --columns"
+  echo "        type: string"
+  echo "        List of columns in the annotation file, e.g."
+  echo "        CHROM,POS,REF,ALT,-,INFO/TAG."
+  echo "        See man page for details."
+  echo ""
+  echo "    --C, --columns_file"
+  echo "        type: file, file must exist"
+  echo "        Read -c columns from FILE, one name per row, with optional --merge_logic"
+  echo "        TYPE: NAME[ TYPE]."
+  echo ""
+  echo "    --e, --exclude"
+  echo "        type: string"
+  echo "        example: QUAL >= 30 && DP >= 10"
+  echo "        Exclude sites for which the expression is true."
+  echo "        See https://samtools.github.io/bcftools/bcftools.html#expressions for"
+  echo "        details."
+  echo ""
+  echo "    --force"
+  echo "        type: boolean_true"
+  echo "        continue even when parsing errors, such as undefined tags, are"
+  echo "        encountered."
+  echo "        Note this can be an unsafe operation and can result in corrupted BCF"
+  echo "        files."
+  echo "        If this option is used, make sure to sanity check the result thoroughly."
+  echo ""
+  echo "    --H, --header_line"
+  echo "        type: string"
+  echo "        Header line which should be appended to the VCF header, can be given"
+  echo "        multiple times."
+  echo ""
+  echo "    --h, --header_lines"
+  echo "        type: file, file must exist"
+  echo "        File with header lines to append to the VCF header."
+  echo "        For example:"
+  echo "          ##INFO=<ID=NUMERIC_TAG,Number=1,Type=Integer,Description=\"Example"
+  echo "        header line\">"
+  echo "          ##INFO=<ID=STRING_TAG,Number=1,Type=String,Description=\"Yet another"
+  echo "        header line\">"
+  echo ""
+  echo "    --I, --set_id"
+  echo "        type: string"
+  echo "        Set ID column using a \`bcftools query\`-like expression, see man page for"
+  echo "        details."
+  echo ""
+  echo "    --include"
+  echo "        type: string"
+  echo "        example: QUAL >= 30 && DP >= 10"
+  echo "        Select sites for which the expression is true."
+  echo "        See https://samtools.github.io/bcftools/bcftools.html#expressions for"
+  echo "        details."
+  echo ""
+  echo "    --k, --keep_sites"
+  echo "        type: boolean_true"
+  echo "        Leave --include/--exclude sites unchanged instead of discarding them."
+  echo ""
+  echo "    --l, --merge_logic"
+  echo "        type: string"
+  echo "        When multiple regions overlap a single record, this option defines how"
+  echo "        to treat multiple annotation values."
+  echo "        See man page for more details."
+  echo ""
+  echo "    --m, --mark_sites"
+  echo "        type: string"
+  echo "        Annotate sites which are present (\"+\") or absent (\"-\") in the -a file"
+  echo "        with a new INFO/TAG flag."
+  echo ""
+  echo "    --min_overlap"
+  echo "        type: string"
+  echo "        Minimum overlap required as a fraction of the variant in the annotation"
+  echo "        -a file (ANN),"
+  echo "        in the target VCF file (:VCF), or both for reciprocal overlap (ANN:VCF)."
+  echo "        By default overlaps of arbitrary length are sufficient."
+  echo "        The option can be used only with the tab-delimited annotation -a file"
+  echo "        and with BEG and END columns present."
+  echo ""
+  echo "    --no_version"
+  echo "        type: boolean_true"
+  echo "        Do not append version and command line information to the output VCF"
+  echo "        header."
+  echo ""
+  echo "    --O, --output_type"
+  echo "        type: string"
+  echo "        choices: [ u, z, b, v ]"
+  echo "        Output type:"
+  echo "          u: uncompressed BCF"
+  echo "          z: compressed VCF"
+  echo "          b: compressed BCF"
+  echo "          v: uncompressed VCF"
+  echo ""
+  echo "    --pair_logic"
+  echo "        type: string"
+  echo "        choices: [ snps, indels, both, all, some, exact ]"
+  echo "        Controls how to match records from the annotation file to the target"
+  echo "        VCF."
+  echo "        Effective only when -a is a VCF or BCF file."
+  echo "        The option replaces the former uninuitive --collapse."
+  echo "        See Common Options for more."
+  echo ""
+  echo "    --r, --regions"
+  echo "        type: string"
+  echo "        example: 20:1000000-2000000"
+  echo "        Restrict to comma-separated list of regions."
+  echo "        Following formats are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​]."
+  echo ""
+  echo "    --R, --regions_file"
+  echo "        type: file, file must exist"
+  echo "        Restrict to regions listed in a file."
+  echo "        Regions can be specified either on a VCF, BED, or tab-delimited file"
+  echo "        (the default)."
+  echo "        For more information check manual."
+  echo ""
+  echo "    --regions_overlap"
+  echo "        type: string"
+  echo "        choices: [ pos, record, variant, 0, 1, 2 ]"
+  echo "        This option controls how overlapping records are determined:"
+  echo "        set to 'pos' or '0' if the VCF record has to have POS inside a region"
+  echo "        (this corresponds to the default behavior of -t/-T);"
+  echo "        set to 'record' or '1' if also overlapping records with POS outside a"
+  echo "        region should be included (this is the default behavior of -r/-R,"
+  echo "        and includes indels with POS at the end of a region, which are"
+  echo "        technically outside the region);"
+  echo "        or set to 'variant' or '2' to include only true overlapping variation"
+  echo "        (compare the full VCF representation \"TA>T-\" vs the true sequence"
+  echo "        variation \"A>-\")."
+  echo ""
+  echo "    --rename_annotations"
+  echo "        type: file, file must exist"
+  echo "        Rename annotations: TYPE/old\\tnew, where TYPE is one of"
+  echo "        FILTER,INFO,FORMAT."
+  echo ""
+  echo "    --rename_chromosomes"
+  echo "        type: file, file must exist"
+  echo "        Rename chromosomes according to the map in file, with \"old_name"
+  echo "        new_name\\n\" pairs"
+  echo "        separated by whitespaces, each on a separate line."
+  echo ""
+  echo "    --samples"
+  echo "        type: string"
+  echo "        Subset of samples to annotate."
+  echo "        See also"
+  echo "        https://samtools.github.io/bcftools/bcftools.html#common_options."
+  echo ""
+  echo "    --samples_file"
+  echo "        type: file, file must exist"
+  echo "        Subset of samples to annotate in file format."
+  echo "        See also"
+  echo "        https://samtools.github.io/bcftools/bcftools.html#common_options."
+  echo ""
+  echo "    --single_overlaps"
+  echo "        type: boolean_true"
+  echo "        Use this option to keep memory requirements low with very large"
+  echo "        annotation files."
+  echo "        Note, however, that this comes at a cost, only single overlapping"
+  echo "        intervals are considered in this mode."
+  echo "        This was the default mode until the commit af6f0c9 (Feb 24 2019)."
+  echo ""
+  echo "    --x, --remove"
+  echo "        type: string"
+  echo "        List of annotations to remove."
+  echo "        Use \"FILTER\" to remove all filters or \"FILTER/SomeFilter\" to remove a"
+  echo "        specific filter."
+  echo "        Similarly, \"INFO\" can be used to remove all INFO tags and \"FORMAT\" to"
+  echo "        remove all FORMAT tags except GT."
+  echo "        To remove all INFO tags except \"FOO\" and \"BAR\", use \"^INFO/FOO,INFO/BAR\""
+  echo "        (and similarly for FORMAT and FILTER)."
+  echo "        \"INFO\" can be abbreviated to \"INF\" and \"FORMAT\" to \"FMT\"."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/bcftools/bcftools_concat/.config.vsh.yaml b/target/executable/bcftools/bcftools_concat/.config.vsh.yaml
index 84657444..f2b99752 100644
--- a/target/executable/bcftools/bcftools_concat/.config.vsh.yaml
+++ b/target/executable/bcftools/bcftools_concat/.config.vsh.yaml
@@ -221,6 +221,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -334,16 +337,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/bcftools/bcftools_concat"
   executable: "target/executable/bcftools/bcftools_concat/bcftools_concat"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/bcftools/bcftools_concat/bcftools_concat b/target/executable/bcftools/bcftools_concat/bcftools_concat
index f17af7f3..6ffb3bd7 100755
--- a/target/executable/bcftools/bcftools_concat/bcftools_concat
+++ b/target/executable/bcftools/bcftools_concat/bcftools_concat
@@ -2,7 +2,7 @@
 
 # bcftools_concat main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,116 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "bcftools_concat main"
-  echo ""
-  echo "Concatenate or combine VCF/BCF files. All source files must have the same sample"
-  echo "columns appearing in the same order. The program can be used, for example, to"
-  echo "concatenate chromosome VCFs into one VCF, or combine a SNP VCF and an indel"
-  echo "VCF into one. The input files must be sorted by chr and position. The files"
-  echo "must be given in the correct order to produce sorted VCF on output unless"
-  echo "the -a, --allow-overlaps option is specified. With the --naive option, the files"
-  echo "are concatenated without being recompressed, which is very fast."
-  echo ""
-  echo "Inputs:"
-  echo "    -i, --input"
-  echo "        type: file, multiple values allowed, file must exist"
-  echo "        Input VCF/BCF files to concatenate."
-  echo ""
-  echo "    -f, --file_list"
-  echo "        type: file, file must exist"
-  echo "        Read the list of VCF/BCF files from a file, one file name per line."
-  echo ""
-  echo "Outputs:"
-  echo "    -o, --output"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        Output concatenated VCF/BCF file."
-  echo ""
-  echo "Options:"
-  echo "    -a, --allow_overlaps"
-  echo "        type: boolean_true"
-  echo "        First coordinate of the next file can precede last record of the current"
-  echo "        file."
-  echo ""
-  echo "    -c, --compact_PS"
-  echo "        type: boolean_true"
-  echo "        Do not output PS tag at each site, only at the start of a new phase set"
-  echo "        block."
-  echo ""
-  echo "    -d, --remove_duplicates"
-  echo "        type: string"
-  echo "        choices: [ snps, indels, both, all, exact, none ]"
-  echo "        Output duplicate records present in multiple files only once:"
-  echo "        <snps|indels|both|all|exact>."
-  echo ""
-  echo "    -l, --ligate"
-  echo "        type: boolean_true"
-  echo "        Ligate phased VCFs by matching phase at overlapping haplotypes."
-  echo ""
-  echo "    --ligate_force"
-  echo "        type: boolean_true"
-  echo "        Ligate even non-overlapping chunks, keep all sites."
-  echo ""
-  echo "    --ligate_warn"
-  echo "        type: boolean_true"
-  echo "        Drop sites in imperfect overlaps."
-  echo ""
-  echo "    --no_version"
-  echo "        type: boolean_true"
-  echo "        Do not append version and command line information to the header."
-  echo ""
-  echo "    -n, --naive"
-  echo "        type: boolean_true"
-  echo "        Concatenate files without recompression, a header check compatibility is"
-  echo "        performed."
-  echo ""
-  echo "    --naive_force"
-  echo "        type: boolean_true"
-  echo "        Same as --naive, but header compatibility is not checked."
-  echo "        Dangerous, use with caution."
-  echo ""
-  echo "    -O, --output_type"
-  echo "        type: string"
-  echo "        choices: [ u, z, b, v ]"
-  echo "        Output type:"
-  echo "          u: uncompressed BCF"
-  echo "          z: compressed VCF"
-  echo "          b: compressed BCF"
-  echo "          v: uncompressed VCF"
-  echo ""
-  echo "    -q, --min_PQ"
-  echo "        type: integer"
-  echo "        example: 30"
-  echo "        Break phase set if phasing quality is lower than <int>."
-  echo ""
-  echo "    -r, --regions"
-  echo "        type: string"
-  echo "        example: 20:1000000-2000000"
-  echo "        Restrict to comma-separated list of regions."
-  echo "        Following formats are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​]."
-  echo ""
-  echo "    -R, --regions_file"
-  echo "        type: file, file must exist"
-  echo "        Restrict to regions listed in a file."
-  echo "        Regions can be specified either on a VCF, BED, or tab-delimited file"
-  echo "        (the default)."
-  echo "        For more information check manual."
-  echo ""
-  echo "    --regions_overlap"
-  echo "        type: string"
-  echo "        choices: [ pos, record, variant, 0, 1, 2 ]"
-  echo "        This option controls how overlapping records are determined:"
-  echo "        set to 'pos' or '0' if the VCF record has to have POS inside a region"
-  echo "        (this corresponds to the default behavior of -t/-T);"
-  echo "        set to 'record' or '1' if also overlapping records with POS outside a"
-  echo "        region should be included (this is the default behavior of -r/-R,"
-  echo "        and includes indels with POS at the end of a region, which are"
-  echo "        technically outside the region);"
-  echo "        or set to 'variant' or '2' to include only true overlapping variation"
-  echo "        (compare the full VCF representation \"TA>T-\" vs the true sequence"
-  echo "        variation \"A>-\")."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -566,9 +456,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo
 
 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_concat"
-LABEL org.opencontainers.image.created="2024-12-03T10:34:02Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:36Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -683,6 +573,142 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "bcftools_concat main"
+  echo ""
+  echo "Concatenate or combine VCF/BCF files. All source files must have the same sample"
+  echo "columns appearing in the same order. The program can be used, for example, to"
+  echo "concatenate chromosome VCFs into one VCF, or combine a SNP VCF and an indel"
+  echo "VCF into one. The input files must be sorted by chr and position. The files"
+  echo "must be given in the correct order to produce sorted VCF on output unless"
+  echo "the -a, --allow-overlaps option is specified. With the --naive option, the files"
+  echo "are concatenated without being recompressed, which is very fast."
+  echo ""
+  echo "Inputs:"
+  echo "    -i, --input"
+  echo "        type: file, multiple values allowed, file must exist"
+  echo "        Input VCF/BCF files to concatenate."
+  echo ""
+  echo "    -f, --file_list"
+  echo "        type: file, file must exist"
+  echo "        Read the list of VCF/BCF files from a file, one file name per line."
+  echo ""
+  echo "Outputs:"
+  echo "    -o, --output"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        Output concatenated VCF/BCF file."
+  echo ""
+  echo "Options:"
+  echo "    -a, --allow_overlaps"
+  echo "        type: boolean_true"
+  echo "        First coordinate of the next file can precede last record of the current"
+  echo "        file."
+  echo ""
+  echo "    -c, --compact_PS"
+  echo "        type: boolean_true"
+  echo "        Do not output PS tag at each site, only at the start of a new phase set"
+  echo "        block."
+  echo ""
+  echo "    -d, --remove_duplicates"
+  echo "        type: string"
+  echo "        choices: [ snps, indels, both, all, exact, none ]"
+  echo "        Output duplicate records present in multiple files only once:"
+  echo "        <snps|indels|both|all|exact>."
+  echo ""
+  echo "    -l, --ligate"
+  echo "        type: boolean_true"
+  echo "        Ligate phased VCFs by matching phase at overlapping haplotypes."
+  echo ""
+  echo "    --ligate_force"
+  echo "        type: boolean_true"
+  echo "        Ligate even non-overlapping chunks, keep all sites."
+  echo ""
+  echo "    --ligate_warn"
+  echo "        type: boolean_true"
+  echo "        Drop sites in imperfect overlaps."
+  echo ""
+  echo "    --no_version"
+  echo "        type: boolean_true"
+  echo "        Do not append version and command line information to the header."
+  echo ""
+  echo "    -n, --naive"
+  echo "        type: boolean_true"
+  echo "        Concatenate files without recompression, a header check compatibility is"
+  echo "        performed."
+  echo ""
+  echo "    --naive_force"
+  echo "        type: boolean_true"
+  echo "        Same as --naive, but header compatibility is not checked."
+  echo "        Dangerous, use with caution."
+  echo ""
+  echo "    -O, --output_type"
+  echo "        type: string"
+  echo "        choices: [ u, z, b, v ]"
+  echo "        Output type:"
+  echo "          u: uncompressed BCF"
+  echo "          z: compressed VCF"
+  echo "          b: compressed BCF"
+  echo "          v: uncompressed VCF"
+  echo ""
+  echo "    -q, --min_PQ"
+  echo "        type: integer"
+  echo "        example: 30"
+  echo "        Break phase set if phasing quality is lower than <int>."
+  echo ""
+  echo "    -r, --regions"
+  echo "        type: string"
+  echo "        example: 20:1000000-2000000"
+  echo "        Restrict to comma-separated list of regions."
+  echo "        Following formats are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​]."
+  echo ""
+  echo "    -R, --regions_file"
+  echo "        type: file, file must exist"
+  echo "        Restrict to regions listed in a file."
+  echo "        Regions can be specified either on a VCF, BED, or tab-delimited file"
+  echo "        (the default)."
+  echo "        For more information check manual."
+  echo ""
+  echo "    --regions_overlap"
+  echo "        type: string"
+  echo "        choices: [ pos, record, variant, 0, 1, 2 ]"
+  echo "        This option controls how overlapping records are determined:"
+  echo "        set to 'pos' or '0' if the VCF record has to have POS inside a region"
+  echo "        (this corresponds to the default behavior of -t/-T);"
+  echo "        set to 'record' or '1' if also overlapping records with POS outside a"
+  echo "        region should be included (this is the default behavior of -r/-R,"
+  echo "        and includes indels with POS at the end of a region, which are"
+  echo "        technically outside the region);"
+  echo "        or set to 'variant' or '2' to include only true overlapping variation"
+  echo "        (compare the full VCF representation \"TA>T-\" vs the true sequence"
+  echo "        variation \"A>-\")."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/bcftools/bcftools_norm/.config.vsh.yaml b/target/executable/bcftools/bcftools_norm/.config.vsh.yaml
index 6b1552e2..a203a903 100644
--- a/target/executable/bcftools/bcftools_norm/.config.vsh.yaml
+++ b/target/executable/bcftools/bcftools_norm/.config.vsh.yaml
@@ -302,6 +302,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -415,16 +418,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/bcftools/bcftools_norm"
   executable: "target/executable/bcftools/bcftools_norm/bcftools_norm"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/bcftools/bcftools_norm/bcftools_norm b/target/executable/bcftools/bcftools_norm/bcftools_norm
index 3e78cb60..72c0c76a 100755
--- a/target/executable/bcftools/bcftools_norm/bcftools_norm
+++ b/target/executable/bcftools/bcftools_norm/bcftools_norm
@@ -2,7 +2,7 @@
 
 # bcftools_norm main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,139 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "bcftools_norm main"
-  echo ""
-  echo "Left-align and normalize indels, check if REF alleles match the reference, split"
-  echo "multiallelic sites into multiple rows;"
-  echo "recover multiallelics from multiple rows."
-  echo ""
-  echo "Inputs:"
-  echo "    -i, --input"
-  echo "        type: file, required parameter, file must exist"
-  echo "        Input VCF/BCF file."
-  echo ""
-  echo "Outputs:"
-  echo "    -o, --output"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        Output normalized VCF/BCF file."
-  echo ""
-  echo "Options:"
-  echo "    -a, --atomize"
-  echo "        type: boolean_true"
-  echo "        Decompose complex variants (e.g., MNVs become consecutive SNVs)."
-  echo ""
-  echo "    --atom_overlaps"
-  echo "        type: string"
-  echo "        choices: [ ., * ]"
-  echo "        Use the star allele (*) for overlapping alleles or set to missing (.)."
-  echo ""
-  echo "    -c, --check_ref"
-  echo "        type: string"
-  echo "        choices: [ e, w, x, s ]"
-  echo "        Check REF alleles and exit (e), warn (w), exclude (x), or set (s) bad"
-  echo "        sites."
-  echo ""
-  echo "    -d, --remove_duplicates"
-  echo "        type: string"
-  echo "        choices: [ snps, indels, both, all, exact, none ]"
-  echo "        Remove duplicate snps, indels, both, all, exact matches, or none (old -D"
-  echo "        option)."
-  echo ""
-  echo "    -f, --fasta_ref"
-  echo "        type: file, file must exist"
-  echo "        Reference fasta sequence file."
-  echo ""
-  echo "    --force"
-  echo "        type: boolean_true"
-  echo "        Try to proceed even if malformed tags are encountered."
-  echo "        Experimental, use at your own risk."
-  echo ""
-  echo "    --keep_sum"
-  echo "        type: string"
-  echo "        Keep vector sum constant when splitting multiallelics (see github issue"
-  echo "        #360)."
-  echo ""
-  echo "    -m, --multiallelics"
-  echo "        type: string"
-  echo "        choices: [ +snps, +indels, +both, +any, -snps, -indels, -both, -any ]"
-  echo "        Split multiallelics (-) or join biallelics (+), type: snps, indels,"
-  echo "        both, any [default: both]."
-  echo ""
-  echo "    --no_version"
-  echo "        type: boolean_true"
-  echo "        Do not append version and command line information to the header."
-  echo ""
-  echo "    -N, --do_not_normalize"
-  echo "        type: boolean_true"
-  echo "        Do not normalize indels (with -m or -c s)."
-  echo ""
-  echo "    --O, --output_type"
-  echo "        type: string"
-  echo "        choices: [ u, z, b, v ]"
-  echo "        Output type:"
-  echo "          u: uncompressed BCF"
-  echo "          z: compressed VCF"
-  echo "          b: compressed BCF"
-  echo "          v: uncompressed VCF"
-  echo ""
-  echo "    --old_rec_tag"
-  echo "        type: string"
-  echo "        Annotate modified records with INFO/STR indicating the original variant."
-  echo ""
-  echo "    --r, --regions"
-  echo "        type: string"
-  echo "        example: 20:1000000-2000000"
-  echo "        Restrict to comma-separated list of regions."
-  echo "        Following formats are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​]."
-  echo ""
-  echo "    --R, --regions_file"
-  echo "        type: file, file must exist"
-  echo "        Restrict to regions listed in a file."
-  echo "        Regions can be specified either on a VCF, BED, or tab-delimited file"
-  echo "        (the default)."
-  echo "        For more information check manual."
-  echo ""
-  echo "    --regions_overlap"
-  echo "        type: string"
-  echo "        choices: [ pos, record, variant, 0, 1, 2 ]"
-  echo "        This option controls how overlapping records are determined:"
-  echo "        set to 'pos' or '0' if the VCF record has to have POS inside a region"
-  echo "        (this corresponds to the default behavior of -t/-T);"
-  echo "        set to 'record' or '1' if also overlapping records with POS outside a"
-  echo "        region should be included (this is the default behavior of -r/-R,"
-  echo "        and includes indels with POS at the end of a region, which are"
-  echo "        technically outside the region);"
-  echo "        or set to 'variant' or '2' to include only true overlapping variation"
-  echo "        (compare the full VCF representation \"TA>T-\" vs the true sequence"
-  echo "        variation \"A>-\")."
-  echo ""
-  echo "    -w, --site_win"
-  echo "        type: integer"
-  echo "        Buffer for sorting lines that changed position during realignment."
-  echo ""
-  echo "    -s, --strict_filter"
-  echo "        type: boolean_true"
-  echo "        When merging (-m+), merged site is PASS only if all sites being merged"
-  echo "        PASS."
-  echo ""
-  echo "    -t, --targets"
-  echo "        type: string"
-  echo "        example: 20:1000000-2000000"
-  echo "        Similar to --regions but streams rather than index-jumps."
-  echo ""
-  echo "    -T, --targets_file"
-  echo "        type: file, file must exist"
-  echo "        Similar to --regions_file but streams rather than index-jumps."
-  echo ""
-  echo "    --targets_overlap"
-  echo "        type: string"
-  echo "        choices: [ pos, record, variant, 0, 1, 2 ]"
-  echo "        Include if POS in the region (0), record overlaps (1), variant overlaps"
-  echo "        (2)."
-  echo "        Similar to --regions_overlap."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -589,9 +456,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo
 
 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_norm"
-LABEL org.opencontainers.image.created="2024-12-03T10:34:03Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:46Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -706,6 +573,165 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "bcftools_norm main"
+  echo ""
+  echo "Left-align and normalize indels, check if REF alleles match the reference, split"
+  echo "multiallelic sites into multiple rows;"
+  echo "recover multiallelics from multiple rows."
+  echo ""
+  echo "Inputs:"
+  echo "    -i, --input"
+  echo "        type: file, required parameter, file must exist"
+  echo "        Input VCF/BCF file."
+  echo ""
+  echo "Outputs:"
+  echo "    -o, --output"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        Output normalized VCF/BCF file."
+  echo ""
+  echo "Options:"
+  echo "    -a, --atomize"
+  echo "        type: boolean_true"
+  echo "        Decompose complex variants (e.g., MNVs become consecutive SNVs)."
+  echo ""
+  echo "    --atom_overlaps"
+  echo "        type: string"
+  echo "        choices: [ ., * ]"
+  echo "        Use the star allele (*) for overlapping alleles or set to missing (.)."
+  echo ""
+  echo "    -c, --check_ref"
+  echo "        type: string"
+  echo "        choices: [ e, w, x, s ]"
+  echo "        Check REF alleles and exit (e), warn (w), exclude (x), or set (s) bad"
+  echo "        sites."
+  echo ""
+  echo "    -d, --remove_duplicates"
+  echo "        type: string"
+  echo "        choices: [ snps, indels, both, all, exact, none ]"
+  echo "        Remove duplicate snps, indels, both, all, exact matches, or none (old -D"
+  echo "        option)."
+  echo ""
+  echo "    -f, --fasta_ref"
+  echo "        type: file, file must exist"
+  echo "        Reference fasta sequence file."
+  echo ""
+  echo "    --force"
+  echo "        type: boolean_true"
+  echo "        Try to proceed even if malformed tags are encountered."
+  echo "        Experimental, use at your own risk."
+  echo ""
+  echo "    --keep_sum"
+  echo "        type: string"
+  echo "        Keep vector sum constant when splitting multiallelics (see github issue"
+  echo "        #360)."
+  echo ""
+  echo "    -m, --multiallelics"
+  echo "        type: string"
+  echo "        choices: [ +snps, +indels, +both, +any, -snps, -indels, -both, -any ]"
+  echo "        Split multiallelics (-) or join biallelics (+), type: snps, indels,"
+  echo "        both, any [default: both]."
+  echo ""
+  echo "    --no_version"
+  echo "        type: boolean_true"
+  echo "        Do not append version and command line information to the header."
+  echo ""
+  echo "    -N, --do_not_normalize"
+  echo "        type: boolean_true"
+  echo "        Do not normalize indels (with -m or -c s)."
+  echo ""
+  echo "    --O, --output_type"
+  echo "        type: string"
+  echo "        choices: [ u, z, b, v ]"
+  echo "        Output type:"
+  echo "          u: uncompressed BCF"
+  echo "          z: compressed VCF"
+  echo "          b: compressed BCF"
+  echo "          v: uncompressed VCF"
+  echo ""
+  echo "    --old_rec_tag"
+  echo "        type: string"
+  echo "        Annotate modified records with INFO/STR indicating the original variant."
+  echo ""
+  echo "    --r, --regions"
+  echo "        type: string"
+  echo "        example: 20:1000000-2000000"
+  echo "        Restrict to comma-separated list of regions."
+  echo "        Following formats are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​]."
+  echo ""
+  echo "    --R, --regions_file"
+  echo "        type: file, file must exist"
+  echo "        Restrict to regions listed in a file."
+  echo "        Regions can be specified either on a VCF, BED, or tab-delimited file"
+  echo "        (the default)."
+  echo "        For more information check manual."
+  echo ""
+  echo "    --regions_overlap"
+  echo "        type: string"
+  echo "        choices: [ pos, record, variant, 0, 1, 2 ]"
+  echo "        This option controls how overlapping records are determined:"
+  echo "        set to 'pos' or '0' if the VCF record has to have POS inside a region"
+  echo "        (this corresponds to the default behavior of -t/-T);"
+  echo "        set to 'record' or '1' if also overlapping records with POS outside a"
+  echo "        region should be included (this is the default behavior of -r/-R,"
+  echo "        and includes indels with POS at the end of a region, which are"
+  echo "        technically outside the region);"
+  echo "        or set to 'variant' or '2' to include only true overlapping variation"
+  echo "        (compare the full VCF representation \"TA>T-\" vs the true sequence"
+  echo "        variation \"A>-\")."
+  echo ""
+  echo "    -w, --site_win"
+  echo "        type: integer"
+  echo "        Buffer for sorting lines that changed position during realignment."
+  echo ""
+  echo "    -s, --strict_filter"
+  echo "        type: boolean_true"
+  echo "        When merging (-m+), merged site is PASS only if all sites being merged"
+  echo "        PASS."
+  echo ""
+  echo "    -t, --targets"
+  echo "        type: string"
+  echo "        example: 20:1000000-2000000"
+  echo "        Similar to --regions but streams rather than index-jumps."
+  echo ""
+  echo "    -T, --targets_file"
+  echo "        type: file, file must exist"
+  echo "        Similar to --regions_file but streams rather than index-jumps."
+  echo ""
+  echo "    --targets_overlap"
+  echo "        type: string"
+  echo "        choices: [ pos, record, variant, 0, 1, 2 ]"
+  echo "        Include if POS in the region (0), record overlaps (1), variant overlaps"
+  echo "        (2)."
+  echo "        Similar to --regions_overlap."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/bcftools/bcftools_sort/.config.vsh.yaml b/target/executable/bcftools/bcftools_sort/.config.vsh.yaml
index 3c4bd419..48d0ff9d 100644
--- a/target/executable/bcftools/bcftools_sort/.config.vsh.yaml
+++ b/target/executable/bcftools/bcftools_sort/.config.vsh.yaml
@@ -76,6 +76,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -184,16 +187,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/bcftools/bcftools_sort"
   executable: "target/executable/bcftools/bcftools_sort/bcftools_sort"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/bcftools/bcftools_sort/bcftools_sort b/target/executable/bcftools/bcftools_sort/bcftools_sort
index 2b5f3881..7d17c81e 100755
--- a/target/executable/bcftools/bcftools_sort/bcftools_sort
+++ b/target/executable/bcftools/bcftools_sort/bcftools_sort
@@ -2,7 +2,7 @@
 
 # bcftools_sort main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,33 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "bcftools_sort main"
-  echo ""
-  echo "Sorts VCF/BCF files."
-  echo ""
-  echo "Inputs:"
-  echo "    -i, --input"
-  echo "        type: file, required parameter, file must exist"
-  echo "        Input VCF/BCF file."
-  echo ""
-  echo "Outputs:"
-  echo "    -o, --output"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        Output sorted VCF/BCF file."
-  echo ""
-  echo "Options:"
-  echo "    -O, --output_type"
-  echo "        type: string"
-  echo "        choices: [ b, u, z, v ]"
-  echo "        Compresses or uncompresses the output."
-  echo "        The options are:"
-  echo "          b: compressed BCF,"
-  echo "          u: uncompressed BCF,"
-  echo "          z: compressed VCF,"
-  echo "          v: uncompressed VCF."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -483,9 +456,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo
 
 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_sort"
-LABEL org.opencontainers.image.created="2024-12-03T10:34:02Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:35Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -600,6 +573,59 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "bcftools_sort main"
+  echo ""
+  echo "Sorts VCF/BCF files."
+  echo ""
+  echo "Inputs:"
+  echo "    -i, --input"
+  echo "        type: file, required parameter, file must exist"
+  echo "        Input VCF/BCF file."
+  echo ""
+  echo "Outputs:"
+  echo "    -o, --output"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        Output sorted VCF/BCF file."
+  echo ""
+  echo "Options:"
+  echo "    -O, --output_type"
+  echo "        type: string"
+  echo "        choices: [ b, u, z, v ]"
+  echo "        Compresses or uncompresses the output."
+  echo "        The options are:"
+  echo "          b: compressed BCF,"
+  echo "          u: uncompressed BCF,"
+  echo "          z: compressed VCF,"
+  echo "          v: uncompressed VCF."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/bcftools/bcftools_stats/.config.vsh.yaml b/target/executable/bcftools/bcftools_stats/.config.vsh.yaml
index 3cc2973e..9625263c 100644
--- a/target/executable/bcftools/bcftools_stats/.config.vsh.yaml
+++ b/target/executable/bcftools/bcftools_stats/.config.vsh.yaml
@@ -344,6 +344,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -457,16 +460,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/bcftools/bcftools_stats"
   executable: "target/executable/bcftools/bcftools_stats/bcftools_stats"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/bcftools/bcftools_stats/bcftools_stats b/target/executable/bcftools/bcftools_stats/bcftools_stats
index 06a2d5e2..6097790f 100755
--- a/target/executable/bcftools/bcftools_stats/bcftools_stats
+++ b/target/executable/bcftools/bcftools_stats/bcftools_stats
@@ -2,7 +2,7 @@
 
 # bcftools_stats main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,176 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "bcftools_stats main"
-  echo ""
-  echo "Parses VCF or BCF and produces a txt stats file which can be plotted using"
-  echo "plot-vcfstats."
-  echo "When two files are given, the program generates separate stats for intersection"
-  echo "and the complements. By default only sites are compared, -s/-S must given to"
-  echo "include"
-  echo "also sample columns."
-  echo ""
-  echo "Inputs:"
-  echo "    -i, --input"
-  echo "        type: file, required parameter, multiple values allowed, file must exist"
-  echo "        Input VCF/BCF file. Maximum of two files."
-  echo ""
-  echo "Outputs:"
-  echo "    -o, --output"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        Output txt statistics file."
-  echo ""
-  echo "Options:"
-  echo "    --af_bins, --allele_frequency_bins"
-  echo "        type: string"
-  echo "        example: 0.1,0.5,1"
-  echo "        Allele frequency bins, a list of bin values (0.1,0.5,1)."
-  echo ""
-  echo "    --af_bins_file, --allele_frequency_bins_file"
-  echo "        type: file, file must exist"
-  echo "        Same as allele_frequency_bins, but in a file."
-  echo "        Format of file is one value per line."
-  echo "        e.g."
-  echo "          0.1"
-  echo "          0.5"
-  echo "          1"
-  echo ""
-  echo "    --af_tag, --allele_frequency_tag"
-  echo "        type: string"
-  echo "        Allele frequency tag to use, by default estimated from AN,AC or GT."
-  echo ""
-  echo "    --first_only, --first_allele_only"
-  echo "        type: boolean_true"
-  echo "        Include only 1st allele at multiallelic sites."
-  echo ""
-  echo "    --c, --collapse"
-  echo "        type: string"
-  echo "        choices: [ snps, indels, both, all, some, none ]"
-  echo "        Treat as identical records with <snps|indels|both|all|some|none>."
-  echo "        See https://samtools.github.io/bcftools/bcftools.html#common_options for"
-  echo "        details."
-  echo ""
-  echo "    --d, --depth"
-  echo "        type: string"
-  echo "        example: 0,500,1"
-  echo "        Depth distribution: min,max,bin size."
-  echo ""
-  echo "    --e, --exclude"
-  echo "        type: string"
-  echo "        example: QUAL < 30 && DP < 10"
-  echo "        Exclude sites for which the expression is true."
-  echo "        See https://samtools.github.io/bcftools/bcftools.html#expressions for"
-  echo "        details."
-  echo ""
-  echo "    --E, --exons"
-  echo "        type: file, file must exist"
-  echo "        tab-delimited file with exons for indel frameshifts statistics."
-  echo "        The columns of the file are CHR, FROM, TO, with 1-based, inclusive,"
-  echo "        positions."
-  echo "        The file is BGZF-compressed and indexed with tabix (e.g. tabix -s1 -b2"
-  echo "        -e3 file.gz)."
-  echo ""
-  echo "    --f, --apply_filters"
-  echo "        type: string"
-  echo "        Require at least one of the listed FILTER strings (e.g. \"PASS,.\")."
-  echo ""
-  echo "    --F, --fasta_reference"
-  echo "        type: file, file must exist"
-  echo "        Faidx indexed reference sequence file to determine INDEL context."
-  echo ""
-  echo "    --i, --include"
-  echo "        type: string"
-  echo "        example: QUAL >= 30 && DP >= 10"
-  echo "        Select sites for which the expression is true."
-  echo "        See https://samtools.github.io/bcftools/bcftools.html#expressions for"
-  echo "        details."
-  echo ""
-  echo "    --I, --split_by_ID"
-  echo "        type: boolean_true"
-  echo "        Collect stats for sites with ID separately (known vs novel)."
-  echo ""
-  echo "    --r, --regions"
-  echo "        type: string"
-  echo "        example: 20:1000000-2000000"
-  echo "        Restrict to comma-separated list of regions."
-  echo "        Following formats are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​]."
-  echo ""
-  echo "    --R, --regions_file"
-  echo "        type: file, file must exist"
-  echo "        Restrict to regions listed in a file."
-  echo "        Regions can be specified either on a VCF, BED, or tab-delimited file"
-  echo "        (the default)."
-  echo "        For more information check manual."
-  echo ""
-  echo "    --regions_overlap"
-  echo "        type: string"
-  echo "        choices: [ pos, record, variant, 0, 1, 2 ]"
-  echo "        This option controls how overlapping records are determined:"
-  echo "        set to 'pos' or '0' if the VCF record has to have POS inside a region"
-  echo "        (this corresponds to the default behavior of -t/-T);"
-  echo "        set to 'record' or '1' if also overlapping records with POS outside a"
-  echo "        region should be included (this is the default behavior of -r/-R,"
-  echo "        and includes indels with POS at the end of a region, which are"
-  echo "        technically outside the region);"
-  echo "        or set to 'variant' or '2' to include only true overlapping variation"
-  echo "        (compare the full VCF representation \"TA>T-\" vs the true sequence"
-  echo "        variation \"A>-\")."
-  echo ""
-  echo "    --s, --samples"
-  echo "        type: string"
-  echo "        List of samples for sample stats, \"-\" to include all samples."
-  echo ""
-  echo "    --S, --samples_file"
-  echo "        type: file, file must exist"
-  echo "        File of samples to include."
-  echo "        e.g."
-  echo "          sample1    1"
-  echo "          sample2    2"
-  echo "          sample3    2"
-  echo ""
-  echo "    --t, --targets"
-  echo "        type: string"
-  echo "        example: 20:1000000-2000000"
-  echo "        Similar as -r, --regions, but the next position is accessed by streaming"
-  echo "        the whole VCF/BCF"
-  echo "        rather than using the tbi/csi index. Both -r and -t options can be"
-  echo "        applied simultaneously: -r uses the"
-  echo "        index to jump to a region and -t discards positions which are not in the"
-  echo "        targets. Unlike -r, targets"
-  echo "        can be prefixed with \"^\" to request logical complement. For example,"
-  echo "        \"^X,Y,MT\" indicates that"
-  echo "        sequences X, Y and MT should be skipped. Yet another difference between"
-  echo "        the -t/-T and -r/-R is"
-  echo "        that -r/-R checks for proper overlaps and considers both POS and the end"
-  echo "        position of an indel,"
-  echo "        while -t/-T considers the POS coordinate only (by default; see also"
-  echo "        --regions-overlap and --targets-overlap)."
-  echo "        Note that -t cannot be used in combination with -T."
-  echo "        Following formats are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​]."
-  echo ""
-  echo "    --T, --targets_file"
-  echo "        type: file, file must exist"
-  echo "        Similar to --regions_file option but streams rather than index-jumps."
-  echo ""
-  echo "    --targets_overlaps"
-  echo "        type: string"
-  echo "        choices: [ pos, record, variant, 0, 1, 2 ]"
-  echo "        Include if POS in the region (0), record overlaps (1), variant overlaps"
-  echo "        (2)."
-  echo ""
-  echo "    --u, --user_tstv"
-  echo "        type: string"
-  echo "        Collect Ts/Tv stats for any tag using the given binning [0:1:100]."
-  echo "        Format is <TAG[:min:max:n]>."
-  echo "        A subfield can be selected as e.g. 'PV4[0]', here the first value of the"
-  echo "        PV4 tag."
-  echo ""
-  echo "    --v, --verbose"
-  echo "        type: boolean_true"
-  echo "        Produce verbose per-site and per-sample output."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -626,9 +456,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo
 
 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_stats"
-LABEL org.opencontainers.image.created="2024-12-03T10:34:03Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:35Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -743,6 +573,202 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "bcftools_stats main"
+  echo ""
+  echo "Parses VCF or BCF and produces a txt stats file which can be plotted using"
+  echo "plot-vcfstats."
+  echo "When two files are given, the program generates separate stats for intersection"
+  echo "and the complements. By default only sites are compared, -s/-S must given to"
+  echo "include"
+  echo "also sample columns."
+  echo ""
+  echo "Inputs:"
+  echo "    -i, --input"
+  echo "        type: file, required parameter, multiple values allowed, file must exist"
+  echo "        Input VCF/BCF file. Maximum of two files."
+  echo ""
+  echo "Outputs:"
+  echo "    -o, --output"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        Output txt statistics file."
+  echo ""
+  echo "Options:"
+  echo "    --af_bins, --allele_frequency_bins"
+  echo "        type: string"
+  echo "        example: 0.1,0.5,1"
+  echo "        Allele frequency bins, a list of bin values (0.1,0.5,1)."
+  echo ""
+  echo "    --af_bins_file, --allele_frequency_bins_file"
+  echo "        type: file, file must exist"
+  echo "        Same as allele_frequency_bins, but in a file."
+  echo "        Format of file is one value per line."
+  echo "        e.g."
+  echo "          0.1"
+  echo "          0.5"
+  echo "          1"
+  echo ""
+  echo "    --af_tag, --allele_frequency_tag"
+  echo "        type: string"
+  echo "        Allele frequency tag to use, by default estimated from AN,AC or GT."
+  echo ""
+  echo "    --first_only, --first_allele_only"
+  echo "        type: boolean_true"
+  echo "        Include only 1st allele at multiallelic sites."
+  echo ""
+  echo "    --c, --collapse"
+  echo "        type: string"
+  echo "        choices: [ snps, indels, both, all, some, none ]"
+  echo "        Treat as identical records with <snps|indels|both|all|some|none>."
+  echo "        See https://samtools.github.io/bcftools/bcftools.html#common_options for"
+  echo "        details."
+  echo ""
+  echo "    --d, --depth"
+  echo "        type: string"
+  echo "        example: 0,500,1"
+  echo "        Depth distribution: min,max,bin size."
+  echo ""
+  echo "    --e, --exclude"
+  echo "        type: string"
+  echo "        example: QUAL < 30 && DP < 10"
+  echo "        Exclude sites for which the expression is true."
+  echo "        See https://samtools.github.io/bcftools/bcftools.html#expressions for"
+  echo "        details."
+  echo ""
+  echo "    --E, --exons"
+  echo "        type: file, file must exist"
+  echo "        tab-delimited file with exons for indel frameshifts statistics."
+  echo "        The columns of the file are CHR, FROM, TO, with 1-based, inclusive,"
+  echo "        positions."
+  echo "        The file is BGZF-compressed and indexed with tabix (e.g. tabix -s1 -b2"
+  echo "        -e3 file.gz)."
+  echo ""
+  echo "    --f, --apply_filters"
+  echo "        type: string"
+  echo "        Require at least one of the listed FILTER strings (e.g. \"PASS,.\")."
+  echo ""
+  echo "    --F, --fasta_reference"
+  echo "        type: file, file must exist"
+  echo "        Faidx indexed reference sequence file to determine INDEL context."
+  echo ""
+  echo "    --i, --include"
+  echo "        type: string"
+  echo "        example: QUAL >= 30 && DP >= 10"
+  echo "        Select sites for which the expression is true."
+  echo "        See https://samtools.github.io/bcftools/bcftools.html#expressions for"
+  echo "        details."
+  echo ""
+  echo "    --I, --split_by_ID"
+  echo "        type: boolean_true"
+  echo "        Collect stats for sites with ID separately (known vs novel)."
+  echo ""
+  echo "    --r, --regions"
+  echo "        type: string"
+  echo "        example: 20:1000000-2000000"
+  echo "        Restrict to comma-separated list of regions."
+  echo "        Following formats are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​]."
+  echo ""
+  echo "    --R, --regions_file"
+  echo "        type: file, file must exist"
+  echo "        Restrict to regions listed in a file."
+  echo "        Regions can be specified either on a VCF, BED, or tab-delimited file"
+  echo "        (the default)."
+  echo "        For more information check manual."
+  echo ""
+  echo "    --regions_overlap"
+  echo "        type: string"
+  echo "        choices: [ pos, record, variant, 0, 1, 2 ]"
+  echo "        This option controls how overlapping records are determined:"
+  echo "        set to 'pos' or '0' if the VCF record has to have POS inside a region"
+  echo "        (this corresponds to the default behavior of -t/-T);"
+  echo "        set to 'record' or '1' if also overlapping records with POS outside a"
+  echo "        region should be included (this is the default behavior of -r/-R,"
+  echo "        and includes indels with POS at the end of a region, which are"
+  echo "        technically outside the region);"
+  echo "        or set to 'variant' or '2' to include only true overlapping variation"
+  echo "        (compare the full VCF representation \"TA>T-\" vs the true sequence"
+  echo "        variation \"A>-\")."
+  echo ""
+  echo "    --s, --samples"
+  echo "        type: string"
+  echo "        List of samples for sample stats, \"-\" to include all samples."
+  echo ""
+  echo "    --S, --samples_file"
+  echo "        type: file, file must exist"
+  echo "        File of samples to include."
+  echo "        e.g."
+  echo "          sample1    1"
+  echo "          sample2    2"
+  echo "          sample3    2"
+  echo ""
+  echo "    --t, --targets"
+  echo "        type: string"
+  echo "        example: 20:1000000-2000000"
+  echo "        Similar as -r, --regions, but the next position is accessed by streaming"
+  echo "        the whole VCF/BCF"
+  echo "        rather than using the tbi/csi index. Both -r and -t options can be"
+  echo "        applied simultaneously: -r uses the"
+  echo "        index to jump to a region and -t discards positions which are not in the"
+  echo "        targets. Unlike -r, targets"
+  echo "        can be prefixed with \"^\" to request logical complement. For example,"
+  echo "        \"^X,Y,MT\" indicates that"
+  echo "        sequences X, Y and MT should be skipped. Yet another difference between"
+  echo "        the -t/-T and -r/-R is"
+  echo "        that -r/-R checks for proper overlaps and considers both POS and the end"
+  echo "        position of an indel,"
+  echo "        while -t/-T considers the POS coordinate only (by default; see also"
+  echo "        --regions-overlap and --targets-overlap)."
+  echo "        Note that -t cannot be used in combination with -T."
+  echo "        Following formats are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​]."
+  echo ""
+  echo "    --T, --targets_file"
+  echo "        type: file, file must exist"
+  echo "        Similar to --regions_file option but streams rather than index-jumps."
+  echo ""
+  echo "    --targets_overlaps"
+  echo "        type: string"
+  echo "        choices: [ pos, record, variant, 0, 1, 2 ]"
+  echo "        Include if POS in the region (0), record overlaps (1), variant overlaps"
+  echo "        (2)."
+  echo ""
+  echo "    --u, --user_tstv"
+  echo "        type: string"
+  echo "        Collect Ts/Tv stats for any tag using the given binning [0:1:100]."
+  echo "        Format is <TAG[:min:max:n]>."
+  echo "        A subfield can be selected as e.g. 'PV4[0]', here the first value of the"
+  echo "        PV4 tag."
+  echo ""
+  echo "    --v, --verbose"
+  echo "        type: boolean_true"
+  echo "        Produce verbose per-site and per-sample output."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/bcl_convert/.config.vsh.yaml b/target/executable/bcl_convert/.config.vsh.yaml
index 03da7f15..66821963 100644
--- a/target/executable/bcl_convert/.config.vsh.yaml
+++ b/target/executable/bcl_convert/.config.vsh.yaml
@@ -290,6 +290,16 @@ argument_groups:
     direction: "output"
     multiple: false
     multiple_sep: ";"
+  - type: "boolean"
+    name: "--force"
+    description: "Allow destination directory to already exist and overwrite files.\n"
+    info: null
+    example:
+    - true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
 resources:
 - type: "bash_script"
   path: "script.sh"
@@ -303,6 +313,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -417,16 +430,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/bcl_convert"
   executable: "target/executable/bcl_convert/bcl_convert"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/bcl_convert/bcl_convert b/target/executable/bcl_convert/bcl_convert
index c8e2bc66..d73d6552 100755
--- a/target/executable/bcl_convert/bcl_convert
+++ b/target/executable/bcl_convert/bcl_convert
@@ -2,7 +2,7 @@
 
 # bcl_convert main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -173,143 +173,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "bcl_convert main"
-  echo ""
-  echo "Convert bcl files to fastq files using bcl-convert."
-  echo "Information about upgrading from bcl2fastq via"
-  echo "[Upgrading from bcl2fastq to BCL"
-  echo "Convert](https://emea.support.illumina.com/bulletins/2020/10/upgrading-from-bcl2fastq-to-bcl-convert.html)"
-  echo "and [BCL Convert Compatible"
-  echo "Products](https://support.illumina.com/sequencing/sequencing_software/bcl-convert/compatibility.html)"
-  echo ""
-  echo "Input arguments:"
-  echo "    -i, --bcl_input_directory"
-  echo "        type: file, required parameter, file must exist"
-  echo "        example: bcl_dir"
-  echo "        Input run directory"
-  echo ""
-  echo "    -s, --sample_sheet"
-  echo "        type: file, file must exist"
-  echo "        example: bcl_dir/sample_sheet.csv"
-  echo "        Path to SampleSheet.csv file (default searched for in"
-  echo "        --bcl_input_directory)"
-  echo ""
-  echo "    --run_info"
-  echo "        type: file, file must exist"
-  echo "        example: bcl_dir/RunInfo.xml"
-  echo "        Path to RunInfo.xml file (default root of BCL input directory)"
-  echo ""
-  echo "Lane and tile settings:"
-  echo "    --bcl_only_lane"
-  echo "        type: integer"
-  echo "        example: 1"
-  echo "        Convert only specified lane number (default all lanes)"
-  echo ""
-  echo "    --first_tile_only"
-  echo "        type: boolean"
-  echo "        example: true"
-  echo "        Only convert first tile of input (for testing & debugging)"
-  echo ""
-  echo "    --tiles"
-  echo "        type: string"
-  echo "        example: s_[0-9]+_1"
-  echo "        Process only a subset of tiles by a regular expression"
-  echo ""
-  echo "    --exclude_tiles"
-  echo "        type: string"
-  echo "        example: s_[0-9]+_1"
-  echo "        Exclude set of tiles by a regular expression"
-  echo ""
-  echo "Resource arguments:"
-  echo "    --shared_thread_odirect_output"
-  echo "        type: boolean"
-  echo "        example: true"
-  echo "        Use linux native asynchronous io (io_submit) for file output"
-  echo "        (Default=false)"
-  echo ""
-  echo "    --bcl_num_parallel_tiles"
-  echo "        type: integer"
-  echo "        example: 1"
-  echo "        \\# of tiles to process in parallel (default 1)"
-  echo ""
-  echo "    --bcl_num_conversion_threads"
-  echo "        type: integer"
-  echo "        example: 1"
-  echo "        \\# of threads for conversion (per tile, default # cpu threads)"
-  echo ""
-  echo "    --bcl_num_compression_threads"
-  echo "        type: integer"
-  echo "        example: 1"
-  echo "        \\# of threads for fastq.gz output compression (per tile, default # cpu"
-  echo "        threads, or HW+12)"
-  echo ""
-  echo "    --bcl_num_decompression_threads"
-  echo "        type: integer"
-  echo "        example: 1"
-  echo "        \\# of threads for bcl/cbcl input decompression (per tile, default half #"
-  echo "        cpu threads, or HW+8). Only applies when preloading files"
-  echo ""
-  echo "Run arguments:"
-  echo "    --bcl_only_matched_reads"
-  echo "        type: boolean"
-  echo "        example: true"
-  echo "        For pure BCL conversion, do not output files for 'Undetermined'"
-  echo "        [unmatched] reads (output by default)"
-  echo ""
-  echo "    --no_lane_splitting"
-  echo "        type: boolean"
-  echo "        example: true"
-  echo "        Do not split FASTQ file by lane (false by default)"
-  echo ""
-  echo "    --num_unknown_barcodes_reported"
-  echo "        type: integer"
-  echo "        example: 1000"
-  echo "        \\# of Top Unknown Barcodes to output (1000 by default)"
-  echo ""
-  echo "    --bcl_validate_sample_sheet_only"
-  echo "        type: boolean"
-  echo "        example: true"
-  echo "        Only validate RunInfo.xml & SampleSheet files (produce no FASTQ files)"
-  echo ""
-  echo "    --strict_mode"
-  echo "        type: boolean"
-  echo "        example: true"
-  echo "        Abort if any files are missing (false by default)"
-  echo ""
-  echo "    --sample_name_column_enabled"
-  echo "        type: boolean"
-  echo "        example: true"
-  echo "        Use sample sheet 'Sample_Name' column when naming fastq files &"
-  echo "        subdirectories"
-  echo ""
-  echo "Output arguments:"
-  echo "    -o, --output_directory"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        example: fastq_dir"
-  echo "        Output directory containig fastq files"
-  echo ""
-  echo "    --bcl_sampleproject_subdirectories"
-  echo "        type: boolean"
-  echo "        example: true"
-  echo "        Output to subdirectories based upon sample sheet 'Sample_Project' column"
-  echo ""
-  echo "    --fastq_gzip_compression_level"
-  echo "        type: integer"
-  echo "        example: 1"
-  echo "        Set fastq output compression level 0-9 (default 1)"
-  echo ""
-  echo "    --reports"
-  echo "        type: file, output, file must exist"
-  echo "        example: reports_dir"
-  echo "        Reports directory"
-  echo ""
-  echo "    --logs"
-  echo "        type: file, output, file must exist"
-  echo "        example: logs_dir"
-  echo "        Reports directory"
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -599,9 +462,9 @@ RUN echo "bcl-convert: \"$(bcl-convert -V 2>&1 >/dev/null | sed -n '/Version/ s/
 
 LABEL org.opencontainers.image.authors="Toni Verbeiren, Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component bcl_convert"
-LABEL org.opencontainers.image.created="2024-12-03T10:34:01Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:44Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -716,6 +579,174 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "bcl_convert main"
+  echo ""
+  echo "Convert bcl files to fastq files using bcl-convert."
+  echo "Information about upgrading from bcl2fastq via"
+  echo "[Upgrading from bcl2fastq to BCL"
+  echo "Convert](https://emea.support.illumina.com/bulletins/2020/10/upgrading-from-bcl2fastq-to-bcl-convert.html)"
+  echo "and [BCL Convert Compatible"
+  echo "Products](https://support.illumina.com/sequencing/sequencing_software/bcl-convert/compatibility.html)"
+  echo ""
+  echo "Input arguments:"
+  echo "    -i, --bcl_input_directory"
+  echo "        type: file, required parameter, file must exist"
+  echo "        example: bcl_dir"
+  echo "        Input run directory"
+  echo ""
+  echo "    -s, --sample_sheet"
+  echo "        type: file, file must exist"
+  echo "        example: bcl_dir/sample_sheet.csv"
+  echo "        Path to SampleSheet.csv file (default searched for in"
+  echo "        --bcl_input_directory)"
+  echo ""
+  echo "    --run_info"
+  echo "        type: file, file must exist"
+  echo "        example: bcl_dir/RunInfo.xml"
+  echo "        Path to RunInfo.xml file (default root of BCL input directory)"
+  echo ""
+  echo "Lane and tile settings:"
+  echo "    --bcl_only_lane"
+  echo "        type: integer"
+  echo "        example: 1"
+  echo "        Convert only specified lane number (default all lanes)"
+  echo ""
+  echo "    --first_tile_only"
+  echo "        type: boolean"
+  echo "        example: true"
+  echo "        Only convert first tile of input (for testing & debugging)"
+  echo ""
+  echo "    --tiles"
+  echo "        type: string"
+  echo "        example: s_[0-9]+_1"
+  echo "        Process only a subset of tiles by a regular expression"
+  echo ""
+  echo "    --exclude_tiles"
+  echo "        type: string"
+  echo "        example: s_[0-9]+_1"
+  echo "        Exclude set of tiles by a regular expression"
+  echo ""
+  echo "Resource arguments:"
+  echo "    --shared_thread_odirect_output"
+  echo "        type: boolean"
+  echo "        example: true"
+  echo "        Use linux native asynchronous io (io_submit) for file output"
+  echo "        (Default=false)"
+  echo ""
+  echo "    --bcl_num_parallel_tiles"
+  echo "        type: integer"
+  echo "        example: 1"
+  echo "        \\# of tiles to process in parallel (default 1)"
+  echo ""
+  echo "    --bcl_num_conversion_threads"
+  echo "        type: integer"
+  echo "        example: 1"
+  echo "        \\# of threads for conversion (per tile, default # cpu threads)"
+  echo ""
+  echo "    --bcl_num_compression_threads"
+  echo "        type: integer"
+  echo "        example: 1"
+  echo "        \\# of threads for fastq.gz output compression (per tile, default # cpu"
+  echo "        threads, or HW+12)"
+  echo ""
+  echo "    --bcl_num_decompression_threads"
+  echo "        type: integer"
+  echo "        example: 1"
+  echo "        \\# of threads for bcl/cbcl input decompression (per tile, default half #"
+  echo "        cpu threads, or HW+8). Only applies when preloading files"
+  echo ""
+  echo "Run arguments:"
+  echo "    --bcl_only_matched_reads"
+  echo "        type: boolean"
+  echo "        example: true"
+  echo "        For pure BCL conversion, do not output files for 'Undetermined'"
+  echo "        [unmatched] reads (output by default)"
+  echo ""
+  echo "    --no_lane_splitting"
+  echo "        type: boolean"
+  echo "        example: true"
+  echo "        Do not split FASTQ file by lane (false by default)"
+  echo ""
+  echo "    --num_unknown_barcodes_reported"
+  echo "        type: integer"
+  echo "        example: 1000"
+  echo "        \\# of Top Unknown Barcodes to output (1000 by default)"
+  echo ""
+  echo "    --bcl_validate_sample_sheet_only"
+  echo "        type: boolean"
+  echo "        example: true"
+  echo "        Only validate RunInfo.xml & SampleSheet files (produce no FASTQ files)"
+  echo ""
+  echo "    --strict_mode"
+  echo "        type: boolean"
+  echo "        example: true"
+  echo "        Abort if any files are missing (false by default)"
+  echo ""
+  echo "    --sample_name_column_enabled"
+  echo "        type: boolean"
+  echo "        example: true"
+  echo "        Use sample sheet 'Sample_Name' column when naming fastq files &"
+  echo "        subdirectories"
+  echo ""
+  echo "Output arguments:"
+  echo "    -o, --output_directory"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        example: fastq_dir"
+  echo "        Output directory containig fastq files"
+  echo ""
+  echo "    --bcl_sampleproject_subdirectories"
+  echo "        type: boolean"
+  echo "        example: true"
+  echo "        Output to subdirectories based upon sample sheet 'Sample_Project' column"
+  echo ""
+  echo "    --fastq_gzip_compression_level"
+  echo "        type: integer"
+  echo "        example: 1"
+  echo "        Set fastq output compression level 0-9 (default 1)"
+  echo ""
+  echo "    --reports"
+  echo "        type: file, output, file must exist"
+  echo "        example: reports_dir"
+  echo "        Reports directory"
+  echo ""
+  echo "    --logs"
+  echo "        type: file, output, file must exist"
+  echo "        example: logs_dir"
+  echo "        Reports directory"
+  echo ""
+  echo "    --force"
+  echo "        type: boolean"
+  echo "        example: true"
+  echo "        Allow destination directory to already exist and overwrite files."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
@@ -1012,6 +1043,17 @@ while [[ $# -gt 0 ]]; do
             VIASH_PAR_LOGS=$(ViashRemoveFlags "$1")
             shift 1
             ;;
+        --force)
+            [ -n "$VIASH_PAR_FORCE" ] && ViashError Bad arguments for option \'--force\': \'$VIASH_PAR_FORCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_FORCE="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --force. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --force=*)
+            [ -n "$VIASH_PAR_FORCE" ] && ViashError Bad arguments for option \'--force=*\': \'$VIASH_PAR_FORCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_FORCE=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
         ---engine)
             VIASH_ENGINE_ID="$2"
             shift 2
@@ -1322,6 +1364,12 @@ if [[ -n "$VIASH_PAR_FASTQ_GZIP_COMPRESSION_LEVEL" ]]; then
     exit 1
   fi
 fi
+if [[ -n "$VIASH_PAR_FORCE" ]]; then
+  if ! [[ "$VIASH_PAR_FORCE" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
+    ViashError '--force' has to be a boolean. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
 if [[ -n "$VIASH_META_CPUS" ]]; then
   if ! [[ "$VIASH_META_CPUS" =~ ^[-+]?[0-9]+$ ]]; then
     ViashError 'cpus' has to be an integer. Use "--help" to get more information on the parameters.
@@ -1537,6 +1585,7 @@ $( if [ ! -z ${VIASH_PAR_BCL_SAMPLEPROJECT_SUBDIRECTORIES+x} ]; then echo "${VIA
 $( if [ ! -z ${VIASH_PAR_FASTQ_GZIP_COMPRESSION_LEVEL+x} ]; then echo "${VIASH_PAR_FASTQ_GZIP_COMPRESSION_LEVEL}" | sed "s#'#'\"'\"'#g;s#.*#par_fastq_gzip_compression_level='&'#" ; else echo "# par_fastq_gzip_compression_level="; fi )
 $( if [ ! -z ${VIASH_PAR_REPORTS+x} ]; then echo "${VIASH_PAR_REPORTS}" | sed "s#'#'\"'\"'#g;s#.*#par_reports='&'#" ; else echo "# par_reports="; fi )
 $( if [ ! -z ${VIASH_PAR_LOGS+x} ]; then echo "${VIASH_PAR_LOGS}" | sed "s#'#'\"'\"'#g;s#.*#par_logs='&'#" ; else echo "# par_logs="; fi )
+$( if [ ! -z ${VIASH_PAR_FORCE+x} ]; then echo "${VIASH_PAR_FORCE}" | sed "s#'#'\"'\"'#g;s#.*#par_force='&'#" ; else echo "# par_force="; fi )
 $( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "${VIASH_META_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_name='&'#" ; else echo "# meta_name="; fi )
 $( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "${VIASH_META_FUNCTIONALITY_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_functionality_name='&'#" ; else echo "# meta_functionality_name="; fi )
 $( if [ ! -z ${VIASH_META_RESOURCES_DIR+x} ]; then echo "${VIASH_META_RESOURCES_DIR}" | sed "s#'#'\"'\"'#g;s#.*#meta_resources_dir='&'#" ; else echo "# meta_resources_dir="; fi )
@@ -1561,9 +1610,13 @@ $( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}"
 
 set -eo pipefail
 
+[[ "\$par_force" == "false" ]] && unset par_force
+
+
 \$(which bcl-convert) \\
  --bcl-input-directory "\$par_bcl_input_directory" \\
  --output-directory "\$par_output_directory" \\
+  \${par_force:+--force} \\
   \${par_sample_sheet:+ --sample-sheet "\$par_sample_sheet"} \\
   \${par_run_info:+ --run-info "\$par_run_info"} \\
   \${par_bcl_only_lane:+ --bcl-only-lane "\$par_bcl_only_lane"} \\
diff --git a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml
index 4b94e028..225fbbf3 100644
--- a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml
+++ b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml
@@ -159,6 +159,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -273,16 +276,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/bd_rhapsody/bd_rhapsody_make_reference"
   executable: "target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference
index 793bbbb8..be802d32 100755
--- a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference
+++ b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference
@@ -2,7 +2,7 @@
 
 # bd_rhapsody_make_reference main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -173,95 +173,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "bd_rhapsody_make_reference main"
-  echo ""
-  echo "The Reference Files Generator creates an archive containing Genome Index"
-  echo "and Transcriptome annotation files needed for the BD Rhapsody Sequencing"
-  echo "Analysis Pipeline. The app takes as input one or more FASTA and GTF files"
-  echo "and produces a compressed archive in the form of a tar.gz file. The"
-  echo "archive contains:"
-  echo ""
-  echo "- STAR index"
-  echo "- Filtered GTF file"
-  echo ""
-  echo "Inputs:"
-  echo "    --genome_fasta"
-  echo "        type: file, required parameter, multiple values allowed, file must exist"
-  echo "        example: genome_sequence.fa.gz"
-  echo "        Reference genome file in FASTA or FASTA.GZ format. The BD Rhapsody"
-  echo "        Sequencing Analysis Pipeline uses GRCh38 for Human and GRCm39 for Mouse."
-  echo ""
-  echo "    --gtf"
-  echo "        type: file, required parameter, multiple values allowed, file must exist"
-  echo "        example: transcriptome_annotation.gtf.gz"
-  echo "        File path to the transcript annotation files in GTF or GTF.GZ format."
-  echo "        The Sequence Analysis Pipeline requires the 'gene_name' or"
-  echo "        'gene_id' attribute to be set on each gene and exon feature. Gene and"
-  echo "        exon feature lines must have the same attribute, and exons"
-  echo "        must have a corresponding gene with the same value. For TCR/BCR assays,"
-  echo "        the TCR or BCR gene segments must have the 'gene_type' or"
-  echo "        'gene_biotype' attribute set, and the value should begin with 'TR' or"
-  echo "        'IG', respectively."
-  echo ""
-  echo "    --extra_sequences"
-  echo "        type: file, multiple values allowed, file must exist"
-  echo "        File path to additional sequences in FASTA format to use when building"
-  echo "        the STAR index. (e.g. transgenes or CRISPR guide barcodes)."
-  echo "        GTF lines for these sequences will be automatically generated and"
-  echo "        combined with the main GTF."
-  echo ""
-  echo "Outputs:"
-  echo "    --reference_archive"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        example: star_index.tar.gz"
-  echo "        A Compressed archive containing the Reference Genome Index and"
-  echo "        annotation GTF files. This archive is meant to be used as an"
-  echo "        input in the BD Rhapsody Sequencing Analysis Pipeline."
-  echo ""
-  echo "Arguments:"
-  echo "    --mitochondrial_contigs"
-  echo "        type: string, multiple values allowed"
-  echo "        default: chrM;chrMT;M;MT"
-  echo "        Names of the Mitochondrial contigs in the provided Reference Genome."
-  echo "        Fragments originating from contigs other than these are"
-  echo "        identified as 'nuclear fragments' in the ATACseq analysis pipeline."
-  echo ""
-  echo "    --filtering_off"
-  echo "        type: boolean_true"
-  echo "        By default the input Transcript Annotation files are filtered based on"
-  echo "        the gene_type/gene_biotype attribute. Only features"
-  echo "        having the following attribute values are kept:"
-  echo "          - protein_coding"
-  echo "          - lncRNA (lincRNA and antisense for Gencode < v31/M22/Ensembl97)"
-  echo "          - IG_LV_gene"
-  echo "          - IG_V_gene"
-  echo "          - IG_V_pseudogene"
-  echo "          - IG_D_gene"
-  echo "          - IG_J_gene"
-  echo "          - IG_J_pseudogene"
-  echo "          - IG_C_gene"
-  echo "          - IG_C_pseudogene"
-  echo "          - TR_V_gene"
-  echo "          - TR_V_pseudogene"
-  echo "          - TR_D_gene"
-  echo "          - TR_J_gene"
-  echo "          - TR_J_pseudogene"
-  echo "          - TR_C_gene"
-  echo "          If you have already pre-filtered the input Annotation files and/or"
-  echo "        wish to turn-off the filtering, please set this option to True."
-  echo ""
-  echo "    --wta_only_index"
-  echo "        type: boolean_true"
-  echo "        Build a WTA only index, otherwise builds a WTA + ATAC index."
-  echo ""
-  echo "    --extra_star_params"
-  echo "        type: string"
-  echo "        example: --limitGenomeGenerateRAM 48000 --genomeSAindexNbases 11"
-  echo "        Additional parameters to pass to STAR when building the genome index."
-  echo "        Specify exactly like how you would on the command line."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -554,9 +465,9 @@ RUN VERSION=$(ls -v /var/bd_rhapsody_cwl | grep '^v' | sed 's#v##' | tail -1)
 RUN echo "bdgenomics/rhapsody: \"$VERSION\"" > /var/software_versions.txt
 LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Weiwei Schultz"
 LABEL org.opencontainers.image.description="Companion container for running component bd_rhapsody bd_rhapsody_make_reference"
-LABEL org.opencontainers.image.created="2024-12-03T10:34:04Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:41Z"
 LABEL org.opencontainers.image.source="https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1/Extra_Utilities/"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -671,6 +582,121 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "bd_rhapsody_make_reference main"
+  echo ""
+  echo "The Reference Files Generator creates an archive containing Genome Index"
+  echo "and Transcriptome annotation files needed for the BD Rhapsody Sequencing"
+  echo "Analysis Pipeline. The app takes as input one or more FASTA and GTF files"
+  echo "and produces a compressed archive in the form of a tar.gz file. The"
+  echo "archive contains:"
+  echo ""
+  echo "- STAR index"
+  echo "- Filtered GTF file"
+  echo ""
+  echo "Inputs:"
+  echo "    --genome_fasta"
+  echo "        type: file, required parameter, multiple values allowed, file must exist"
+  echo "        example: genome_sequence.fa.gz"
+  echo "        Reference genome file in FASTA or FASTA.GZ format. The BD Rhapsody"
+  echo "        Sequencing Analysis Pipeline uses GRCh38 for Human and GRCm39 for Mouse."
+  echo ""
+  echo "    --gtf"
+  echo "        type: file, required parameter, multiple values allowed, file must exist"
+  echo "        example: transcriptome_annotation.gtf.gz"
+  echo "        File path to the transcript annotation files in GTF or GTF.GZ format."
+  echo "        The Sequence Analysis Pipeline requires the 'gene_name' or"
+  echo "        'gene_id' attribute to be set on each gene and exon feature. Gene and"
+  echo "        exon feature lines must have the same attribute, and exons"
+  echo "        must have a corresponding gene with the same value. For TCR/BCR assays,"
+  echo "        the TCR or BCR gene segments must have the 'gene_type' or"
+  echo "        'gene_biotype' attribute set, and the value should begin with 'TR' or"
+  echo "        'IG', respectively."
+  echo ""
+  echo "    --extra_sequences"
+  echo "        type: file, multiple values allowed, file must exist"
+  echo "        File path to additional sequences in FASTA format to use when building"
+  echo "        the STAR index. (e.g. transgenes or CRISPR guide barcodes)."
+  echo "        GTF lines for these sequences will be automatically generated and"
+  echo "        combined with the main GTF."
+  echo ""
+  echo "Outputs:"
+  echo "    --reference_archive"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        example: star_index.tar.gz"
+  echo "        A Compressed archive containing the Reference Genome Index and"
+  echo "        annotation GTF files. This archive is meant to be used as an"
+  echo "        input in the BD Rhapsody Sequencing Analysis Pipeline."
+  echo ""
+  echo "Arguments:"
+  echo "    --mitochondrial_contigs"
+  echo "        type: string, multiple values allowed"
+  echo "        default: chrM;chrMT;M;MT"
+  echo "        Names of the Mitochondrial contigs in the provided Reference Genome."
+  echo "        Fragments originating from contigs other than these are"
+  echo "        identified as 'nuclear fragments' in the ATACseq analysis pipeline."
+  echo ""
+  echo "    --filtering_off"
+  echo "        type: boolean_true"
+  echo "        By default the input Transcript Annotation files are filtered based on"
+  echo "        the gene_type/gene_biotype attribute. Only features"
+  echo "        having the following attribute values are kept:"
+  echo "          - protein_coding"
+  echo "          - lncRNA (lincRNA and antisense for Gencode < v31/M22/Ensembl97)"
+  echo "          - IG_LV_gene"
+  echo "          - IG_V_gene"
+  echo "          - IG_V_pseudogene"
+  echo "          - IG_D_gene"
+  echo "          - IG_J_gene"
+  echo "          - IG_J_pseudogene"
+  echo "          - IG_C_gene"
+  echo "          - IG_C_pseudogene"
+  echo "          - TR_V_gene"
+  echo "          - TR_V_pseudogene"
+  echo "          - TR_D_gene"
+  echo "          - TR_J_gene"
+  echo "          - TR_J_pseudogene"
+  echo "          - TR_C_gene"
+  echo "          If you have already pre-filtered the input Annotation files and/or"
+  echo "        wish to turn-off the filtering, please set this option to True."
+  echo ""
+  echo "    --wta_only_index"
+  echo "        type: boolean_true"
+  echo "        Build a WTA only index, otherwise builds a WTA + ATAC index."
+  echo ""
+  echo "    --extra_star_params"
+  echo "        type: string"
+  echo "        example: --limitGenomeGenerateRAM 48000 --genomeSAindexNbases 11"
+  echo "        Additional parameters to pass to STAR when building the genome index."
+  echo "        Specify exactly like how you would on the command line."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml b/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml
index 009876f7..bb09ea18 100644
--- a/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml
+++ b/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml
@@ -989,6 +989,9 @@ test_resources:
   path: "helpers"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -1114,16 +1117,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis"
   executable: "target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/bd_rhapsody_sequence_analysis"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/bd_rhapsody_sequence_analysis b/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/bd_rhapsody_sequence_analysis
index f98066ab..7cda8bae 100755
--- a/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/bd_rhapsody_sequence_analysis
+++ b/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/bd_rhapsody_sequence_analysis
@@ -2,7 +2,7 @@
 
 # bd_rhapsody_sequence_analysis main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -173,6 +173,416 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
+
+# initialise variables
+VIASH_MODE='run'
+VIASH_ENGINE_ID='docker'
+
+######## Helper functions for setting up Docker images for viash ########
+# expects: ViashDockerBuild
+
+# ViashDockerInstallationCheck: check whether Docker is installed correctly
+#
+# examples:
+#   ViashDockerInstallationCheck
+function ViashDockerInstallationCheck {
+  ViashDebug "Checking whether Docker is installed"
+  if [ ! command -v docker &> /dev/null ]; then
+    ViashCritical "Docker doesn't seem to be installed. See 'https://docs.docker.com/get-docker/' for instructions."
+    exit 1
+  fi
+
+  ViashDebug "Checking whether the Docker daemon is running"
+  local save=$-; set +e
+  local docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
+  local out=$?
+  [[ $save =~ e ]] && set -e
+  if [ $out -ne 0 ]; then
+    ViashCritical "Docker daemon does not seem to be running. Try one of the following:"
+    ViashCritical "- Try running 'dockerd' in the command line"
+    ViashCritical "- See https://docs.docker.com/config/daemon/"
+    exit 1
+  fi
+}
+
+# ViashDockerRemoteTagCheck: check whether a Docker image is available 
+# on a remote. Assumes `docker login` has been performed, if relevant.
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   ViashDockerRemoteTagCheck python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerRemoteTagCheck sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerRemoteTagCheck {
+  docker manifest inspect $1 > /dev/null 2> /dev/null
+}
+
+# ViashDockerLocalTagCheck: check whether a Docker image is available locally
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   docker pull python:latest
+#   ViashDockerLocalTagCheck python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerLocalTagCheck sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerLocalTagCheck {
+  [ -n "$(docker images -q $1)" ]
+}
+
+# ViashDockerPull: pull a Docker image
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   ViashDockerPull python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerPull sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerPull {
+  ViashNotice "Checking if Docker image is available at '$1'"
+  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
+    docker pull $1 && return 0 || return 1
+  else
+    local save=$-; set +e
+    docker pull $1 2> /dev/null > /dev/null
+    local out=$?
+    [[ $save =~ e ]] && set -e
+    if [ $out -ne 0 ]; then
+      ViashWarning "Could not pull from '$1'. Docker image doesn't exist or is not accessible."
+    fi
+    return $out
+  fi
+}
+
+# ViashDockerPush: push a Docker image
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   ViashDockerPush python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerPush sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerPush {
+  ViashNotice "Pushing image to '$1'"
+  local save=$-; set +e
+  local out
+  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
+    docker push $1
+    out=$?
+  else
+    docker push $1 2> /dev/null > /dev/null
+    out=$?
+  fi
+  [[ $save =~ e ]] && set -e
+  if [ $out -eq 0 ]; then
+    ViashNotice "Container '$1' push succeeded."
+  else
+    ViashError "Container '$1' push errored. You might not be logged in or have the necessary permissions."
+  fi
+  return $out
+}
+
+# ViashDockerPullElseBuild: pull a Docker image, else build it
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# ViashDockerBuild    : a Bash function which builds a docker image, takes image identifier as argument.
+# examples:
+#   ViashDockerPullElseBuild mynewcomponent
+function ViashDockerPullElseBuild {
+  local save=$-; set +e
+  ViashDockerPull $1
+  local out=$?
+  [[ $save =~ e ]] && set -e
+  if [ $out -ne 0 ]; then
+    ViashDockerBuild $@
+  fi
+}
+
+# ViashDockerSetup: create a Docker image, according to specified docker setup strategy
+#
+# $1          : image identifier with format `[registry/]image[:tag]`
+# $2          : docker setup strategy, see DockerSetupStrategy.scala
+# examples:
+#   ViashDockerSetup mynewcomponent alwaysbuild
+function ViashDockerSetup {
+  local image_id="$1"
+  local setup_strategy="$2"
+  if [ "$setup_strategy" == "alwaysbuild" -o "$setup_strategy" == "build" -o "$setup_strategy" == "b" ]; then
+    ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+  elif [ "$setup_strategy" == "alwayspull" -o "$setup_strategy" == "pull" -o "$setup_strategy" == "p" ]; then
+    ViashDockerPull $image_id
+  elif [ "$setup_strategy" == "alwayspullelsebuild" -o "$setup_strategy" == "pullelsebuild" ]; then
+    ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+  elif [ "$setup_strategy" == "alwayspullelsecachedbuild" -o "$setup_strategy" == "pullelsecachedbuild" ]; then
+    ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+  elif [ "$setup_strategy" == "alwayscachedbuild" -o "$setup_strategy" == "cachedbuild" -o "$setup_strategy" == "cb" ]; then
+    ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+  elif [[ "$setup_strategy" =~ ^ifneedbe ]]; then
+    local save=$-; set +e
+    ViashDockerLocalTagCheck $image_id
+    local outCheck=$?
+    [[ $save =~ e ]] && set -e
+    if [ $outCheck -eq 0 ]; then
+      ViashInfo "Image $image_id already exists"
+    elif [ "$setup_strategy" == "ifneedbebuild" ]; then
+      ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+    elif [ "$setup_strategy" == "ifneedbecachedbuild" ]; then
+      ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+    elif [ "$setup_strategy" == "ifneedbepull" ]; then
+      ViashDockerPull $image_id
+    elif [ "$setup_strategy" == "ifneedbepullelsebuild" ]; then
+      ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+    elif [ "$setup_strategy" == "ifneedbepullelsecachedbuild" ]; then
+      ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+    else
+      ViashError "Unrecognised Docker strategy: $setup_strategy"
+      exit 1
+    fi
+  elif [ "$setup_strategy" == "push" -o "$setup_strategy" == "forcepush" -o "$setup_strategy" == "alwayspush" ]; then
+    ViashDockerPush "$image_id"
+  elif [ "$setup_strategy" == "pushifnotpresent" -o "$setup_strategy" == "gentlepush" -o "$setup_strategy" == "maybepush" ]; then
+    local save=$-; set +e
+    ViashDockerRemoteTagCheck $image_id
+    local outCheck=$?
+    [[ $save =~ e ]] && set -e
+    if [ $outCheck -eq 0 ]; then
+      ViashNotice "Container '$image_id' exists, doing nothing."
+    else
+      ViashNotice "Container '$image_id' does not yet exist."
+      ViashDockerPush "$image_id"
+    fi
+  elif [ "$setup_strategy" == "donothing" -o "$setup_strategy" == "meh" ]; then
+    ViashNotice "Skipping setup."
+  else
+    ViashError "Unrecognised Docker strategy: $setup_strategy"
+    exit 1
+  fi
+}
+
+# ViashDockerCheckCommands: Check whether a docker container has the required commands
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# $@                  : commands to verify being present
+# examples:
+#   ViashDockerCheckCommands bash:4.0 bash ps foo
+function ViashDockerCheckCommands {
+  local image_id="$1"
+  shift 1
+  local commands="$@"
+  local save=$-; set +e
+  local missing # mark 'missing' as local in advance, otherwise the exit code of the command will be missing and always be '0'
+  missing=$(docker run --rm --entrypoint=sh "$image_id" -c "for command in $commands; do command -v \$command >/dev/null 2>&1; if [ \$? -ne 0 ]; then echo \$command; exit 1; fi; done")
+  local outCheck=$?
+  [[ $save =~ e ]] && set -e
+  if [ $outCheck -ne 0 ]; then
+  	ViashError "Docker container '$image_id' does not contain command '$missing'."
+  	exit 1
+  fi
+}
+
+# ViashDockerBuild: build a docker image
+# $1                               : image identifier with format `[registry/]image[:tag]`
+# $...                             : additional arguments to pass to docker build
+# $VIASH_META_TEMP_DIR             : temporary directory to store dockerfile & optional resources in
+# $VIASH_META_NAME                 : name of the component
+# $VIASH_META_RESOURCES_DIR        : directory containing the resources
+# $VIASH_VERBOSITY                 : verbosity level
+# exit code $?                     : whether or not the image was built successfully
+function ViashDockerBuild {
+  local image_id="$1"
+  shift 1
+
+  # create temporary directory to store dockerfile & optional resources in
+  local tmpdir=$(mktemp -d "$VIASH_META_TEMP_DIR/dockerbuild-$VIASH_META_NAME-XXXXXX")
+  local dockerfile="$tmpdir/Dockerfile"
+  function clean_up {
+    rm -rf "$tmpdir"
+  }
+  trap clean_up EXIT
+
+  # store dockerfile and resources
+  ViashDockerfile "$VIASH_ENGINE_ID" > "$dockerfile"
+
+  # generate the build command
+  local docker_build_cmd="docker build -t '$image_id' $@ '$VIASH_META_RESOURCES_DIR' -f '$dockerfile'"
+
+  # build the container
+  ViashNotice "Building container '$image_id' with Dockerfile"
+  ViashInfo "$docker_build_cmd"
+  local save=$-; set +e
+  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
+    eval $docker_build_cmd
+  else
+    eval $docker_build_cmd &> "$tmpdir/docker_build.log"
+  fi
+
+  # check exit code
+  local out=$?
+  [[ $save =~ e ]] && set -e
+  if [ $out -ne 0 ]; then
+    ViashError "Error occurred while building container '$image_id'"
+    if [ $VIASH_VERBOSITY -lt $VIASH_LOGCODE_INFO ]; then
+      ViashError "Transcript: --------------------------------"
+      cat "$tmpdir/docker_build.log"
+      ViashError "End of transcript --------------------------"
+    fi
+    exit 1
+  fi
+}
+
+######## End of helper functions for setting up Docker images for viash ########
+
+# ViashDockerFile: print the dockerfile to stdout
+# $1    : engine identifier
+# return : dockerfile required to run this component
+# examples:
+#   ViashDockerFile
+function ViashDockerfile {
+  local engine_id="$1"
+
+  if [[ "$engine_id" == "docker" ]]; then
+    cat << 'VIASHDOCKER'
+FROM bdgenomics/rhapsody:2.2.1
+ENTRYPOINT []
+RUN apt-get update && \
+  DEBIAN_FRONTEND=noninteractive apt-get install -y procps git && \
+  rm -rf /var/lib/apt/lists/*
+
+RUN pip install --upgrade pip && \
+  pip install --upgrade --no-cache-dir "cwlref-runner" "cwl-runner"
+
+RUN mkdir /var/bd_rhapsody_cwl && \
+  cd /var/bd_rhapsody_cwl && \
+  git clone https://bitbucket.org/CRSwDev/cwl.git . && \
+  git checkout 8feeace1141b24749ea6003f8e6ad6d3ad5232de
+
+RUN VERSION=$(ls -v /var/bd_rhapsody_cwl | grep '^v' | sed 's#v##' | tail -1)
+RUN echo "bdgenomics/rhapsody: \"$VERSION\"" > /var/software_versions.txt
+LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Weiwei Schultz"
+LABEL org.opencontainers.image.description="Companion container for running component bd_rhapsody bd_rhapsody_sequence_analysis"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:41Z"
+LABEL org.opencontainers.image.source="https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+LABEL org.opencontainers.image.version="main"
+
+VIASHDOCKER
+  fi
+}
+
+# ViashDockerBuildArgs: return the arguments to pass to docker build
+# $1    : engine identifier
+# return : arguments to pass to docker build
+function ViashDockerBuildArgs {
+  local engine_id="$1"
+
+  if [[ "$engine_id" == "docker" ]]; then
+    echo ""
+  fi
+}
+
+# ViashAbsolutePath: generate absolute path from relative path
+# borrowed from https://stackoverflow.com/a/21951256
+# $1     : relative filename
+# return : absolute path
+# examples:
+#   ViashAbsolutePath some_file.txt   # returns /path/to/some_file.txt
+#   ViashAbsolutePath /foo/bar/..     # returns /foo
+function ViashAbsolutePath {
+  local thePath
+  local parr
+  local outp
+  local len
+  if [[ ! "$1" =~ ^/ ]]; then
+    thePath="$PWD/$1"
+  else
+    thePath="$1"
+  fi
+  echo "$thePath" | (
+    IFS=/
+    read -a parr
+    declare -a outp
+    for i in "${parr[@]}"; do
+      case "$i" in
+      ''|.) continue ;;
+      ..)
+        len=${#outp[@]}
+        if ((len==0)); then
+          continue
+        else
+          unset outp[$((len-1))]
+        fi
+        ;;
+      *)
+        len=${#outp[@]}
+        outp[$len]="$i"
+      ;;
+      esac
+    done
+    echo /"${outp[*]}"
+  )
+}
+# ViashDockerAutodetectMount: auto configuring docker mounts from parameters
+# $1                             : The parameter value
+# returns                        : New parameter
+# $VIASH_DIRECTORY_MOUNTS        : Added another parameter to be passed to docker
+# $VIASH_DOCKER_AUTOMOUNT_PREFIX : The prefix to be used for the automounts
+# examples:
+#   ViashDockerAutodetectMount /path/to/bar      # returns '/viash_automount/path/to/bar'
+#   ViashDockerAutodetectMountArg /path/to/bar   # returns '--volume="/path/to:/viash_automount/path/to"'
+function ViashDockerAutodetectMount {
+  local abs_path=$(ViashAbsolutePath "$1")
+  local mount_source
+  local base_name
+  if [ -d "$abs_path" ]; then
+    mount_source="$abs_path"
+    base_name=""
+  else
+    mount_source=`dirname "$abs_path"`
+    base_name=`basename "$abs_path"`
+  fi
+  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
+  if [ -z "$base_name" ]; then
+    echo "$mount_target"
+  else
+    echo "$mount_target/$base_name"
+  fi
+}
+function ViashDockerAutodetectMountArg {
+  local abs_path=$(ViashAbsolutePath "$1")
+  local mount_source
+  local base_name
+  if [ -d "$abs_path" ]; then
+    mount_source="$abs_path"
+    base_name=""
+  else
+    mount_source=`dirname "$abs_path"`
+    base_name=`basename "$abs_path"`
+  fi
+  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
+  ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target"
+  echo "--volume=\"$mount_source:$mount_target\""
+}
+function ViashDockerStripAutomount {
+  local abs_path=$(ViashAbsolutePath "$1")
+  echo "${abs_path#$VIASH_DOCKER_AUTOMOUNT_PREFIX}"
+}
+# initialise variables
+VIASH_DIRECTORY_MOUNTS=()
+
+# configure default docker automount prefix if it is unset
+if [ -z "${VIASH_DOCKER_AUTOMOUNT_PREFIX+x}" ]; then
+  VIASH_DOCKER_AUTOMOUNT_PREFIX="/viash_automount"
+fi
+
+# initialise docker variables
+VIASH_DOCKER_RUN_ARGS=(-i --rm)
+
+
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
   echo "bd_rhapsody_sequence_analysis main"
@@ -661,416 +1071,32 @@ function ViashHelp {
   echo ""
   echo "    --write_filtered_reads"
   echo "        type: boolean"
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
 }
 
-# initialise variables
-VIASH_MODE='run'
-VIASH_ENGINE_ID='docker'
-
-######## Helper functions for setting up Docker images for viash ########
-# expects: ViashDockerBuild
-
-# ViashDockerInstallationCheck: check whether Docker is installed correctly
-#
-# examples:
-#   ViashDockerInstallationCheck
-function ViashDockerInstallationCheck {
-  ViashDebug "Checking whether Docker is installed"
-  if [ ! command -v docker &> /dev/null ]; then
-    ViashCritical "Docker doesn't seem to be installed. See 'https://docs.docker.com/get-docker/' for instructions."
-    exit 1
-  fi
-
-  ViashDebug "Checking whether the Docker daemon is running"
-  local save=$-; set +e
-  local docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
-  local out=$?
-  [[ $save =~ e ]] && set -e
-  if [ $out -ne 0 ]; then
-    ViashCritical "Docker daemon does not seem to be running. Try one of the following:"
-    ViashCritical "- Try running 'dockerd' in the command line"
-    ViashCritical "- See https://docs.docker.com/config/daemon/"
-    exit 1
-  fi
-}
-
-# ViashDockerRemoteTagCheck: check whether a Docker image is available 
-# on a remote. Assumes `docker login` has been performed, if relevant.
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   ViashDockerRemoteTagCheck python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerRemoteTagCheck sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerRemoteTagCheck {
-  docker manifest inspect $1 > /dev/null 2> /dev/null
-}
-
-# ViashDockerLocalTagCheck: check whether a Docker image is available locally
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   docker pull python:latest
-#   ViashDockerLocalTagCheck python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerLocalTagCheck sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerLocalTagCheck {
-  [ -n "$(docker images -q $1)" ]
-}
-
-# ViashDockerPull: pull a Docker image
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   ViashDockerPull python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerPull sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerPull {
-  ViashNotice "Checking if Docker image is available at '$1'"
-  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
-    docker pull $1 && return 0 || return 1
-  else
-    local save=$-; set +e
-    docker pull $1 2> /dev/null > /dev/null
-    local out=$?
-    [[ $save =~ e ]] && set -e
-    if [ $out -ne 0 ]; then
-      ViashWarning "Could not pull from '$1'. Docker image doesn't exist or is not accessible."
-    fi
-    return $out
-  fi
-}
-
-# ViashDockerPush: push a Docker image
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   ViashDockerPush python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerPush sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerPush {
-  ViashNotice "Pushing image to '$1'"
-  local save=$-; set +e
-  local out
-  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
-    docker push $1
-    out=$?
-  else
-    docker push $1 2> /dev/null > /dev/null
-    out=$?
-  fi
-  [[ $save =~ e ]] && set -e
-  if [ $out -eq 0 ]; then
-    ViashNotice "Container '$1' push succeeded."
-  else
-    ViashError "Container '$1' push errored. You might not be logged in or have the necessary permissions."
-  fi
-  return $out
-}
-
-# ViashDockerPullElseBuild: pull a Docker image, else build it
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# ViashDockerBuild    : a Bash function which builds a docker image, takes image identifier as argument.
-# examples:
-#   ViashDockerPullElseBuild mynewcomponent
-function ViashDockerPullElseBuild {
-  local save=$-; set +e
-  ViashDockerPull $1
-  local out=$?
-  [[ $save =~ e ]] && set -e
-  if [ $out -ne 0 ]; then
-    ViashDockerBuild $@
-  fi
-}
-
-# ViashDockerSetup: create a Docker image, according to specified docker setup strategy
-#
-# $1          : image identifier with format `[registry/]image[:tag]`
-# $2          : docker setup strategy, see DockerSetupStrategy.scala
-# examples:
-#   ViashDockerSetup mynewcomponent alwaysbuild
-function ViashDockerSetup {
-  local image_id="$1"
-  local setup_strategy="$2"
-  if [ "$setup_strategy" == "alwaysbuild" -o "$setup_strategy" == "build" -o "$setup_strategy" == "b" ]; then
-    ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-  elif [ "$setup_strategy" == "alwayspull" -o "$setup_strategy" == "pull" -o "$setup_strategy" == "p" ]; then
-    ViashDockerPull $image_id
-  elif [ "$setup_strategy" == "alwayspullelsebuild" -o "$setup_strategy" == "pullelsebuild" ]; then
-    ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-  elif [ "$setup_strategy" == "alwayspullelsecachedbuild" -o "$setup_strategy" == "pullelsecachedbuild" ]; then
-    ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-  elif [ "$setup_strategy" == "alwayscachedbuild" -o "$setup_strategy" == "cachedbuild" -o "$setup_strategy" == "cb" ]; then
-    ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-  elif [[ "$setup_strategy" =~ ^ifneedbe ]]; then
-    local save=$-; set +e
-    ViashDockerLocalTagCheck $image_id
-    local outCheck=$?
-    [[ $save =~ e ]] && set -e
-    if [ $outCheck -eq 0 ]; then
-      ViashInfo "Image $image_id already exists"
-    elif [ "$setup_strategy" == "ifneedbebuild" ]; then
-      ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-    elif [ "$setup_strategy" == "ifneedbecachedbuild" ]; then
-      ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-    elif [ "$setup_strategy" == "ifneedbepull" ]; then
-      ViashDockerPull $image_id
-    elif [ "$setup_strategy" == "ifneedbepullelsebuild" ]; then
-      ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-    elif [ "$setup_strategy" == "ifneedbepullelsecachedbuild" ]; then
-      ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-    else
-      ViashError "Unrecognised Docker strategy: $setup_strategy"
-      exit 1
-    fi
-  elif [ "$setup_strategy" == "push" -o "$setup_strategy" == "forcepush" -o "$setup_strategy" == "alwayspush" ]; then
-    ViashDockerPush "$image_id"
-  elif [ "$setup_strategy" == "pushifnotpresent" -o "$setup_strategy" == "gentlepush" -o "$setup_strategy" == "maybepush" ]; then
-    local save=$-; set +e
-    ViashDockerRemoteTagCheck $image_id
-    local outCheck=$?
-    [[ $save =~ e ]] && set -e
-    if [ $outCheck -eq 0 ]; then
-      ViashNotice "Container '$image_id' exists, doing nothing."
-    else
-      ViashNotice "Container '$image_id' does not yet exist."
-      ViashDockerPush "$image_id"
-    fi
-  elif [ "$setup_strategy" == "donothing" -o "$setup_strategy" == "meh" ]; then
-    ViashNotice "Skipping setup."
-  else
-    ViashError "Unrecognised Docker strategy: $setup_strategy"
-    exit 1
-  fi
-}
-
-# ViashDockerCheckCommands: Check whether a docker container has the required commands
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# $@                  : commands to verify being present
-# examples:
-#   ViashDockerCheckCommands bash:4.0 bash ps foo
-function ViashDockerCheckCommands {
-  local image_id="$1"
-  shift 1
-  local commands="$@"
-  local save=$-; set +e
-  local missing # mark 'missing' as local in advance, otherwise the exit code of the command will be missing and always be '0'
-  missing=$(docker run --rm --entrypoint=sh "$image_id" -c "for command in $commands; do command -v \$command >/dev/null 2>&1; if [ \$? -ne 0 ]; then echo \$command; exit 1; fi; done")
-  local outCheck=$?
-  [[ $save =~ e ]] && set -e
-  if [ $outCheck -ne 0 ]; then
-  	ViashError "Docker container '$image_id' does not contain command '$missing'."
-  	exit 1
-  fi
-}
-
-# ViashDockerBuild: build a docker image
-# $1                               : image identifier with format `[registry/]image[:tag]`
-# $...                             : additional arguments to pass to docker build
-# $VIASH_META_TEMP_DIR             : temporary directory to store dockerfile & optional resources in
-# $VIASH_META_NAME                 : name of the component
-# $VIASH_META_RESOURCES_DIR        : directory containing the resources
-# $VIASH_VERBOSITY                 : verbosity level
-# exit code $?                     : whether or not the image was built successfully
-function ViashDockerBuild {
-  local image_id="$1"
-  shift 1
-
-  # create temporary directory to store dockerfile & optional resources in
-  local tmpdir=$(mktemp -d "$VIASH_META_TEMP_DIR/dockerbuild-$VIASH_META_NAME-XXXXXX")
-  local dockerfile="$tmpdir/Dockerfile"
-  function clean_up {
-    rm -rf "$tmpdir"
-  }
-  trap clean_up EXIT
-
-  # store dockerfile and resources
-  ViashDockerfile "$VIASH_ENGINE_ID" > "$dockerfile"
-
-  # generate the build command
-  local docker_build_cmd="docker build -t '$image_id' $@ '$VIASH_META_RESOURCES_DIR' -f '$dockerfile'"
-
-  # build the container
-  ViashNotice "Building container '$image_id' with Dockerfile"
-  ViashInfo "$docker_build_cmd"
-  local save=$-; set +e
-  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
-    eval $docker_build_cmd
-  else
-    eval $docker_build_cmd &> "$tmpdir/docker_build.log"
-  fi
-
-  # check exit code
-  local out=$?
-  [[ $save =~ e ]] && set -e
-  if [ $out -ne 0 ]; then
-    ViashError "Error occurred while building container '$image_id'"
-    if [ $VIASH_VERBOSITY -lt $VIASH_LOGCODE_INFO ]; then
-      ViashError "Transcript: --------------------------------"
-      cat "$tmpdir/docker_build.log"
-      ViashError "End of transcript --------------------------"
-    fi
-    exit 1
-  fi
-}
-
-######## End of helper functions for setting up Docker images for viash ########
-
-# ViashDockerFile: print the dockerfile to stdout
-# $1    : engine identifier
-# return : dockerfile required to run this component
-# examples:
-#   ViashDockerFile
-function ViashDockerfile {
-  local engine_id="$1"
-
-  if [[ "$engine_id" == "docker" ]]; then
-    cat << 'VIASHDOCKER'
-FROM bdgenomics/rhapsody:2.2.1
-ENTRYPOINT []
-RUN apt-get update && \
-  DEBIAN_FRONTEND=noninteractive apt-get install -y procps git && \
-  rm -rf /var/lib/apt/lists/*
-
-RUN pip install --upgrade pip && \
-  pip install --upgrade --no-cache-dir "cwlref-runner" "cwl-runner"
-
-RUN mkdir /var/bd_rhapsody_cwl && \
-  cd /var/bd_rhapsody_cwl && \
-  git clone https://bitbucket.org/CRSwDev/cwl.git . && \
-  git checkout 8feeace1141b24749ea6003f8e6ad6d3ad5232de
-
-RUN VERSION=$(ls -v /var/bd_rhapsody_cwl | grep '^v' | sed 's#v##' | tail -1)
-RUN echo "bdgenomics/rhapsody: \"$VERSION\"" > /var/software_versions.txt
-LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Weiwei Schultz"
-LABEL org.opencontainers.image.description="Companion container for running component bd_rhapsody bd_rhapsody_sequence_analysis"
-LABEL org.opencontainers.image.created="2024-12-03T10:34:04Z"
-LABEL org.opencontainers.image.source="https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-LABEL org.opencontainers.image.version="main"
-
-VIASHDOCKER
-  fi
-}
-
-# ViashDockerBuildArgs: return the arguments to pass to docker build
-# $1    : engine identifier
-# return : arguments to pass to docker build
-function ViashDockerBuildArgs {
-  local engine_id="$1"
-
-  if [[ "$engine_id" == "docker" ]]; then
-    echo ""
-  fi
-}
-
-# ViashAbsolutePath: generate absolute path from relative path
-# borrowed from https://stackoverflow.com/a/21951256
-# $1     : relative filename
-# return : absolute path
-# examples:
-#   ViashAbsolutePath some_file.txt   # returns /path/to/some_file.txt
-#   ViashAbsolutePath /foo/bar/..     # returns /foo
-function ViashAbsolutePath {
-  local thePath
-  local parr
-  local outp
-  local len
-  if [[ ! "$1" =~ ^/ ]]; then
-    thePath="$PWD/$1"
-  else
-    thePath="$1"
-  fi
-  echo "$thePath" | (
-    IFS=/
-    read -a parr
-    declare -a outp
-    for i in "${parr[@]}"; do
-      case "$i" in
-      ''|.) continue ;;
-      ..)
-        len=${#outp[@]}
-        if ((len==0)); then
-          continue
-        else
-          unset outp[$((len-1))]
-        fi
-        ;;
-      *)
-        len=${#outp[@]}
-        outp[$len]="$i"
-      ;;
-      esac
-    done
-    echo /"${outp[*]}"
-  )
-}
-# ViashDockerAutodetectMount: auto configuring docker mounts from parameters
-# $1                             : The parameter value
-# returns                        : New parameter
-# $VIASH_DIRECTORY_MOUNTS        : Added another parameter to be passed to docker
-# $VIASH_DOCKER_AUTOMOUNT_PREFIX : The prefix to be used for the automounts
-# examples:
-#   ViashDockerAutodetectMount /path/to/bar      # returns '/viash_automount/path/to/bar'
-#   ViashDockerAutodetectMountArg /path/to/bar   # returns '--volume="/path/to:/viash_automount/path/to"'
-function ViashDockerAutodetectMount {
-  local abs_path=$(ViashAbsolutePath "$1")
-  local mount_source
-  local base_name
-  if [ -d "$abs_path" ]; then
-    mount_source="$abs_path"
-    base_name=""
-  else
-    mount_source=`dirname "$abs_path"`
-    base_name=`basename "$abs_path"`
-  fi
-  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
-  if [ -z "$base_name" ]; then
-    echo "$mount_target"
-  else
-    echo "$mount_target/$base_name"
-  fi
-}
-function ViashDockerAutodetectMountArg {
-  local abs_path=$(ViashAbsolutePath "$1")
-  local mount_source
-  local base_name
-  if [ -d "$abs_path" ]; then
-    mount_source="$abs_path"
-    base_name=""
-  else
-    mount_source=`dirname "$abs_path"`
-    base_name=`basename "$abs_path"`
-  fi
-  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
-  ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target"
-  echo "--volume=\"$mount_source:$mount_target\""
-}
-function ViashDockerStripAutomount {
-  local abs_path=$(ViashAbsolutePath "$1")
-  echo "${abs_path#$VIASH_DOCKER_AUTOMOUNT_PREFIX}"
-}
-# initialise variables
-VIASH_DIRECTORY_MOUNTS=()
-
-# configure default docker automount prefix if it is unset
-if [ -z "${VIASH_DOCKER_AUTOMOUNT_PREFIX+x}" ]; then
-  VIASH_DOCKER_AUTOMOUNT_PREFIX="/viash_automount"
-fi
-
-# initialise docker variables
-VIASH_DOCKER_RUN_ARGS=(-i --rm)
-
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/bedtools/bedtools_bamtobed/.config.vsh.yaml b/target/executable/bedtools/bedtools_bamtobed/.config.vsh.yaml
index 468bb595..88ef0fcc 100644
--- a/target/executable/bedtools/bedtools_bamtobed/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_bamtobed/.config.vsh.yaml
@@ -124,6 +124,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -234,16 +237,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/bedtools/bedtools_bamtobed"
   executable: "target/executable/bedtools/bedtools_bamtobed/bedtools_bamtobed"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/bedtools/bedtools_bamtobed/bedtools_bamtobed b/target/executable/bedtools/bedtools_bamtobed/bedtools_bamtobed
index 146ef3fc..9770fb9b 100755
--- a/target/executable/bedtools/bedtools_bamtobed/bedtools_bamtobed
+++ b/target/executable/bedtools/bedtools_bamtobed/bedtools_bamtobed
@@ -2,7 +2,7 @@
 
 # bedtools_bamtobed main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,72 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "bedtools_bamtobed main"
-  echo ""
-  echo "Converts BAM alignments to BED6 or BEDPE format."
-  echo ""
-  echo "Inputs:"
-  echo "    -i, --input"
-  echo "        type: file, required parameter, file must exist"
-  echo "        Input BAM file."
-  echo ""
-  echo "Outputs:"
-  echo "    -o, --output"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        Output BED file."
-  echo ""
-  echo "Options:"
-  echo "    --bedpe"
-  echo "        type: boolean_true"
-  echo "        Write BEDPE format. Requires BAM to be grouped or sorted by query."
-  echo ""
-  echo "    --mate1"
-  echo "        type: boolean_true"
-  echo "        When writing BEDPE (-bedpe) format, always report mate one as the first"
-  echo "        BEDPE \"block\"."
-  echo ""
-  echo "    --bed12"
-  echo "        type: boolean_true"
-  echo "        Write \"blocked\" BED format (aka \"BED12\"). Forces -split."
-  echo "        See http://genome-test.cse.ucsc.edu/FAQ/FAQformat#format1"
-  echo ""
-  echo "    --split"
-  echo "        type: boolean_true"
-  echo "        Report \"split\" BAM alignments as separate BED entries."
-  echo "        Splits only on N CIGAR operations."
-  echo ""
-  echo "    --splitD"
-  echo "        type: boolean_true"
-  echo "        Split alignments based on N and D CIGAR operators."
-  echo "        Forces -split."
-  echo ""
-  echo "    -ed, --edit_distance"
-  echo "        type: boolean_true"
-  echo "        Use BAM edit distance (NM tag) for BED score."
-  echo "        - Default for BED is to use mapping quality."
-  echo "        - Default for BEDPE is to use the minimum of"
-  echo "          the two mapping qualities for the pair."
-  echo "        - When -ed is used with -bedpe, the total edit"
-  echo "          distance from the two mates is reported."
-  echo ""
-  echo "    --tag"
-  echo "        type: string"
-  echo "        example: SM"
-  echo "        Use other NUMERIC BAM alignment tag for BED score."
-  echo "        Default for BED is to use mapping quality. Disallowed with BEDPE output."
-  echo ""
-  echo "    --color"
-  echo "        type: string"
-  echo "        example: 250,250,250"
-  echo "        An R,G,B string for the color used with BED12 format."
-  echo "        Default is (255,0,0)."
-  echo ""
-  echo "    --cigar"
-  echo "        type: boolean_true"
-  echo "        Add the CIGAR string to the BED entry as a 7th column."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -522,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
 
 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bamtobed"
-LABEL org.opencontainers.image.created="2024-12-03T10:34:01Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:42Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -639,6 +573,98 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "bedtools_bamtobed main"
+  echo ""
+  echo "Converts BAM alignments to BED6 or BEDPE format."
+  echo ""
+  echo "Inputs:"
+  echo "    -i, --input"
+  echo "        type: file, required parameter, file must exist"
+  echo "        Input BAM file."
+  echo ""
+  echo "Outputs:"
+  echo "    -o, --output"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        Output BED file."
+  echo ""
+  echo "Options:"
+  echo "    --bedpe"
+  echo "        type: boolean_true"
+  echo "        Write BEDPE format. Requires BAM to be grouped or sorted by query."
+  echo ""
+  echo "    --mate1"
+  echo "        type: boolean_true"
+  echo "        When writing BEDPE (-bedpe) format, always report mate one as the first"
+  echo "        BEDPE \"block\"."
+  echo ""
+  echo "    --bed12"
+  echo "        type: boolean_true"
+  echo "        Write \"blocked\" BED format (aka \"BED12\"). Forces -split."
+  echo "        See http://genome-test.cse.ucsc.edu/FAQ/FAQformat#format1"
+  echo ""
+  echo "    --split"
+  echo "        type: boolean_true"
+  echo "        Report \"split\" BAM alignments as separate BED entries."
+  echo "        Splits only on N CIGAR operations."
+  echo ""
+  echo "    --splitD"
+  echo "        type: boolean_true"
+  echo "        Split alignments based on N and D CIGAR operators."
+  echo "        Forces -split."
+  echo ""
+  echo "    -ed, --edit_distance"
+  echo "        type: boolean_true"
+  echo "        Use BAM edit distance (NM tag) for BED score."
+  echo "        - Default for BED is to use mapping quality."
+  echo "        - Default for BEDPE is to use the minimum of"
+  echo "          the two mapping qualities for the pair."
+  echo "        - When -ed is used with -bedpe, the total edit"
+  echo "          distance from the two mates is reported."
+  echo ""
+  echo "    --tag"
+  echo "        type: string"
+  echo "        example: SM"
+  echo "        Use other NUMERIC BAM alignment tag for BED score."
+  echo "        Default for BED is to use mapping quality. Disallowed with BEDPE output."
+  echo ""
+  echo "    --color"
+  echo "        type: string"
+  echo "        example: 250,250,250"
+  echo "        An R,G,B string for the color used with BED12 format."
+  echo "        Default is (255,0,0)."
+  echo ""
+  echo "    --cigar"
+  echo "        type: boolean_true"
+  echo "        Add the CIGAR string to the BED entry as a 7th column."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml b/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml
index dbfede3a..15ae4813 100644
--- a/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml
@@ -78,6 +78,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -186,16 +189,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/bedtools/bedtools_bamtofastq"
   executable: "target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq b/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq
index c982db9a..5e970cd2 100755
--- a/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq
+++ b/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq
@@ -2,7 +2,7 @@
 
 # bedtools_bamtofastq main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,33 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "bedtools_bamtofastq main"
-  echo ""
-  echo "Conversion tool for extracting FASTQ records from sequence alignments in BAM"
-  echo "format."
-  echo ""
-  echo "Inputs:"
-  echo "    -i, --input"
-  echo "        type: file, required parameter, file must exist"
-  echo "        Input BAM file to be converted to FASTQ."
-  echo ""
-  echo "Outputs:"
-  echo "    -fq, --fastq"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        Output FASTQ file."
-  echo ""
-  echo "    -fq2, --fastq2"
-  echo "        type: file, output, file must exist"
-  echo "        FASTQ for second end. Used if BAM contains paired-end data."
-  echo "        BAM should be sorted by query name is creating paired FASTQ."
-  echo ""
-  echo "Options:"
-  echo "    --tags"
-  echo "        type: boolean_true"
-  echo "        Create FASTQ based on the mate info in the BAM R2 and Q2 tags."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -483,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
 
 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bamtofastq"
-LABEL org.opencontainers.image.created="2024-12-03T10:34:02Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:42Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -600,6 +573,59 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "bedtools_bamtofastq main"
+  echo ""
+  echo "Conversion tool for extracting FASTQ records from sequence alignments in BAM"
+  echo "format."
+  echo ""
+  echo "Inputs:"
+  echo "    -i, --input"
+  echo "        type: file, required parameter, file must exist"
+  echo "        Input BAM file to be converted to FASTQ."
+  echo ""
+  echo "Outputs:"
+  echo "    -fq, --fastq"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        Output FASTQ file."
+  echo ""
+  echo "    -fq2, --fastq2"
+  echo "        type: file, output, file must exist"
+  echo "        FASTQ for second end. Used if BAM contains paired-end data."
+  echo "        BAM should be sorted by query name is creating paired FASTQ."
+  echo ""
+  echo "Options:"
+  echo "    --tags"
+  echo "        type: boolean_true"
+  echo "        Create FASTQ based on the mate info in the BAM R2 and Q2 tags."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml b/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml
index d64b9723..ef96e839 100644
--- a/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml
@@ -67,6 +67,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -175,16 +178,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/bedtools/bedtools_bed12tobed6"
   executable: "target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6 b/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6
index 4240d74f..a4b878d0 100755
--- a/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6
+++ b/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6
@@ -2,7 +2,7 @@
 
 # bedtools_bed12tobed6 main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,30 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "bedtools_bed12tobed6 main"
-  echo ""
-  echo "Converts BED features in BED12 (a.k.a. “blocked” BED features such as genes) to"
-  echo "discrete BED6 features."
-  echo "For example, in the case of a gene with six exons, bed12ToBed6 would create six"
-  echo "separate BED6 features (i.e., one for each exon)."
-  echo ""
-  echo "Inputs:"
-  echo "    -i, --input"
-  echo "        type: file, required parameter, file must exist"
-  echo "        Input BED12 file."
-  echo ""
-  echo "Outputs:"
-  echo "    -o, --output"
-  echo "        type: file, output, file must exist"
-  echo "        Output BED6 file to be written."
-  echo ""
-  echo "Options:"
-  echo "    -n, --n_score"
-  echo "        type: boolean_true"
-  echo "        Force the score to be the (1-based) block number from the BED12."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -480,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
 
 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bed12tobed6"
-LABEL org.opencontainers.image.created="2024-12-03T10:34:03Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:44Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -597,6 +573,56 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "bedtools_bed12tobed6 main"
+  echo ""
+  echo "Converts BED features in BED12 (a.k.a. “blocked” BED features such as genes) to"
+  echo "discrete BED6 features."
+  echo "For example, in the case of a gene with six exons, bed12ToBed6 would create six"
+  echo "separate BED6 features (i.e., one for each exon)."
+  echo ""
+  echo "Inputs:"
+  echo "    -i, --input"
+  echo "        type: file, required parameter, file must exist"
+  echo "        Input BED12 file."
+  echo ""
+  echo "Outputs:"
+  echo "    -o, --output"
+  echo "        type: file, output, file must exist"
+  echo "        Output BED6 file to be written."
+  echo ""
+  echo "Options:"
+  echo "    -n, --n_score"
+  echo "        type: boolean_true"
+  echo "        Force the score to be the (1-based) block number from the BED12."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml b/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml
index 13ea77e9..5ef81590 100644
--- a/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml
@@ -98,6 +98,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -213,16 +216,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/bedtools/bedtools_bedtobam"
   executable: "target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam b/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam
index e908f0bf..c550c110 100755
--- a/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam
+++ b/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam
@@ -2,7 +2,7 @@
 
 # bedtools_bedtobam main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,46 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "bedtools_bedtobam main"
-  echo ""
-  echo "Converts feature records (bed/gff/vcf) to BAM format."
-  echo ""
-  echo "Inputs:"
-  echo "    -i, --input"
-  echo "        type: file, required parameter, file must exist"
-  echo "        Input file (bed/gff/vcf)."
-  echo ""
-  echo "    -g, --genome"
-  echo "        type: file, required parameter, file must exist"
-  echo "        Input genome file."
-  echo "        NOTE: This is not a fasta file. This is a two-column tab-delimited file"
-  echo "        where the first column is the chromosome name and the second their"
-  echo "        sizes."
-  echo ""
-  echo "Outputs:"
-  echo "    -o, --output"
-  echo "        type: file, output, file must exist"
-  echo "        Output BAM file to be written."
-  echo ""
-  echo "Options:"
-  echo "    -mapq, --map_quality"
-  echo "        type: integer"
-  echo "        default: 255"
-  echo "        min: 0"
-  echo "        max: 255"
-  echo "        Set the mappinq quality for the BAM records."
-  echo ""
-  echo "    --bed12"
-  echo "        type: boolean_true"
-  echo "        The BED file is in BED12 format. The BAM CIGAR"
-  echo "        string will reflect BED \"blocks\"."
-  echo ""
-  echo "    -ubam, --uncompress_bam"
-  echo "        type: boolean_true"
-  echo "        Write uncompressed BAM output. Default writes compressed BAM."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -496,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
 
 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bedtobam"
-LABEL org.opencontainers.image.created="2024-12-03T10:34:04Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:43Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -613,6 +573,72 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "bedtools_bedtobam main"
+  echo ""
+  echo "Converts feature records (bed/gff/vcf) to BAM format."
+  echo ""
+  echo "Inputs:"
+  echo "    -i, --input"
+  echo "        type: file, required parameter, file must exist"
+  echo "        Input file (bed/gff/vcf)."
+  echo ""
+  echo "    -g, --genome"
+  echo "        type: file, required parameter, file must exist"
+  echo "        Input genome file."
+  echo "        NOTE: This is not a fasta file. This is a two-column tab-delimited file"
+  echo "        where the first column is the chromosome name and the second their"
+  echo "        sizes."
+  echo ""
+  echo "Outputs:"
+  echo "    -o, --output"
+  echo "        type: file, output, file must exist"
+  echo "        Output BAM file to be written."
+  echo ""
+  echo "Options:"
+  echo "    -mapq, --map_quality"
+  echo "        type: integer"
+  echo "        default: 255"
+  echo "        min: 0"
+  echo "        max: 255"
+  echo "        Set the mappinq quality for the BAM records."
+  echo ""
+  echo "    --bed12"
+  echo "        type: boolean_true"
+  echo "        The BED file is in BED12 format. The BAM CIGAR"
+  echo "        string will reflect BED \"blocks\"."
+  echo ""
+  echo "    -ubam, --uncompress_bam"
+  echo "        type: boolean_true"
+  echo "        Write uncompressed BAM output. Default writes compressed BAM."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/bedtools/bedtools_genomecov/.config.vsh.yaml b/target/executable/bedtools/bedtools_genomecov/.config.vsh.yaml
index bad39651..10960ab1 100644
--- a/target/executable/bedtools/bedtools_genomecov/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_genomecov/.config.vsh.yaml
@@ -226,6 +226,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -336,16 +339,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/bedtools/bedtools_genomecov"
   executable: "target/executable/bedtools/bedtools_genomecov/bedtools_genomecov"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/bedtools/bedtools_genomecov/bedtools_genomecov b/target/executable/bedtools/bedtools_genomecov/bedtools_genomecov
index 8a28fb4f..6c91a29b 100755
--- a/target/executable/bedtools/bedtools_genomecov/bedtools_genomecov
+++ b/target/executable/bedtools/bedtools_genomecov/bedtools_genomecov
@@ -2,7 +2,7 @@
 
 # bedtools_genomecov main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,141 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "bedtools_genomecov main"
-  echo ""
-  echo "Compute the coverage of a feature file among a genome."
-  echo ""
-  echo "Inputs:"
-  echo "    -i, --input"
-  echo "        type: file, file must exist"
-  echo "        example: input.bed"
-  echo "        The input file (BED/GFF/VCF) to be used."
-  echo ""
-  echo "    -ibam, --input_bam"
-  echo "        type: file, file must exist"
-  echo "        The input file is in BAM format."
-  echo "        Note: BAM _must_ be sorted by positions."
-  echo "        '--genome' option is ignored if you use '--input_bam' option!"
-  echo ""
-  echo "    -g, --genome"
-  echo "        type: file, file must exist"
-  echo "        example: genome.txt"
-  echo "        The genome file to be used."
-  echo ""
-  echo "Outputs:"
-  echo "    --output"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        example: output.bed"
-  echo "        The output BED file."
-  echo ""
-  echo "Options:"
-  echo "    -d, --depth"
-  echo "        type: boolean_true"
-  echo "        Report the depth at each genome position (with one-based coordinates)."
-  echo "        Default behavior is to report a histogram."
-  echo ""
-  echo "    -dz, --depth_zero"
-  echo "        type: boolean_true"
-  echo "        Report the depth at each genome position (with zero-based coordinates)."
-  echo "        Reports only non-zero positions."
-  echo "        Default behavior is to report a histogram."
-  echo ""
-  echo "    -bg, --bed_graph"
-  echo "        type: boolean_true"
-  echo "        Report depth in BedGraph format. For details, see:"
-  echo "        genome.ucsc.edu/goldenPath/help/bedgraph.html"
-  echo ""
-  echo "    -bga, --bed_graph_zero_coverage"
-  echo "        type: boolean_true"
-  echo "        Report depth in BedGraph format, as above (-bg)."
-  echo "        However with this option, regions with zero"
-  echo "        coverage are also reported. This allows one to"
-  echo "        quickly extract all regions of a genome with 0"
-  echo "        coverage by applying: \"grep -w 0\$\" to the output."
-  echo ""
-  echo "    --split"
-  echo "        type: boolean_true"
-  echo "        Treat \"split\" BAM or BED12 entries as distinct BED intervals."
-  echo "        when computing coverage."
-  echo "        For BAM files, this uses the CIGAR \"N\" and \"D\" operations"
-  echo "        to infer the blocks for computing coverage."
-  echo "        For BED12 files, this uses the BlockCount, BlockStarts, and BlockEnds"
-  echo "        fields (i.e., columns 10,11,12)."
-  echo ""
-  echo "    -ignoreD, --ignore_deletion"
-  echo "        type: boolean_true"
-  echo "        Ignore local deletions (CIGAR \"D\" operations) in BAM entries"
-  echo "        when computing coverage."
-  echo ""
-  echo "    --strand"
-  echo "        type: string"
-  echo "        choices: [ +, - ]"
-  echo "        Calculate coverage of intervals from a specific strand."
-  echo "        With BED files, requires at least 6 columns (strand is column 6)."
-  echo ""
-  echo "    -pc, --pair_end_coverage"
-  echo "        type: boolean_true"
-  echo "        Calculate coverage of pair-end fragments."
-  echo "        Works for BAM files only"
-  echo ""
-  echo "    -fs, --fragment_size"
-  echo "        type: boolean_true"
-  echo "        Force to use provided fragment size instead of read length"
-  echo "        Works for BAM files only"
-  echo ""
-  echo "    --du"
-  echo "        type: boolean_true"
-  echo "        Change strand af the mate read (so both reads from the same strand)"
-  echo "        useful for strand specific"
-  echo "        Works for BAM files only"
-  echo ""
-  echo "    -5, --five_prime"
-  echo "        type: boolean_true"
-  echo "        Calculate coverage of 5\" positions (instead of entire interval)."
-  echo ""
-  echo "    -3, --three_prime"
-  echo "        type: boolean_true"
-  echo "        Calculate coverage of 3\" positions (instead of entire interval)."
-  echo ""
-  echo "    --max"
-  echo "        type: integer"
-  echo "        min: 0"
-  echo "        Combine all positions with a depth >= max into"
-  echo "        a single bin in the histogram. Irrelevant"
-  echo "        for -d and -bedGraph"
-  echo "        - (INTEGER)"
-  echo ""
-  echo "    --scale"
-  echo "        type: double"
-  echo "        min: 0.0"
-  echo "        Scale the coverage by a constant factor."
-  echo "        Each coverage value is multiplied by this factor before being reported."
-  echo "        Useful for normalizing coverage by, e.g., reads per million (RPM)."
-  echo "        - Default is 1.0; i.e., unscaled."
-  echo "        - (FLOAT)"
-  echo ""
-  echo "    --trackline"
-  echo "        type: boolean_true"
-  echo "        Adds a UCSC/Genome-Browser track line definition in the first line of"
-  echo "        the output."
-  echo "        - See here for more details about track line definition:"
-  echo "              http://genome.ucsc.edu/goldenPath/help/bedgraph.html"
-  echo "        - NOTE: When adding a trackline definition, the output BedGraph can be"
-  echo "        easily"
-  echo "              uploaded to the Genome Browser as a custom track,"
-  echo "              BUT CAN NOT be converted into a BigWig file (w/o removing the"
-  echo "        first line)."
-  echo ""
-  echo "    --trackopts"
-  echo "        type: string, multiple values allowed"
-  echo "        Writes additional track line definition parameters in the first line."
-  echo "        - Example:"
-  echo "          -trackopts 'name=\"My Track\" visibility=2 color=255,30,30'"
-  echo "          Note the use of single-quotes if you have spaces in your parameters."
-  echo "        - (TEXT)"
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -591,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
 
 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_genomecov"
-LABEL org.opencontainers.image.created="2024-12-03T10:34:04Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:42Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -708,6 +573,167 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "bedtools_genomecov main"
+  echo ""
+  echo "Compute the coverage of a feature file among a genome."
+  echo ""
+  echo "Inputs:"
+  echo "    -i, --input"
+  echo "        type: file, file must exist"
+  echo "        example: input.bed"
+  echo "        The input file (BED/GFF/VCF) to be used."
+  echo ""
+  echo "    -ibam, --input_bam"
+  echo "        type: file, file must exist"
+  echo "        The input file is in BAM format."
+  echo "        Note: BAM _must_ be sorted by positions."
+  echo "        '--genome' option is ignored if you use '--input_bam' option!"
+  echo ""
+  echo "    -g, --genome"
+  echo "        type: file, file must exist"
+  echo "        example: genome.txt"
+  echo "        The genome file to be used."
+  echo ""
+  echo "Outputs:"
+  echo "    --output"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        example: output.bed"
+  echo "        The output BED file."
+  echo ""
+  echo "Options:"
+  echo "    -d, --depth"
+  echo "        type: boolean_true"
+  echo "        Report the depth at each genome position (with one-based coordinates)."
+  echo "        Default behavior is to report a histogram."
+  echo ""
+  echo "    -dz, --depth_zero"
+  echo "        type: boolean_true"
+  echo "        Report the depth at each genome position (with zero-based coordinates)."
+  echo "        Reports only non-zero positions."
+  echo "        Default behavior is to report a histogram."
+  echo ""
+  echo "    -bg, --bed_graph"
+  echo "        type: boolean_true"
+  echo "        Report depth in BedGraph format. For details, see:"
+  echo "        genome.ucsc.edu/goldenPath/help/bedgraph.html"
+  echo ""
+  echo "    -bga, --bed_graph_zero_coverage"
+  echo "        type: boolean_true"
+  echo "        Report depth in BedGraph format, as above (-bg)."
+  echo "        However with this option, regions with zero"
+  echo "        coverage are also reported. This allows one to"
+  echo "        quickly extract all regions of a genome with 0"
+  echo "        coverage by applying: \"grep -w 0\$\" to the output."
+  echo ""
+  echo "    --split"
+  echo "        type: boolean_true"
+  echo "        Treat \"split\" BAM or BED12 entries as distinct BED intervals."
+  echo "        when computing coverage."
+  echo "        For BAM files, this uses the CIGAR \"N\" and \"D\" operations"
+  echo "        to infer the blocks for computing coverage."
+  echo "        For BED12 files, this uses the BlockCount, BlockStarts, and BlockEnds"
+  echo "        fields (i.e., columns 10,11,12)."
+  echo ""
+  echo "    -ignoreD, --ignore_deletion"
+  echo "        type: boolean_true"
+  echo "        Ignore local deletions (CIGAR \"D\" operations) in BAM entries"
+  echo "        when computing coverage."
+  echo ""
+  echo "    --strand"
+  echo "        type: string"
+  echo "        choices: [ +, - ]"
+  echo "        Calculate coverage of intervals from a specific strand."
+  echo "        With BED files, requires at least 6 columns (strand is column 6)."
+  echo ""
+  echo "    -pc, --pair_end_coverage"
+  echo "        type: boolean_true"
+  echo "        Calculate coverage of pair-end fragments."
+  echo "        Works for BAM files only"
+  echo ""
+  echo "    -fs, --fragment_size"
+  echo "        type: boolean_true"
+  echo "        Force to use provided fragment size instead of read length"
+  echo "        Works for BAM files only"
+  echo ""
+  echo "    --du"
+  echo "        type: boolean_true"
+  echo "        Change strand af the mate read (so both reads from the same strand)"
+  echo "        useful for strand specific"
+  echo "        Works for BAM files only"
+  echo ""
+  echo "    -5, --five_prime"
+  echo "        type: boolean_true"
+  echo "        Calculate coverage of 5\" positions (instead of entire interval)."
+  echo ""
+  echo "    -3, --three_prime"
+  echo "        type: boolean_true"
+  echo "        Calculate coverage of 3\" positions (instead of entire interval)."
+  echo ""
+  echo "    --max"
+  echo "        type: integer"
+  echo "        min: 0"
+  echo "        Combine all positions with a depth >= max into"
+  echo "        a single bin in the histogram. Irrelevant"
+  echo "        for -d and -bedGraph"
+  echo "        - (INTEGER)"
+  echo ""
+  echo "    --scale"
+  echo "        type: double"
+  echo "        min: 0.0"
+  echo "        Scale the coverage by a constant factor."
+  echo "        Each coverage value is multiplied by this factor before being reported."
+  echo "        Useful for normalizing coverage by, e.g., reads per million (RPM)."
+  echo "        - Default is 1.0; i.e., unscaled."
+  echo "        - (FLOAT)"
+  echo ""
+  echo "    --trackline"
+  echo "        type: boolean_true"
+  echo "        Adds a UCSC/Genome-Browser track line definition in the first line of"
+  echo "        the output."
+  echo "        - See here for more details about track line definition:"
+  echo "              http://genome.ucsc.edu/goldenPath/help/bedgraph.html"
+  echo "        - NOTE: When adding a trackline definition, the output BedGraph can be"
+  echo "        easily"
+  echo "              uploaded to the Genome Browser as a custom track,"
+  echo "              BUT CAN NOT be converted into a BigWig file (w/o removing the"
+  echo "        first line)."
+  echo ""
+  echo "    --trackopts"
+  echo "        type: string, multiple values allowed"
+  echo "        Writes additional track line definition parameters in the first line."
+  echo "        - Example:"
+  echo "          -trackopts 'name=\"My Track\" visibility=2 color=255,30,30'"
+  echo "          Note the use of single-quotes if you have spaces in your parameters."
+  echo "        - (TEXT)"
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml b/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml
index 6fc44a04..9998ae82 100644
--- a/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml
@@ -123,6 +123,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -231,16 +234,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/bedtools/bedtools_getfasta"
   executable: "target/executable/bedtools/bedtools_getfasta/bedtools_getfasta"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta b/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta
index 8211df9a..c4677746 100755
--- a/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta
+++ b/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta
@@ -2,7 +2,7 @@
 
 # bedtools_getfasta main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,76 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "bedtools_getfasta main"
-  echo ""
-  echo "Extract sequences from a FASTA file for each of the intervals defined in a"
-  echo "BED/GFF/VCF file."
-  echo ""
-  echo "Input arguments:"
-  echo "    --input_fasta"
-  echo "        type: file, file must exist"
-  echo "        FASTA file containing sequences for each interval specified in the input"
-  echo "        BED file."
-  echo "        The headers in the input FASTA file must exactly match the chromosome"
-  echo "        column in the BED file."
-  echo ""
-  echo "    --input_bed"
-  echo "        type: file, file must exist"
-  echo "        BED file containing intervals to extract from the FASTA file."
-  echo "        BED files containing a single region require a newline character"
-  echo "        at the end of the line, otherwise a blank output file is produced."
-  echo ""
-  echo "    --rna"
-  echo "        type: boolean_true"
-  echo "        The FASTA is RNA not DNA. Reverse complementation handled accordingly."
-  echo ""
-  echo "Run arguments:"
-  echo "    -s, --strandedness"
-  echo "        type: boolean_true"
-  echo "        Force strandedness. If the feature occupies the antisense strand, the"
-  echo "        output sequence will"
-  echo "        be reverse complemented. By default strandedness is not taken into"
-  echo "        account."
-  echo ""
-  echo "Output arguments:"
-  echo "    -o, --output"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        Output file where the output from the 'bedtools getfasta' commend will"
-  echo "        be written to."
-  echo ""
-  echo "    --tab"
-  echo "        type: boolean_true"
-  echo "        Report extract sequences in a tab-delimited format instead of in FASTA"
-  echo "        format."
-  echo ""
-  echo "    --bed_out"
-  echo "        type: boolean_true"
-  echo "        Report extract sequences in a tab-delimited BED format instead of in"
-  echo "        FASTA format."
-  echo ""
-  echo "    --name"
-  echo "        type: boolean_true"
-  echo "        Set the FASTA header for each extracted sequence to be the \"name\" and"
-  echo "        coordinate columns from the BED feature."
-  echo ""
-  echo "    --name_only"
-  echo "        type: boolean_true"
-  echo "        Set the FASTA header for each extracted sequence to be the \"name\""
-  echo "        columns from the BED feature."
-  echo ""
-  echo "    --split"
-  echo "        type: boolean_true"
-  echo "        When --input is in BED12 format, create a separate fasta entry for each"
-  echo "        block in a BED12 record,"
-  echo "        blocks being described in the 11th and 12th column of the BED."
-  echo ""
-  echo "    --full_header"
-  echo "        type: boolean_true"
-  echo "        Use full fasta header. By default, only the word before the first space"
-  echo "        or tab is used."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -526,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_getfasta"
-LABEL org.opencontainers.image.created="2024-12-03T10:34:02Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:43Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -643,6 +573,102 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "bedtools_getfasta main"
+  echo ""
+  echo "Extract sequences from a FASTA file for each of the intervals defined in a"
+  echo "BED/GFF/VCF file."
+  echo ""
+  echo "Input arguments:"
+  echo "    --input_fasta"
+  echo "        type: file, file must exist"
+  echo "        FASTA file containing sequences for each interval specified in the input"
+  echo "        BED file."
+  echo "        The headers in the input FASTA file must exactly match the chromosome"
+  echo "        column in the BED file."
+  echo ""
+  echo "    --input_bed"
+  echo "        type: file, file must exist"
+  echo "        BED file containing intervals to extract from the FASTA file."
+  echo "        BED files containing a single region require a newline character"
+  echo "        at the end of the line, otherwise a blank output file is produced."
+  echo ""
+  echo "    --rna"
+  echo "        type: boolean_true"
+  echo "        The FASTA is RNA not DNA. Reverse complementation handled accordingly."
+  echo ""
+  echo "Run arguments:"
+  echo "    -s, --strandedness"
+  echo "        type: boolean_true"
+  echo "        Force strandedness. If the feature occupies the antisense strand, the"
+  echo "        output sequence will"
+  echo "        be reverse complemented. By default strandedness is not taken into"
+  echo "        account."
+  echo ""
+  echo "Output arguments:"
+  echo "    -o, --output"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        Output file where the output from the 'bedtools getfasta' commend will"
+  echo "        be written to."
+  echo ""
+  echo "    --tab"
+  echo "        type: boolean_true"
+  echo "        Report extract sequences in a tab-delimited format instead of in FASTA"
+  echo "        format."
+  echo ""
+  echo "    --bed_out"
+  echo "        type: boolean_true"
+  echo "        Report extract sequences in a tab-delimited BED format instead of in"
+  echo "        FASTA format."
+  echo ""
+  echo "    --name"
+  echo "        type: boolean_true"
+  echo "        Set the FASTA header for each extracted sequence to be the \"name\" and"
+  echo "        coordinate columns from the BED feature."
+  echo ""
+  echo "    --name_only"
+  echo "        type: boolean_true"
+  echo "        Set the FASTA header for each extracted sequence to be the \"name\""
+  echo "        columns from the BED feature."
+  echo ""
+  echo "    --split"
+  echo "        type: boolean_true"
+  echo "        When --input is in BED12 format, create a separate fasta entry for each"
+  echo "        block in a BED12 record,"
+  echo "        blocks being described in the 11th and 12th column of the BED."
+  echo ""
+  echo "    --full_header"
+  echo "        type: boolean_true"
+  echo "        Use full fasta header. By default, only the word before the first space"
+  echo "        or tab is used."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml b/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml
index b1f46153..24183173 100644
--- a/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml
@@ -165,6 +165,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -272,16 +275,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/bedtools/bedtools_groupby"
   executable: "target/executable/bedtools/bedtools_groupby/bedtools_groupby"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/bedtools/bedtools_groupby/bedtools_groupby b/target/executable/bedtools/bedtools_groupby/bedtools_groupby
index 4ce69b09..d367f977 100755
--- a/target/executable/bedtools/bedtools_groupby/bedtools_groupby
+++ b/target/executable/bedtools/bedtools_groupby/bedtools_groupby
@@ -2,7 +2,7 @@
 
 # bedtools_groupby main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,102 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "bedtools_groupby main"
-  echo ""
-  echo "Summarizes a dataset column based upon common column groupings."
-  echo "Akin to the SQL \"group by\" command."
-  echo ""
-  echo "Inputs:"
-  echo "    -i, --input"
-  echo "        type: file, required parameter, file must exist"
-  echo "        example: input_a.bed"
-  echo "        The input BED file to be used."
-  echo ""
-  echo "Outputs:"
-  echo "    --output"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        example: output.bed"
-  echo "        The output groupby BED file."
-  echo ""
-  echo "Options:"
-  echo "    -g, -grp, --groupby"
-  echo "        type: string, required parameter"
-  echo "        Specify the columns (1-based) for the grouping."
-  echo "        The columns must be comma separated."
-  echo "        - Default: 1,2,3"
-  echo ""
-  echo "    -c, -opCols, --column"
-  echo "        type: integer, required parameter"
-  echo "        Specify the column (1-based) that should be summarized."
-  echo ""
-  echo "    -o, -ops, --operation"
-  echo "        type: string"
-  echo "        Specify the operation that should be applied to opCol."
-  echo "        Valid operations:"
-  echo "            sum, count, count_distinct, min, max,"
-  echo "            mean, median, mode, antimode,"
-  echo "            stdev, sstdev (sample standard dev.),"
-  echo "            collapse (i.e., print a comma separated list (duplicates allowed)),"
-  echo "            distinct (i.e., print a comma separated list (NO duplicates"
-  echo "        allowed)),"
-  echo "            distinct_sort_num (as distinct, but sorted numerically, ascending),"
-  echo "            distinct_sort_num_desc (as distinct, but sorted numerically,"
-  echo "        descending),"
-  echo "            concat   (i.e., merge values into a single, non-delimited string),"
-  echo "            freqdesc (i.e., print desc. list of values:freq)"
-  echo "            freqasc (i.e., print asc. list of values:freq)"
-  echo "            first (i.e., print first value)"
-  echo "            last (i.e., print last value)"
-  echo "        Default value: sum"
-  echo "        If there is only column, but multiple operations, all operations will be"
-  echo "        applied on that column. Likewise, if there is only one operation, but"
-  echo "        multiple columns, that operation will be applied to all columns."
-  echo "        Otherwise, the number of columns must match the the number of"
-  echo "        operations,"
-  echo "        and will be applied in respective order."
-  echo "        E.g., \"-c 5,4,6 -o sum,mean,count\" will give the sum of column 5,"
-  echo "        the mean of column 4, and the count of column 6."
-  echo "        The order of output columns will match the ordering given in the"
-  echo "        command."
-  echo ""
-  echo "    --full"
-  echo "        type: boolean_true"
-  echo "        Print all columns from input file. The first line in the group is used."
-  echo "        Default: print only grouped columns."
-  echo ""
-  echo "    --inheader"
-  echo "        type: boolean_true"
-  echo "        Input file has a header line - the first line will be ignored."
-  echo ""
-  echo "    --outheader"
-  echo "        type: boolean_true"
-  echo "        Print header line in the output, detailing the column names."
-  echo "        If the input file has headers (-inheader), the output file"
-  echo "        will use the input's column names."
-  echo "        If the input file has no headers, the output file"
-  echo "        will use \"col_1\", \"col_2\", etc. as the column names."
-  echo ""
-  echo "    --header"
-  echo "        type: boolean_true"
-  echo "        same as '-inheader -outheader'."
-  echo ""
-  echo "    --ignorecase"
-  echo "        type: boolean_true"
-  echo "        Group values regardless of upper/lower case."
-  echo ""
-  echo "    -prec, --precision"
-  echo "        type: integer"
-  echo "        default: 5"
-  echo "        Sets the decimal precision for output."
-  echo ""
-  echo "    -delim, --delimiter"
-  echo "        type: string"
-  echo "        default: ,"
-  echo "        example: |"
-  echo "        Specify a custom delimiter for the collapse operations."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -552,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
 
 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_groupby"
-LABEL org.opencontainers.image.created="2024-12-03T10:34:02Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:44Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -669,6 +573,128 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "bedtools_groupby main"
+  echo ""
+  echo "Summarizes a dataset column based upon common column groupings."
+  echo "Akin to the SQL \"group by\" command."
+  echo ""
+  echo "Inputs:"
+  echo "    -i, --input"
+  echo "        type: file, required parameter, file must exist"
+  echo "        example: input_a.bed"
+  echo "        The input BED file to be used."
+  echo ""
+  echo "Outputs:"
+  echo "    --output"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        example: output.bed"
+  echo "        The output groupby BED file."
+  echo ""
+  echo "Options:"
+  echo "    -g, -grp, --groupby"
+  echo "        type: string, required parameter"
+  echo "        Specify the columns (1-based) for the grouping."
+  echo "        The columns must be comma separated."
+  echo "        - Default: 1,2,3"
+  echo ""
+  echo "    -c, -opCols, --column"
+  echo "        type: integer, required parameter"
+  echo "        Specify the column (1-based) that should be summarized."
+  echo ""
+  echo "    -o, -ops, --operation"
+  echo "        type: string"
+  echo "        Specify the operation that should be applied to opCol."
+  echo "        Valid operations:"
+  echo "            sum, count, count_distinct, min, max,"
+  echo "            mean, median, mode, antimode,"
+  echo "            stdev, sstdev (sample standard dev.),"
+  echo "            collapse (i.e., print a comma separated list (duplicates allowed)),"
+  echo "            distinct (i.e., print a comma separated list (NO duplicates"
+  echo "        allowed)),"
+  echo "            distinct_sort_num (as distinct, but sorted numerically, ascending),"
+  echo "            distinct_sort_num_desc (as distinct, but sorted numerically,"
+  echo "        descending),"
+  echo "            concat   (i.e., merge values into a single, non-delimited string),"
+  echo "            freqdesc (i.e., print desc. list of values:freq)"
+  echo "            freqasc (i.e., print asc. list of values:freq)"
+  echo "            first (i.e., print first value)"
+  echo "            last (i.e., print last value)"
+  echo "        Default value: sum"
+  echo "        If there is only column, but multiple operations, all operations will be"
+  echo "        applied on that column. Likewise, if there is only one operation, but"
+  echo "        multiple columns, that operation will be applied to all columns."
+  echo "        Otherwise, the number of columns must match the the number of"
+  echo "        operations,"
+  echo "        and will be applied in respective order."
+  echo "        E.g., \"-c 5,4,6 -o sum,mean,count\" will give the sum of column 5,"
+  echo "        the mean of column 4, and the count of column 6."
+  echo "        The order of output columns will match the ordering given in the"
+  echo "        command."
+  echo ""
+  echo "    --full"
+  echo "        type: boolean_true"
+  echo "        Print all columns from input file. The first line in the group is used."
+  echo "        Default: print only grouped columns."
+  echo ""
+  echo "    --inheader"
+  echo "        type: boolean_true"
+  echo "        Input file has a header line - the first line will be ignored."
+  echo ""
+  echo "    --outheader"
+  echo "        type: boolean_true"
+  echo "        Print header line in the output, detailing the column names."
+  echo "        If the input file has headers (-inheader), the output file"
+  echo "        will use the input's column names."
+  echo "        If the input file has no headers, the output file"
+  echo "        will use \"col_1\", \"col_2\", etc. as the column names."
+  echo ""
+  echo "    --header"
+  echo "        type: boolean_true"
+  echo "        same as '-inheader -outheader'."
+  echo ""
+  echo "    --ignorecase"
+  echo "        type: boolean_true"
+  echo "        Group values regardless of upper/lower case."
+  echo ""
+  echo "    -prec, --precision"
+  echo "        type: integer"
+  echo "        default: 5"
+  echo "        Sets the decimal precision for output."
+  echo ""
+  echo "    -delim, --delimiter"
+  echo "        type: string"
+  echo "        default: ,"
+  echo "        example: |"
+  echo "        Specify a custom delimiter for the collapse operations."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml b/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml
index f2a79977..132c6869 100644
--- a/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml
@@ -301,6 +301,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -409,16 +412,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/bedtools/bedtools_intersect"
   executable: "target/executable/bedtools/bedtools_intersect/bedtools_intersect"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/bedtools/bedtools_intersect/bedtools_intersect b/target/executable/bedtools/bedtools_intersect/bedtools_intersect
index 8ae4cfc4..b116bd59 100755
--- a/target/executable/bedtools/bedtools_intersect/bedtools_intersect
+++ b/target/executable/bedtools/bedtools_intersect/bedtools_intersect
@@ -2,7 +2,7 @@
 
 # bedtools_intersect main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,183 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "bedtools_intersect main"
-  echo ""
-  echo "bedtools intersect allows one to screen for overlaps between two sets of genomic"
-  echo "features."
-  echo "Moreover, it allows one to have fine control as to how the intersections are"
-  echo "reported."
-  echo "bedtools intersect works with both BED/GFF/VCF and BAM files as input."
-  echo ""
-  echo "Inputs:"
-  echo "    -a, --input_a"
-  echo "        type: file, required parameter, file must exist"
-  echo "        example: input_a.bed"
-  echo "        The input file (BED/GFF/VCF/BAM) to be used as the -a file."
-  echo ""
-  echo "    -b, --input_b"
-  echo "        type: file, required parameter, multiple values allowed, file must exist"
-  echo "        example: input_b.bed"
-  echo "        The input file(s) (BED/GFF/VCF/BAM) to be used as the -b file(s)."
-  echo ""
-  echo "Outputs:"
-  echo "    --output"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        example: output.bed"
-  echo "        The output BED file."
-  echo ""
-  echo "Options:"
-  echo "    -wa, --write_a"
-  echo "        type: boolean_true"
-  echo "        Write the original A entry for each overlap."
-  echo ""
-  echo "    -wb, --write_b"
-  echo "        type: boolean_true"
-  echo "        Write the original B entry for each overlap."
-  echo "        Useful for knowing _what_ A overlaps. Restricted by -f and -r."
-  echo ""
-  echo "    -loj, --left_outer_join"
-  echo "        type: boolean_true"
-  echo "        Perform a \"left outer join\". That is, for each feature in A report each"
-  echo "        overlap with B."
-  echo "        If no overlaps are found, report a NULL feature for B."
-  echo ""
-  echo "    -wo, --write_overlap"
-  echo "        type: boolean_true"
-  echo "        Write the original A and B entries plus the number of base pairs of"
-  echo "        overlap between the two features."
-  echo "        - Overlaps restricted by -f and -r."
-  echo "          Only A features with overlap are reported."
-  echo ""
-  echo "    -wao, --write_overlap_plus"
-  echo "        type: boolean_true"
-  echo "        Write the original A and B entries plus the number of base pairs of"
-  echo "        overlap between the two features."
-  echo "        - Overlaps restricted by -f and -r."
-  echo "          However, A features w/o overlap are also reported with a NULL B"
-  echo "        feature and overlap = 0."
-  echo ""
-  echo "    -u, --report_A_if_no_overlap"
-  echo "        type: boolean_true"
-  echo "        Write the original A entry _if_ no overlap is found."
-  echo "        - In other words, just report the fact >=1 hit was found."
-  echo "        - Overlaps restricted by -f and -r."
-  echo ""
-  echo "    -c, --number_of_overlaps_A"
-  echo "        type: boolean_true"
-  echo "        For each entry in A, report the number of overlaps with B."
-  echo "        - Reports 0 for A entries that have no overlap with B."
-  echo "        - Overlaps restricted by -f and -r."
-  echo ""
-  echo "    -v, --report_no_overlaps_A"
-  echo "        type: boolean_true"
-  echo "        Only report those entries in A that have _no overlaps_ with B."
-  echo "        - Similar to \"grep -v\" (an homage)."
-  echo ""
-  echo "    -ubam, --uncompressed_bam"
-  echo "        type: boolean_true"
-  echo "        Write uncompressed BAM output. Default writes compressed BAM."
-  echo ""
-  echo "    -s, --same_strand"
-  echo "        type: boolean_true"
-  echo "        Require same strandedness.  That is, only report hits in B."
-  echo "        that overlap A on the _same_ strand."
-  echo "        - By default, overlaps are reported without respect to strand."
-  echo ""
-  echo "    -S, --opposite_strand"
-  echo "        type: boolean_true"
-  echo "        Require different strandedness.  That is, only report hits in B"
-  echo "        that overlap A on the _opposite_ strand."
-  echo "        - By default, overlaps are reported without respect to strand."
-  echo ""
-  echo "    -f, --min_overlap_A"
-  echo "        type: double"
-  echo "        example: 0.5"
-  echo "        Minimum overlap required as a fraction of A."
-  echo "        - Default is 1E-9 (i.e., 1bp)."
-  echo "        - FLOAT (e.g. 0.50)"
-  echo ""
-  echo "    -F, --min_overlap_B"
-  echo "        type: double"
-  echo "        example: 0.5"
-  echo "        Minimum overlap required as a fraction of B."
-  echo "        - Default is 1E-9 (i.e., 1bp)."
-  echo "        - FLOAT (e.g. 0.50)"
-  echo ""
-  echo "    -r, --reciprocal_overlap"
-  echo "        type: boolean_true"
-  echo "        Require that the fraction overlap be reciprocal for A AND B."
-  echo "        - In other words, if -f is 0.90 and -r is used, this requires"
-  echo "        that B overlap 90% of A and A _also_ overlaps 90% of B."
-  echo ""
-  echo "    -e, --either_overlap"
-  echo "        type: boolean_true"
-  echo "        Require that the minimum fraction be satisfied for A OR B."
-  echo "        - In other words, if -e is used with -f 0.90 and -F 0.10 this requires"
-  echo "        that either 90% of A is covered OR 10% of B is covered."
-  echo "        Without -e, both fractions would have to be satisfied."
-  echo ""
-  echo "    --split"
-  echo "        type: boolean_true"
-  echo "        Treat \"split\" BAM or BED12 entries as distinct BED intervals."
-  echo ""
-  echo "    -g, --genome"
-  echo "        type: file, file must exist"
-  echo "        example: genome.txt"
-  echo "        Provide a genome file to enforce consistent chromosome"
-  echo "        sort order across input files. Only applies when used"
-  echo "        with -sorted option."
-  echo ""
-  echo "    --nonamecheck"
-  echo "        type: boolean_true"
-  echo "        For sorted data, don't throw an error if the file"
-  echo "        has different naming conventions for the same chromosome"
-  echo "        (e.g., \"chr1\" vs \"chr01\")."
-  echo ""
-  echo "    --sorted"
-  echo "        type: boolean_true"
-  echo "        Use the \"chromsweep\" algorithm for sorted (-k1,1 -k2,2n) input."
-  echo ""
-  echo "    --names"
-  echo "        type: string"
-  echo "        When using multiple databases, provide an alias"
-  echo "        for each that will appear instead of a fileId when"
-  echo "        also printing the DB record."
-  echo ""
-  echo "    --filenames"
-  echo "        type: boolean_true"
-  echo "        When using multiple databases, show each complete filename instead of a"
-  echo "        fileId when also printing the DB record."
-  echo ""
-  echo "    --sortout"
-  echo "        type: boolean_true"
-  echo "        When using multiple databases, sort the output DB hits for each record."
-  echo ""
-  echo "    --bed"
-  echo "        type: boolean_true"
-  echo "        If using BAM input, write output as BED."
-  echo ""
-  echo "    --header"
-  echo "        type: boolean_true"
-  echo "        Print the header from the A file prior to results."
-  echo ""
-  echo "    --nobuf, --no_buffer_output"
-  echo "        type: boolean_true"
-  echo "        Disable buffered output. Using this option will cause each line"
-  echo "        of output to be printed as it is generated, rather than saved"
-  echo "        in a buffer. This will make printing large output files"
-  echo "        noticeably slower, but can be useful in conjunction with"
-  echo "        other software tools and scripts that need to process one"
-  echo "        line of bedtools output at a time."
-  echo ""
-  echo "    --iobuf, --io_buffer_size"
-  echo "        type: integer"
-  echo "        Specify amount of memory to use for input buffer."
-  echo "        Takes an integer argument. Optional suffixes K/M/G supported."
-  echo "        Note: currently has no effect with compressed files."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -633,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
 
 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_intersect"
-LABEL org.opencontainers.image.created="2024-12-03T10:34:03Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:41Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -750,6 +573,209 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "bedtools_intersect main"
+  echo ""
+  echo "bedtools intersect allows one to screen for overlaps between two sets of genomic"
+  echo "features."
+  echo "Moreover, it allows one to have fine control as to how the intersections are"
+  echo "reported."
+  echo "bedtools intersect works with both BED/GFF/VCF and BAM files as input."
+  echo ""
+  echo "Inputs:"
+  echo "    -a, --input_a"
+  echo "        type: file, required parameter, file must exist"
+  echo "        example: input_a.bed"
+  echo "        The input file (BED/GFF/VCF/BAM) to be used as the -a file."
+  echo ""
+  echo "    -b, --input_b"
+  echo "        type: file, required parameter, multiple values allowed, file must exist"
+  echo "        example: input_b.bed"
+  echo "        The input file(s) (BED/GFF/VCF/BAM) to be used as the -b file(s)."
+  echo ""
+  echo "Outputs:"
+  echo "    --output"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        example: output.bed"
+  echo "        The output BED file."
+  echo ""
+  echo "Options:"
+  echo "    -wa, --write_a"
+  echo "        type: boolean_true"
+  echo "        Write the original A entry for each overlap."
+  echo ""
+  echo "    -wb, --write_b"
+  echo "        type: boolean_true"
+  echo "        Write the original B entry for each overlap."
+  echo "        Useful for knowing _what_ A overlaps. Restricted by -f and -r."
+  echo ""
+  echo "    -loj, --left_outer_join"
+  echo "        type: boolean_true"
+  echo "        Perform a \"left outer join\". That is, for each feature in A report each"
+  echo "        overlap with B."
+  echo "        If no overlaps are found, report a NULL feature for B."
+  echo ""
+  echo "    -wo, --write_overlap"
+  echo "        type: boolean_true"
+  echo "        Write the original A and B entries plus the number of base pairs of"
+  echo "        overlap between the two features."
+  echo "        - Overlaps restricted by -f and -r."
+  echo "          Only A features with overlap are reported."
+  echo ""
+  echo "    -wao, --write_overlap_plus"
+  echo "        type: boolean_true"
+  echo "        Write the original A and B entries plus the number of base pairs of"
+  echo "        overlap between the two features."
+  echo "        - Overlaps restricted by -f and -r."
+  echo "          However, A features w/o overlap are also reported with a NULL B"
+  echo "        feature and overlap = 0."
+  echo ""
+  echo "    -u, --report_A_if_no_overlap"
+  echo "        type: boolean_true"
+  echo "        Write the original A entry _if_ no overlap is found."
+  echo "        - In other words, just report the fact >=1 hit was found."
+  echo "        - Overlaps restricted by -f and -r."
+  echo ""
+  echo "    -c, --number_of_overlaps_A"
+  echo "        type: boolean_true"
+  echo "        For each entry in A, report the number of overlaps with B."
+  echo "        - Reports 0 for A entries that have no overlap with B."
+  echo "        - Overlaps restricted by -f and -r."
+  echo ""
+  echo "    -v, --report_no_overlaps_A"
+  echo "        type: boolean_true"
+  echo "        Only report those entries in A that have _no overlaps_ with B."
+  echo "        - Similar to \"grep -v\" (an homage)."
+  echo ""
+  echo "    -ubam, --uncompressed_bam"
+  echo "        type: boolean_true"
+  echo "        Write uncompressed BAM output. Default writes compressed BAM."
+  echo ""
+  echo "    -s, --same_strand"
+  echo "        type: boolean_true"
+  echo "        Require same strandedness.  That is, only report hits in B."
+  echo "        that overlap A on the _same_ strand."
+  echo "        - By default, overlaps are reported without respect to strand."
+  echo ""
+  echo "    -S, --opposite_strand"
+  echo "        type: boolean_true"
+  echo "        Require different strandedness.  That is, only report hits in B"
+  echo "        that overlap A on the _opposite_ strand."
+  echo "        - By default, overlaps are reported without respect to strand."
+  echo ""
+  echo "    -f, --min_overlap_A"
+  echo "        type: double"
+  echo "        example: 0.5"
+  echo "        Minimum overlap required as a fraction of A."
+  echo "        - Default is 1E-9 (i.e., 1bp)."
+  echo "        - FLOAT (e.g. 0.50)"
+  echo ""
+  echo "    -F, --min_overlap_B"
+  echo "        type: double"
+  echo "        example: 0.5"
+  echo "        Minimum overlap required as a fraction of B."
+  echo "        - Default is 1E-9 (i.e., 1bp)."
+  echo "        - FLOAT (e.g. 0.50)"
+  echo ""
+  echo "    -r, --reciprocal_overlap"
+  echo "        type: boolean_true"
+  echo "        Require that the fraction overlap be reciprocal for A AND B."
+  echo "        - In other words, if -f is 0.90 and -r is used, this requires"
+  echo "        that B overlap 90% of A and A _also_ overlaps 90% of B."
+  echo ""
+  echo "    -e, --either_overlap"
+  echo "        type: boolean_true"
+  echo "        Require that the minimum fraction be satisfied for A OR B."
+  echo "        - In other words, if -e is used with -f 0.90 and -F 0.10 this requires"
+  echo "        that either 90% of A is covered OR 10% of B is covered."
+  echo "        Without -e, both fractions would have to be satisfied."
+  echo ""
+  echo "    --split"
+  echo "        type: boolean_true"
+  echo "        Treat \"split\" BAM or BED12 entries as distinct BED intervals."
+  echo ""
+  echo "    -g, --genome"
+  echo "        type: file, file must exist"
+  echo "        example: genome.txt"
+  echo "        Provide a genome file to enforce consistent chromosome"
+  echo "        sort order across input files. Only applies when used"
+  echo "        with -sorted option."
+  echo ""
+  echo "    --nonamecheck"
+  echo "        type: boolean_true"
+  echo "        For sorted data, don't throw an error if the file"
+  echo "        has different naming conventions for the same chromosome"
+  echo "        (e.g., \"chr1\" vs \"chr01\")."
+  echo ""
+  echo "    --sorted"
+  echo "        type: boolean_true"
+  echo "        Use the \"chromsweep\" algorithm for sorted (-k1,1 -k2,2n) input."
+  echo ""
+  echo "    --names"
+  echo "        type: string"
+  echo "        When using multiple databases, provide an alias"
+  echo "        for each that will appear instead of a fileId when"
+  echo "        also printing the DB record."
+  echo ""
+  echo "    --filenames"
+  echo "        type: boolean_true"
+  echo "        When using multiple databases, show each complete filename instead of a"
+  echo "        fileId when also printing the DB record."
+  echo ""
+  echo "    --sortout"
+  echo "        type: boolean_true"
+  echo "        When using multiple databases, sort the output DB hits for each record."
+  echo ""
+  echo "    --bed"
+  echo "        type: boolean_true"
+  echo "        If using BAM input, write output as BED."
+  echo ""
+  echo "    --header"
+  echo "        type: boolean_true"
+  echo "        Print the header from the A file prior to results."
+  echo ""
+  echo "    --nobuf, --no_buffer_output"
+  echo "        type: boolean_true"
+  echo "        Disable buffered output. Using this option will cause each line"
+  echo "        of output to be printed as it is generated, rather than saved"
+  echo "        in a buffer. This will make printing large output files"
+  echo "        noticeably slower, but can be useful in conjunction with"
+  echo "        other software tools and scripts that need to process one"
+  echo "        line of bedtools output at a time."
+  echo ""
+  echo "    --iobuf, --io_buffer_size"
+  echo "        type: integer"
+  echo "        Specify amount of memory to use for input buffer."
+  echo "        Takes an integer argument. Optional suffixes K/M/G supported."
+  echo "        Note: currently has no effect with compressed files."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/bedtools/bedtools_links/.config.vsh.yaml b/target/executable/bedtools/bedtools_links/.config.vsh.yaml
index bc6afa65..7037157a 100644
--- a/target/executable/bedtools/bedtools_links/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_links/.config.vsh.yaml
@@ -100,6 +100,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -209,16 +212,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/bedtools/bedtools_links"
   executable: "target/executable/bedtools/bedtools_links/bedtools_links"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/bedtools/bedtools_links/bedtools_links b/target/executable/bedtools/bedtools_links/bedtools_links
index 22e16dda..613d51be 100755
--- a/target/executable/bedtools/bedtools_links/bedtools_links
+++ b/target/executable/bedtools/bedtools_links/bedtools_links
@@ -2,7 +2,7 @@
 
 # bedtools_links main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,50 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "bedtools_links main"
-  echo ""
-  echo "Creates an HTML file with links to an instance of the UCSC Genome Browser for"
-  echo "all features / intervals in a file."
-  echo "This is useful for cases when one wants to manually inspect through a large set"
-  echo "of annotations or features."
-  echo ""
-  echo "Inputs:"
-  echo "    -i, --input"
-  echo "        type: file, required parameter, file must exist"
-  echo "        Input file (bed/gff/vcf)."
-  echo ""
-  echo "Outputs:"
-  echo "    -o, --output"
-  echo "        type: file, output, file must exist"
-  echo "        Output HTML file to be written."
-  echo ""
-  echo "Options:"
-  echo "    By default, the links created will point to human (hg18) UCSC browser."
-  echo "    If you have a local mirror, you can override this behavior by supplying"
-  echo "    the -base, -org, and -db options."
-  echo "    For example, if the URL of your local mirror for mouse MM9 is called:"
-  echo "    http://mymirror.myuniversity.edu, then you would use the following:"
-  echo "    --base_url http://mymirror.myuniversity.edu"
-  echo "    --organism mouse"
-  echo "    --database mm9"
-  echo ""
-  echo "    -base, --base_url"
-  echo "        type: string"
-  echo "        default: http://genome.ucsc.edu"
-  echo "        The “basename” for the UCSC browser."
-  echo ""
-  echo "    -org, --organism"
-  echo "        type: string"
-  echo "        default: human"
-  echo "        The organism (e.g. mouse, human)."
-  echo ""
-  echo "    -db, --database"
-  echo "        type: string"
-  echo "        default: hg18"
-  echo "        The genome build."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -500,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
 
 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_links"
-LABEL org.opencontainers.image.created="2024-12-03T10:34:04Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:43Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -617,6 +573,76 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "bedtools_links main"
+  echo ""
+  echo "Creates an HTML file with links to an instance of the UCSC Genome Browser for"
+  echo "all features / intervals in a file."
+  echo "This is useful for cases when one wants to manually inspect through a large set"
+  echo "of annotations or features."
+  echo ""
+  echo "Inputs:"
+  echo "    -i, --input"
+  echo "        type: file, required parameter, file must exist"
+  echo "        Input file (bed/gff/vcf)."
+  echo ""
+  echo "Outputs:"
+  echo "    -o, --output"
+  echo "        type: file, output, file must exist"
+  echo "        Output HTML file to be written."
+  echo ""
+  echo "Options:"
+  echo "    By default, the links created will point to human (hg18) UCSC browser."
+  echo "    If you have a local mirror, you can override this behavior by supplying"
+  echo "    the -base, -org, and -db options."
+  echo "    For example, if the URL of your local mirror for mouse MM9 is called:"
+  echo "    http://mymirror.myuniversity.edu, then you would use the following:"
+  echo "    --base_url http://mymirror.myuniversity.edu"
+  echo "    --organism mouse"
+  echo "    --database mm9"
+  echo ""
+  echo "    -base, --base_url"
+  echo "        type: string"
+  echo "        default: http://genome.ucsc.edu"
+  echo "        The “basename” for the UCSC browser."
+  echo ""
+  echo "    -org, --organism"
+  echo "        type: string"
+  echo "        default: human"
+  echo "        The organism (e.g. mouse, human)."
+  echo ""
+  echo "    -db, --database"
+  echo "        type: string"
+  echo "        default: hg18"
+  echo "        The genome build."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/bedtools/bedtools_merge/.config.vsh.yaml b/target/executable/bedtools/bedtools_merge/.config.vsh.yaml
index 5a26354b..d574fd8a 100644
--- a/target/executable/bedtools/bedtools_merge/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_merge/.config.vsh.yaml
@@ -174,6 +174,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -278,16 +281,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/bedtools/bedtools_merge"
   executable: "target/executable/bedtools/bedtools_merge/bedtools_merge"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/bedtools/bedtools_merge/bedtools_merge b/target/executable/bedtools/bedtools_merge/bedtools_merge
index f54e4ece..1aafa88a 100755
--- a/target/executable/bedtools/bedtools_merge/bedtools_merge
+++ b/target/executable/bedtools/bedtools_merge/bedtools_merge
@@ -2,7 +2,7 @@
 
 # bedtools_merge main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,108 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "bedtools_merge main"
-  echo ""
-  echo "Merges overlapping BED/GFF/VCF entries into a single interval."
-  echo ""
-  echo "Inputs:"
-  echo "    -i, --input"
-  echo "        type: file, required parameter, file must exist"
-  echo "        Input file (BED/GFF/VCF) to be merged."
-  echo ""
-  echo "Outputs:"
-  echo "    --output"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        Output merged file BED to be written."
-  echo ""
-  echo "Options:"
-  echo "    -s, --strand"
-  echo "        type: boolean_true"
-  echo "        Force strandedness. That is, only merge features"
-  echo "        that are on the same strand."
-  echo "        - By default, merging is done without respect to strand."
-  echo ""
-  echo "    -S, --specific_strand"
-  echo "        type: string"
-  echo "        choices: [ +, - ]"
-  echo "        Force merge for one specific strand only."
-  echo "        Follow with + or - to force merge from only"
-  echo "        the forward or reverse strand, respectively."
-  echo "        - By default, merging is done without respect to strand."
-  echo ""
-  echo "    -d, --distance"
-  echo "        type: integer"
-  echo "        Maximum distance between features allowed for features"
-  echo "        to be merged."
-  echo "        - Def. 0. That is, overlapping & book-ended features are merged."
-  echo "        - (INTEGER)"
-  echo "        - Note: negative values enforce the number of b.p. required for overlap."
-  echo ""
-  echo "    -c, --columns"
-  echo "        type: integer"
-  echo "        Specify columns from the B file to map onto intervals in A."
-  echo "        Default: 5."
-  echo "        Multiple columns can be specified in a comma-delimited list."
-  echo ""
-  echo "    -o, --operation"
-  echo "        type: string"
-  echo "        Specify the operation that should be applied to -c."
-  echo "        Valid operations:"
-  echo "            sum, min, max, absmin, absmax,"
-  echo "            mean, median, mode, antimode"
-  echo "            stdev, sstdev"
-  echo "            collapse (i.e., print a delimited list (duplicates allowed)),"
-  echo "            distinct (i.e., print a delimited list (NO duplicates allowed)),"
-  echo "            distinct_sort_num (as distinct, sorted numerically, ascending),"
-  echo "            distinct_sort_num_desc (as distinct, sorted numerically,"
-  echo "        desscending),"
-  echo "            distinct_only (delimited list of only unique values),"
-  echo "            count"
-  echo "            count_distinct (i.e., a count of the unique values in the column),"
-  echo "            first (i.e., just the first value in the column),"
-  echo "            last (i.e., just the last value in the column),"
-  echo "        Default: sum"
-  echo "        Multiple operations can be specified in a comma-delimited list."
-  echo "        If there is only column, but multiple operations, all operations will be"
-  echo "        applied on that column. Likewise, if there is only one operation, but"
-  echo "        multiple columns, that operation will be applied to all columns."
-  echo "        Otherwise, the number of columns must match the the number of"
-  echo "        operations,"
-  echo "        and will be applied in respective order."
-  echo "        E.g., \"-c 5,4,6 -o sum,mean,count\" will give the sum of column 5,"
-  echo "        the mean of column 4, and the count of column 6."
-  echo "        The order of output columns will match the ordering given in the"
-  echo "        command."
-  echo ""
-  echo "    -delim, --delimiter"
-  echo "        type: string"
-  echo "        default: ,"
-  echo "        example: |"
-  echo "        Specify a custom delimiter for the collapse operations."
-  echo ""
-  echo "    -prec, --precision"
-  echo "        type: integer"
-  echo "        Sets the decimal precision for output (Default: 5)."
-  echo ""
-  echo "    --bed"
-  echo "        type: boolean_true"
-  echo "        If using BAM input, write output as BED."
-  echo ""
-  echo "    --header"
-  echo "        type: boolean_true"
-  echo "        Print the header from the A file prior to results."
-  echo ""
-  echo "    -nobuf, --no_buffer"
-  echo "        type: boolean_true"
-  echo "        Disable buffered output. Using this option will cause each line"
-  echo "        of output to be printed as it is generated, rather than saved"
-  echo "        in a buffer. This will make printing large output files"
-  echo "        noticeably slower, but can be useful in conjunction with"
-  echo "        other software tools and scripts that need to process one"
-  echo "        line of bedtools output at a time."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -558,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
 
 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_merge"
-LABEL org.opencontainers.image.created="2024-12-03T10:34:04Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:42Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -675,6 +573,134 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "bedtools_merge main"
+  echo ""
+  echo "Merges overlapping BED/GFF/VCF entries into a single interval."
+  echo ""
+  echo "Inputs:"
+  echo "    -i, --input"
+  echo "        type: file, required parameter, file must exist"
+  echo "        Input file (BED/GFF/VCF) to be merged."
+  echo ""
+  echo "Outputs:"
+  echo "    --output"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        Output merged file BED to be written."
+  echo ""
+  echo "Options:"
+  echo "    -s, --strand"
+  echo "        type: boolean_true"
+  echo "        Force strandedness. That is, only merge features"
+  echo "        that are on the same strand."
+  echo "        - By default, merging is done without respect to strand."
+  echo ""
+  echo "    -S, --specific_strand"
+  echo "        type: string"
+  echo "        choices: [ +, - ]"
+  echo "        Force merge for one specific strand only."
+  echo "        Follow with + or - to force merge from only"
+  echo "        the forward or reverse strand, respectively."
+  echo "        - By default, merging is done without respect to strand."
+  echo ""
+  echo "    -d, --distance"
+  echo "        type: integer"
+  echo "        Maximum distance between features allowed for features"
+  echo "        to be merged."
+  echo "        - Def. 0. That is, overlapping & book-ended features are merged."
+  echo "        - (INTEGER)"
+  echo "        - Note: negative values enforce the number of b.p. required for overlap."
+  echo ""
+  echo "    -c, --columns"
+  echo "        type: integer"
+  echo "        Specify columns from the B file to map onto intervals in A."
+  echo "        Default: 5."
+  echo "        Multiple columns can be specified in a comma-delimited list."
+  echo ""
+  echo "    -o, --operation"
+  echo "        type: string"
+  echo "        Specify the operation that should be applied to -c."
+  echo "        Valid operations:"
+  echo "            sum, min, max, absmin, absmax,"
+  echo "            mean, median, mode, antimode"
+  echo "            stdev, sstdev"
+  echo "            collapse (i.e., print a delimited list (duplicates allowed)),"
+  echo "            distinct (i.e., print a delimited list (NO duplicates allowed)),"
+  echo "            distinct_sort_num (as distinct, sorted numerically, ascending),"
+  echo "            distinct_sort_num_desc (as distinct, sorted numerically,"
+  echo "        desscending),"
+  echo "            distinct_only (delimited list of only unique values),"
+  echo "            count"
+  echo "            count_distinct (i.e., a count of the unique values in the column),"
+  echo "            first (i.e., just the first value in the column),"
+  echo "            last (i.e., just the last value in the column),"
+  echo "        Default: sum"
+  echo "        Multiple operations can be specified in a comma-delimited list."
+  echo "        If there is only column, but multiple operations, all operations will be"
+  echo "        applied on that column. Likewise, if there is only one operation, but"
+  echo "        multiple columns, that operation will be applied to all columns."
+  echo "        Otherwise, the number of columns must match the the number of"
+  echo "        operations,"
+  echo "        and will be applied in respective order."
+  echo "        E.g., \"-c 5,4,6 -o sum,mean,count\" will give the sum of column 5,"
+  echo "        the mean of column 4, and the count of column 6."
+  echo "        The order of output columns will match the ordering given in the"
+  echo "        command."
+  echo ""
+  echo "    -delim, --delimiter"
+  echo "        type: string"
+  echo "        default: ,"
+  echo "        example: |"
+  echo "        Specify a custom delimiter for the collapse operations."
+  echo ""
+  echo "    -prec, --precision"
+  echo "        type: integer"
+  echo "        Sets the decimal precision for output (Default: 5)."
+  echo ""
+  echo "    --bed"
+  echo "        type: boolean_true"
+  echo "        If using BAM input, write output as BED."
+  echo ""
+  echo "    --header"
+  echo "        type: boolean_true"
+  echo "        Print the header from the A file prior to results."
+  echo ""
+  echo "    -nobuf, --no_buffer"
+  echo "        type: boolean_true"
+  echo "        Disable buffered output. Using this option will cause each line"
+  echo "        of output to be printed as it is generated, rather than saved"
+  echo "        in a buffer. This will make printing large output files"
+  echo "        noticeably slower, but can be useful in conjunction with"
+  echo "        other software tools and scripts that need to process one"
+  echo "        line of bedtools output at a time."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/bedtools/bedtools_sort/.config.vsh.yaml b/target/executable/bedtools/bedtools_sort/.config.vsh.yaml
index 6554e8fe..a341b1dc 100644
--- a/target/executable/bedtools/bedtools_sort/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_sort/.config.vsh.yaml
@@ -114,6 +114,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -221,16 +224,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/bedtools/bedtools_sort"
   executable: "target/executable/bedtools/bedtools_sort/bedtools_sort"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/bedtools/bedtools_sort/bedtools_sort b/target/executable/bedtools/bedtools_sort/bedtools_sort
index 941312b3..0d67a470 100755
--- a/target/executable/bedtools/bedtools_sort/bedtools_sort
+++ b/target/executable/bedtools/bedtools_sort/bedtools_sort
@@ -2,7 +2,7 @@
 
 # bedtools_sort main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,59 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "bedtools_sort main"
-  echo ""
-  echo "Sorts a feature file (bed/gff/vcf) by chromosome and other criteria."
-  echo ""
-  echo "Inputs:"
-  echo "    -i, --input"
-  echo "        type: file, required parameter, file must exist"
-  echo "        Input file (bed/gff/vcf) to be sorted."
-  echo ""
-  echo "Outputs:"
-  echo "    -o, --output"
-  echo "        type: file, output, file must exist"
-  echo "        Output sorted file (bed/gff/vcf) to be written."
-  echo ""
-  echo "Options:"
-  echo "    --sizeA"
-  echo "        type: boolean_true"
-  echo "        Sort by feature size in ascending order."
-  echo ""
-  echo "    --sizeD"
-  echo "        type: boolean_true"
-  echo "        Sort by feature size in descending order."
-  echo ""
-  echo "    --chrThenSizeA"
-  echo "        type: boolean_true"
-  echo "        Sort by chrom (asc), then feature size (asc)."
-  echo ""
-  echo "    --chrThenSizeD"
-  echo "        type: boolean_true"
-  echo "        Sort by chrom (asc), then feature size (desc)."
-  echo ""
-  echo "    --chrThenScoreA"
-  echo "        type: boolean_true"
-  echo "        Sort by chrom (asc), then score (asc)."
-  echo ""
-  echo "    --chrThenScoreD"
-  echo "        type: boolean_true"
-  echo "        Sort by chrom (asc), then score (desc)."
-  echo ""
-  echo "    -g, --genome"
-  echo "        type: file, file must exist"
-  echo "        Sort according to the chromosomes declared in \"genome.txt\""
-  echo ""
-  echo "    --faidx"
-  echo "        type: file, file must exist"
-  echo "        Sort according to the chromosomes declared in \"names.txt\""
-  echo ""
-  echo "    --header"
-  echo "        type: boolean_true"
-  echo "        Print the header from the A file prior to results."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -509,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
 
 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_sort"
-LABEL org.opencontainers.image.created="2024-12-03T10:34:03Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:43Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -626,6 +573,85 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "bedtools_sort main"
+  echo ""
+  echo "Sorts a feature file (bed/gff/vcf) by chromosome and other criteria."
+  echo ""
+  echo "Inputs:"
+  echo "    -i, --input"
+  echo "        type: file, required parameter, file must exist"
+  echo "        Input file (bed/gff/vcf) to be sorted."
+  echo ""
+  echo "Outputs:"
+  echo "    -o, --output"
+  echo "        type: file, output, file must exist"
+  echo "        Output sorted file (bed/gff/vcf) to be written."
+  echo ""
+  echo "Options:"
+  echo "    --sizeA"
+  echo "        type: boolean_true"
+  echo "        Sort by feature size in ascending order."
+  echo ""
+  echo "    --sizeD"
+  echo "        type: boolean_true"
+  echo "        Sort by feature size in descending order."
+  echo ""
+  echo "    --chrThenSizeA"
+  echo "        type: boolean_true"
+  echo "        Sort by chrom (asc), then feature size (asc)."
+  echo ""
+  echo "    --chrThenSizeD"
+  echo "        type: boolean_true"
+  echo "        Sort by chrom (asc), then feature size (desc)."
+  echo ""
+  echo "    --chrThenScoreA"
+  echo "        type: boolean_true"
+  echo "        Sort by chrom (asc), then score (asc)."
+  echo ""
+  echo "    --chrThenScoreD"
+  echo "        type: boolean_true"
+  echo "        Sort by chrom (asc), then score (desc)."
+  echo ""
+  echo "    -g, --genome"
+  echo "        type: file, file must exist"
+  echo "        Sort according to the chromosomes declared in \"genome.txt\""
+  echo ""
+  echo "    --faidx"
+  echo "        type: file, file must exist"
+  echo "        Sort according to the chromosomes declared in \"names.txt\""
+  echo ""
+  echo "    --header"
+  echo "        type: boolean_true"
+  echo "        Print the header from the A file prior to results."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/busco/busco_download_datasets/.config.vsh.yaml b/target/executable/busco/busco_download_datasets/.config.vsh.yaml
index b4a40135..12b8f47c 100644
--- a/target/executable/busco/busco_download_datasets/.config.vsh.yaml
+++ b/target/executable/busco/busco_download_datasets/.config.vsh.yaml
@@ -58,6 +58,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -157,16 +160,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/busco/busco_download_datasets"
   executable: "target/executable/busco/busco_download_datasets/busco_download_datasets"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/busco/busco_download_datasets/busco_download_datasets b/target/executable/busco/busco_download_datasets/busco_download_datasets
index 939f9f43..d8dc2fb7 100755
--- a/target/executable/busco/busco_download_datasets/busco_download_datasets
+++ b/target/executable/busco/busco_download_datasets/busco_download_datasets
@@ -2,7 +2,7 @@
 
 # busco_download_datasets main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,29 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "busco_download_datasets main"
-  echo ""
-  echo "Downloads available busco datasets"
-  echo ""
-  echo "Inputs:"
-  echo "    --download"
-  echo "        type: string, required parameter"
-  echo "        example: stramenopiles_odb10"
-  echo "        Download dataset. Possible values are a specific dataset name, \"all\","
-  echo "        \"prokaryota\", \"eukaryota\", or \"virus\"."
-  echo "        The full list of available datasets can be viewed"
-  echo "        [here](https://busco-data.ezlab.org/v5/data/lineages/) or by running the"
-  echo "        busco/busco_list_datasets component."
-  echo ""
-  echo "Outputs:"
-  echo "    --download_path"
-  echo "        type: file, output, file must exist"
-  echo "        default: busco_downloads"
-  echo "        example: busco_downloads"
-  echo "        Local filepath for storing BUSCO dataset downloads"
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -475,9 +452,9 @@ RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_version
 
 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component busco busco_download_datasets"
-LABEL org.opencontainers.image.created="2024-12-03T10:34:01Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:40Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -592,6 +569,55 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "busco_download_datasets main"
+  echo ""
+  echo "Downloads available busco datasets"
+  echo ""
+  echo "Inputs:"
+  echo "    --download"
+  echo "        type: string, required parameter"
+  echo "        example: stramenopiles_odb10"
+  echo "        Download dataset. Possible values are a specific dataset name, \"all\","
+  echo "        \"prokaryota\", \"eukaryota\", or \"virus\"."
+  echo "        The full list of available datasets can be viewed"
+  echo "        [here](https://busco-data.ezlab.org/v5/data/lineages/) or by running the"
+  echo "        busco/busco_list_datasets component."
+  echo ""
+  echo "Outputs:"
+  echo "    --download_path"
+  echo "        type: file, output, file must exist"
+  echo "        default: busco_downloads"
+  echo "        example: busco_downloads"
+  echo "        Local filepath for storing BUSCO dataset downloads"
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/busco/busco_list_datasets/.config.vsh.yaml b/target/executable/busco/busco_list_datasets/.config.vsh.yaml
index 49b5b868..41b1f542 100644
--- a/target/executable/busco/busco_list_datasets/.config.vsh.yaml
+++ b/target/executable/busco/busco_list_datasets/.config.vsh.yaml
@@ -45,6 +45,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -144,16 +147,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/busco/busco_list_datasets"
   executable: "target/executable/busco/busco_list_datasets/busco_list_datasets"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/busco/busco_list_datasets/busco_list_datasets b/target/executable/busco/busco_list_datasets/busco_list_datasets
index 87b4e113..dd7f56de 100755
--- a/target/executable/busco/busco_list_datasets/busco_list_datasets
+++ b/target/executable/busco/busco_list_datasets/busco_list_datasets
@@ -2,7 +2,7 @@
 
 # busco_list_datasets main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,19 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "busco_list_datasets main"
-  echo ""
-  echo "Lists the available busco datasets"
-  echo ""
-  echo "Outputs:"
-  echo "    -o, --output"
-  echo "        type: file, output, file must exist"
-  echo "        default: busco_dataset_list.txt"
-  echo "        example: file.txt"
-  echo "        Output file of the available busco datasets"
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -465,9 +452,9 @@ RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_version
 
 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component busco busco_list_datasets"
-LABEL org.opencontainers.image.created="2024-12-03T10:34:00Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:40Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -582,6 +569,45 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "busco_list_datasets main"
+  echo ""
+  echo "Lists the available busco datasets"
+  echo ""
+  echo "Outputs:"
+  echo "    -o, --output"
+  echo "        type: file, output, file must exist"
+  echo "        default: busco_dataset_list.txt"
+  echo "        example: file.txt"
+  echo "        Output file of the available busco datasets"
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/busco/busco_run/.config.vsh.yaml b/target/executable/busco/busco_run/.config.vsh.yaml
index 26ea3c53..facb6b7c 100644
--- a/target/executable/busco/busco_run/.config.vsh.yaml
+++ b/target/executable/busco/busco_run/.config.vsh.yaml
@@ -322,6 +322,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -422,16 +425,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/busco/busco_run"
   executable: "target/executable/busco/busco_run/busco_run"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/busco/busco_run/busco_run b/target/executable/busco/busco_run/busco_run
index e1f473e9..b0ce61c5 100755
--- a/target/executable/busco/busco_run/busco_run
+++ b/target/executable/busco/busco_run/busco_run
@@ -2,7 +2,7 @@
 
 # busco_run main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,186 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "busco_run main"
-  echo ""
-  echo "Assessment of genome assembly and annotation completeness with single copy"
-  echo "orthologs"
-  echo ""
-  echo "Inputs:"
-  echo "    -i, --input"
-  echo "        type: file, required parameter, file must exist"
-  echo "        example: file.fasta"
-  echo "        Input sequence file in FASTA format. Can be an assembled genome or"
-  echo "        transcriptome (DNA), or protein sequences from an annotated gene set."
-  echo "        Also possible to use a path to a directory containing multiple input"
-  echo "        files."
-  echo ""
-  echo "    -m, --mode"
-  echo "        type: string, required parameter"
-  echo "        example: proteins"
-  echo "        choices: [ genome, geno, transcriptome, tran, proteins, prot ]"
-  echo "        Specify which BUSCO analysis mode to run. There are three valid modes:"
-  echo "          - geno or genome, for genome assemblies (DNA)"
-  echo "          - tran or transcriptome, for transcriptome assemblies (DNA)"
-  echo "          - prot or proteins, for annotated gene sets (protein)"
-  echo ""
-  echo "    -l, --lineage_dataset"
-  echo "        type: string"
-  echo "        example: stramenopiles_odb10"
-  echo "        Specify a BUSCO lineage dataset that is most closely related to the"
-  echo "        assembly or gene set being assessed."
-  echo "        The full list of available datasets can be viewed"
-  echo "        [here](https://busco-data.ezlab.org/v5/data/lineages/) or by running the"
-  echo "        busco/busco_list_datasets component."
-  echo "        When unsure, the \"--auto_lineage\" flag can be set to automatically find"
-  echo "        the optimal lineage path."
-  echo "        BUSCO will automatically download the requested dataset if it is not"
-  echo "        already present in the download folder."
-  echo "        You can optionally provide a path to a local dataset instead of a name,"
-  echo "        e.g. path/to/dataset."
-  echo "        Datasets can be downloaded using the busco/busco_download_dataset"
-  echo "        component."
-  echo ""
-  echo "Outputs:"
-  echo "    --short_summary_json"
-  echo "        type: file, output, file must exist"
-  echo "        example: short_summary.json"
-  echo "        Output file for short summary in JSON format."
-  echo ""
-  echo "    --short_summary_txt"
-  echo "        type: file, output, file must exist"
-  echo "        example: short_summary.txt"
-  echo "        Output file for short summary in TXT format."
-  echo ""
-  echo "    --full_table"
-  echo "        type: file, output, file must exist"
-  echo "        example: full_table.tsv"
-  echo "        Full table output in TSV format."
-  echo ""
-  echo "    --missing_busco_list"
-  echo "        type: file, output, file must exist"
-  echo "        example: missing_busco_list.tsv"
-  echo "        Missing list output in TSV format."
-  echo ""
-  echo "    --output_dir"
-  echo "        type: file, output, file must exist"
-  echo "        example: output_dir"
-  echo "        The full output directory, if so desired."
-  echo ""
-  echo "Resource and Run Settings:"
-  echo "    --force"
-  echo "        type: boolean_true"
-  echo "        Force rewriting of existing files. Must be used when output files with"
-  echo "        the provided name already exist."
-  echo ""
-  echo "    -q, --quiet"
-  echo "        type: boolean_true"
-  echo "        Disable the info logs, displays only errors."
-  echo ""
-  echo "    -r, --restart"
-  echo "        type: boolean_true"
-  echo "        Continue a run that had already partially completed. Restarting skips"
-  echo "        calls to tools that have completed but performs all pre- and"
-  echo "        post-processing steps."
-  echo ""
-  echo "    --tar"
-  echo "        type: boolean_true"
-  echo "        Compress some subdirectories with many files to save space."
-  echo ""
-  echo "Lineage Dataset Settings:"
-  echo "    --auto_lineage"
-  echo "        type: boolean_true"
-  echo "        Run auto-lineage pipelilne to automatically determine BUSCO lineage"
-  echo "        dataset that is most closely related to the assembly or gene set being"
-  echo "        assessed."
-  echo ""
-  echo "    --auto_lineage_euk"
-  echo "        type: boolean_true"
-  echo "        Run auto-placement just on eukaryota tree to find optimal lineage path."
-  echo ""
-  echo "    --auto_lineage_prok"
-  echo "        type: boolean_true"
-  echo "        Run auto_lineage just on prokaryota trees to find optimum lineage path."
-  echo ""
-  echo "    --datasets_version"
-  echo "        type: string"
-  echo "        example: odb10"
-  echo "        Specify the version of BUSCO datasets"
-  echo ""
-  echo "Augustus Settings:"
-  echo "    --augustus"
-  echo "        type: boolean_true"
-  echo "        Use augustus gene predictor for eukaryote runs."
-  echo ""
-  echo "    --augustus_parameters"
-  echo "        type: string"
-  echo "        example: --PARAM1=VALUE1,--PARAM2=VALUE2"
-  echo "        Additional parameters to be passed to Augustus (see Augustus"
-  echo "        documentation:"
-  echo "       "
-  echo "https://github.com/Gaius-Augustus/Augustus/blob/master/docs/RUNNING-AUGUSTUS.md)."
-  echo "        Parameters should be contained within a single string, without"
-  echo "        whitespace and seperated by commas."
-  echo ""
-  echo "    --augustus_species"
-  echo "        type: string"
-  echo "        Specify the augustus species"
-  echo ""
-  echo "    --long"
-  echo "        type: boolean_true"
-  echo "        Optimize Augustus self-training mode. This adds considerably to the run"
-  echo "        time, but can improve results for some non-model organisms."
-  echo ""
-  echo "BBTools Settings:"
-  echo "    --contig_break"
-  echo "        type: integer"
-  echo "        Number of contiguous Ns to signify a break between contigs in BBTools"
-  echo "        analysis."
-  echo ""
-  echo "    --limit"
-  echo "        type: integer"
-  echo "        Number of candidate regions (contig or transcript) from the BLAST output"
-  echo "        to consider per BUSCO."
-  echo "        This option is only effective in pipelines using BLAST, i.e. the genome"
-  echo "        pipeline (see --augustus) or the prokaryota transcriptome pipeline."
-  echo ""
-  echo "    --scaffold_composition"
-  echo "        type: boolean_true"
-  echo "        Writes ACGTN content per scaffold to a file scaffold_composition.txt."
-  echo ""
-  echo "BLAST Settings:"
-  echo "    --e_value"
-  echo "        type: double"
-  echo "        E-value cutoff for BLAST searches."
-  echo ""
-  echo "Protein Gene Prediction settings:"
-  echo "    --miniprot"
-  echo "        type: boolean_true"
-  echo "        Use Miniprot gene predictor."
-  echo ""
-  echo "MetaEuk Settings:"
-  echo "    --metaeuk"
-  echo "        type: boolean_true"
-  echo "        Use Metaeuk gene predictor."
-  echo ""
-  echo "    --metaeuk_parameters"
-  echo "        type: string"
-  echo "        example: --max-overlap=15,--min-exon-aa=15"
-  echo "        Pass additional arguments to Metaeuk for the first run (see Metaeuk"
-  echo "        documentation https://github.com/soedinglab/metaeuk)."
-  echo "        All parameters should be contained within a single string with no white"
-  echo "        space, with each parameter separated by a comma."
-  echo ""
-  echo "    --metaeuk_rerun_parameters"
-  echo "        type: string"
-  echo "        example: --max-overlap=15,--min-exon-aa=15"
-  echo "        Pass additional arguments to Metaeuk for the second run (see Metaeuk"
-  echo "        documentation https://github.com/soedinglab/metaeuk)."
-  echo "        All parameters should be contained within a single string with no white"
-  echo "        space, with each parameter separated by a comma."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -632,9 +452,9 @@ RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_version
 
 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component busco busco_run"
-LABEL org.opencontainers.image.created="2024-12-03T10:34:00Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:40Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -749,6 +569,212 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "busco_run main"
+  echo ""
+  echo "Assessment of genome assembly and annotation completeness with single copy"
+  echo "orthologs"
+  echo ""
+  echo "Inputs:"
+  echo "    -i, --input"
+  echo "        type: file, required parameter, file must exist"
+  echo "        example: file.fasta"
+  echo "        Input sequence file in FASTA format. Can be an assembled genome or"
+  echo "        transcriptome (DNA), or protein sequences from an annotated gene set."
+  echo "        Also possible to use a path to a directory containing multiple input"
+  echo "        files."
+  echo ""
+  echo "    -m, --mode"
+  echo "        type: string, required parameter"
+  echo "        example: proteins"
+  echo "        choices: [ genome, geno, transcriptome, tran, proteins, prot ]"
+  echo "        Specify which BUSCO analysis mode to run. There are three valid modes:"
+  echo "          - geno or genome, for genome assemblies (DNA)"
+  echo "          - tran or transcriptome, for transcriptome assemblies (DNA)"
+  echo "          - prot or proteins, for annotated gene sets (protein)"
+  echo ""
+  echo "    -l, --lineage_dataset"
+  echo "        type: string"
+  echo "        example: stramenopiles_odb10"
+  echo "        Specify a BUSCO lineage dataset that is most closely related to the"
+  echo "        assembly or gene set being assessed."
+  echo "        The full list of available datasets can be viewed"
+  echo "        [here](https://busco-data.ezlab.org/v5/data/lineages/) or by running the"
+  echo "        busco/busco_list_datasets component."
+  echo "        When unsure, the \"--auto_lineage\" flag can be set to automatically find"
+  echo "        the optimal lineage path."
+  echo "        BUSCO will automatically download the requested dataset if it is not"
+  echo "        already present in the download folder."
+  echo "        You can optionally provide a path to a local dataset instead of a name,"
+  echo "        e.g. path/to/dataset."
+  echo "        Datasets can be downloaded using the busco/busco_download_dataset"
+  echo "        component."
+  echo ""
+  echo "Outputs:"
+  echo "    --short_summary_json"
+  echo "        type: file, output, file must exist"
+  echo "        example: short_summary.json"
+  echo "        Output file for short summary in JSON format."
+  echo ""
+  echo "    --short_summary_txt"
+  echo "        type: file, output, file must exist"
+  echo "        example: short_summary.txt"
+  echo "        Output file for short summary in TXT format."
+  echo ""
+  echo "    --full_table"
+  echo "        type: file, output, file must exist"
+  echo "        example: full_table.tsv"
+  echo "        Full table output in TSV format."
+  echo ""
+  echo "    --missing_busco_list"
+  echo "        type: file, output, file must exist"
+  echo "        example: missing_busco_list.tsv"
+  echo "        Missing list output in TSV format."
+  echo ""
+  echo "    --output_dir"
+  echo "        type: file, output, file must exist"
+  echo "        example: output_dir"
+  echo "        The full output directory, if so desired."
+  echo ""
+  echo "Resource and Run Settings:"
+  echo "    --force"
+  echo "        type: boolean_true"
+  echo "        Force rewriting of existing files. Must be used when output files with"
+  echo "        the provided name already exist."
+  echo ""
+  echo "    -q, --quiet"
+  echo "        type: boolean_true"
+  echo "        Disable the info logs, displays only errors."
+  echo ""
+  echo "    -r, --restart"
+  echo "        type: boolean_true"
+  echo "        Continue a run that had already partially completed. Restarting skips"
+  echo "        calls to tools that have completed but performs all pre- and"
+  echo "        post-processing steps."
+  echo ""
+  echo "    --tar"
+  echo "        type: boolean_true"
+  echo "        Compress some subdirectories with many files to save space."
+  echo ""
+  echo "Lineage Dataset Settings:"
+  echo "    --auto_lineage"
+  echo "        type: boolean_true"
+  echo "        Run auto-lineage pipelilne to automatically determine BUSCO lineage"
+  echo "        dataset that is most closely related to the assembly or gene set being"
+  echo "        assessed."
+  echo ""
+  echo "    --auto_lineage_euk"
+  echo "        type: boolean_true"
+  echo "        Run auto-placement just on eukaryota tree to find optimal lineage path."
+  echo ""
+  echo "    --auto_lineage_prok"
+  echo "        type: boolean_true"
+  echo "        Run auto_lineage just on prokaryota trees to find optimum lineage path."
+  echo ""
+  echo "    --datasets_version"
+  echo "        type: string"
+  echo "        example: odb10"
+  echo "        Specify the version of BUSCO datasets"
+  echo ""
+  echo "Augustus Settings:"
+  echo "    --augustus"
+  echo "        type: boolean_true"
+  echo "        Use augustus gene predictor for eukaryote runs."
+  echo ""
+  echo "    --augustus_parameters"
+  echo "        type: string"
+  echo "        example: --PARAM1=VALUE1,--PARAM2=VALUE2"
+  echo "        Additional parameters to be passed to Augustus (see Augustus"
+  echo "        documentation:"
+  echo "       "
+  echo "https://github.com/Gaius-Augustus/Augustus/blob/master/docs/RUNNING-AUGUSTUS.md)."
+  echo "        Parameters should be contained within a single string, without"
+  echo "        whitespace and seperated by commas."
+  echo ""
+  echo "    --augustus_species"
+  echo "        type: string"
+  echo "        Specify the augustus species"
+  echo ""
+  echo "    --long"
+  echo "        type: boolean_true"
+  echo "        Optimize Augustus self-training mode. This adds considerably to the run"
+  echo "        time, but can improve results for some non-model organisms."
+  echo ""
+  echo "BBTools Settings:"
+  echo "    --contig_break"
+  echo "        type: integer"
+  echo "        Number of contiguous Ns to signify a break between contigs in BBTools"
+  echo "        analysis."
+  echo ""
+  echo "    --limit"
+  echo "        type: integer"
+  echo "        Number of candidate regions (contig or transcript) from the BLAST output"
+  echo "        to consider per BUSCO."
+  echo "        This option is only effective in pipelines using BLAST, i.e. the genome"
+  echo "        pipeline (see --augustus) or the prokaryota transcriptome pipeline."
+  echo ""
+  echo "    --scaffold_composition"
+  echo "        type: boolean_true"
+  echo "        Writes ACGTN content per scaffold to a file scaffold_composition.txt."
+  echo ""
+  echo "BLAST Settings:"
+  echo "    --e_value"
+  echo "        type: double"
+  echo "        E-value cutoff for BLAST searches."
+  echo ""
+  echo "Protein Gene Prediction settings:"
+  echo "    --miniprot"
+  echo "        type: boolean_true"
+  echo "        Use Miniprot gene predictor."
+  echo ""
+  echo "MetaEuk Settings:"
+  echo "    --metaeuk"
+  echo "        type: boolean_true"
+  echo "        Use Metaeuk gene predictor."
+  echo ""
+  echo "    --metaeuk_parameters"
+  echo "        type: string"
+  echo "        example: --max-overlap=15,--min-exon-aa=15"
+  echo "        Pass additional arguments to Metaeuk for the first run (see Metaeuk"
+  echo "        documentation https://github.com/soedinglab/metaeuk)."
+  echo "        All parameters should be contained within a single string with no white"
+  echo "        space, with each parameter separated by a comma."
+  echo ""
+  echo "    --metaeuk_rerun_parameters"
+  echo "        type: string"
+  echo "        example: --max-overlap=15,--min-exon-aa=15"
+  echo "        Pass additional arguments to Metaeuk for the second run (see Metaeuk"
+  echo "        documentation https://github.com/soedinglab/metaeuk)."
+  echo "        All parameters should be contained within a single string with no white"
+  echo "        space, with each parameter separated by a comma."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/cellranger/cellranger_mkref/.config.vsh.yaml b/target/executable/cellranger/cellranger_mkref/.config.vsh.yaml
index f9c27765..2c03bf3b 100644
--- a/target/executable/cellranger/cellranger_mkref/.config.vsh.yaml
+++ b/target/executable/cellranger/cellranger_mkref/.config.vsh.yaml
@@ -75,6 +75,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -194,16 +197,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/cellranger/cellranger_mkref"
   executable: "target/executable/cellranger/cellranger_mkref/cellranger_mkref"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/cellranger/cellranger_mkref/cellranger_mkref b/target/executable/cellranger/cellranger_mkref/cellranger_mkref
index dc3f7ab4..18e76d38 100755
--- a/target/executable/cellranger/cellranger_mkref/cellranger_mkref
+++ b/target/executable/cellranger/cellranger_mkref/cellranger_mkref
@@ -2,7 +2,7 @@
 
 # cellranger_mkref main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,33 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "cellranger_mkref main"
-  echo ""
-  echo "Build a Cell Ranger-compatible reference folder from user-supplied genome FASTA"
-  echo "and gene GTF files."
-  echo ""
-  echo "Arguments:"
-  echo "    --genome_fasta"
-  echo "        type: file, required parameter, file must exist"
-  echo "        example: genome_sequence.fa.gz"
-  echo "        Reference genome fasta."
-  echo ""
-  echo "    --transcriptome_gtf"
-  echo "        type: file, required parameter, file must exist"
-  echo "        example: transcriptome_annotation.gtf.gz"
-  echo "        Reference transcriptome annotation."
-  echo ""
-  echo "    --reference_version"
-  echo "        type: string"
-  echo "        Optional reference version string to include with reference"
-  echo ""
-  echo "    --output"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        example: cellranger_reference"
-  echo "        Output folder"
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -481,9 +454,9 @@ RUN apt-get update && \
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component cellranger cellranger_mkref"
-LABEL org.opencontainers.image.created="2024-12-03T10:34:01Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:45Z"
 LABEL org.opencontainers.image.source="https://github.com/10XGenomics/cellranger/blob/main/lib/python/cellranger/reference_builder.py"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -598,6 +571,59 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "cellranger_mkref main"
+  echo ""
+  echo "Build a Cell Ranger-compatible reference folder from user-supplied genome FASTA"
+  echo "and gene GTF files."
+  echo ""
+  echo "Arguments:"
+  echo "    --genome_fasta"
+  echo "        type: file, required parameter, file must exist"
+  echo "        example: genome_sequence.fa.gz"
+  echo "        Reference genome fasta."
+  echo ""
+  echo "    --transcriptome_gtf"
+  echo "        type: file, required parameter, file must exist"
+  echo "        example: transcriptome_annotation.gtf.gz"
+  echo "        Reference transcriptome annotation."
+  echo ""
+  echo "    --reference_version"
+  echo "        type: string"
+  echo "        Optional reference version string to include with reference"
+  echo ""
+  echo "    --output"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        example: cellranger_reference"
+  echo "        Output folder"
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/cutadapt/.config.vsh.yaml b/target/executable/cutadapt/.config.vsh.yaml
index 6eac2dab..af54c8e4 100644
--- a/target/executable/cutadapt/.config.vsh.yaml
+++ b/target/executable/cutadapt/.config.vsh.yaml
@@ -633,6 +633,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -739,16 +742,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/cutadapt"
   executable: "target/executable/cutadapt/cutadapt"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/cutadapt/cutadapt b/target/executable/cutadapt/cutadapt
index 37d90bf0..934ad898 100755
--- a/target/executable/cutadapt/cutadapt
+++ b/target/executable/cutadapt/cutadapt
@@ -2,7 +2,7 @@
 
 # cutadapt main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,6 +172,407 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
+
+# initialise variables
+VIASH_MODE='run'
+VIASH_ENGINE_ID='docker'
+
+######## Helper functions for setting up Docker images for viash ########
+# expects: ViashDockerBuild
+
+# ViashDockerInstallationCheck: check whether Docker is installed correctly
+#
+# examples:
+#   ViashDockerInstallationCheck
+function ViashDockerInstallationCheck {
+  ViashDebug "Checking whether Docker is installed"
+  if [ ! command -v docker &> /dev/null ]; then
+    ViashCritical "Docker doesn't seem to be installed. See 'https://docs.docker.com/get-docker/' for instructions."
+    exit 1
+  fi
+
+  ViashDebug "Checking whether the Docker daemon is running"
+  local save=$-; set +e
+  local docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
+  local out=$?
+  [[ $save =~ e ]] && set -e
+  if [ $out -ne 0 ]; then
+    ViashCritical "Docker daemon does not seem to be running. Try one of the following:"
+    ViashCritical "- Try running 'dockerd' in the command line"
+    ViashCritical "- See https://docs.docker.com/config/daemon/"
+    exit 1
+  fi
+}
+
+# ViashDockerRemoteTagCheck: check whether a Docker image is available 
+# on a remote. Assumes `docker login` has been performed, if relevant.
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   ViashDockerRemoteTagCheck python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerRemoteTagCheck sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerRemoteTagCheck {
+  docker manifest inspect $1 > /dev/null 2> /dev/null
+}
+
+# ViashDockerLocalTagCheck: check whether a Docker image is available locally
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   docker pull python:latest
+#   ViashDockerLocalTagCheck python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerLocalTagCheck sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerLocalTagCheck {
+  [ -n "$(docker images -q $1)" ]
+}
+
+# ViashDockerPull: pull a Docker image
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   ViashDockerPull python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerPull sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerPull {
+  ViashNotice "Checking if Docker image is available at '$1'"
+  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
+    docker pull $1 && return 0 || return 1
+  else
+    local save=$-; set +e
+    docker pull $1 2> /dev/null > /dev/null
+    local out=$?
+    [[ $save =~ e ]] && set -e
+    if [ $out -ne 0 ]; then
+      ViashWarning "Could not pull from '$1'. Docker image doesn't exist or is not accessible."
+    fi
+    return $out
+  fi
+}
+
+# ViashDockerPush: push a Docker image
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   ViashDockerPush python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerPush sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerPush {
+  ViashNotice "Pushing image to '$1'"
+  local save=$-; set +e
+  local out
+  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
+    docker push $1
+    out=$?
+  else
+    docker push $1 2> /dev/null > /dev/null
+    out=$?
+  fi
+  [[ $save =~ e ]] && set -e
+  if [ $out -eq 0 ]; then
+    ViashNotice "Container '$1' push succeeded."
+  else
+    ViashError "Container '$1' push errored. You might not be logged in or have the necessary permissions."
+  fi
+  return $out
+}
+
+# ViashDockerPullElseBuild: pull a Docker image, else build it
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# ViashDockerBuild    : a Bash function which builds a docker image, takes image identifier as argument.
+# examples:
+#   ViashDockerPullElseBuild mynewcomponent
+function ViashDockerPullElseBuild {
+  local save=$-; set +e
+  ViashDockerPull $1
+  local out=$?
+  [[ $save =~ e ]] && set -e
+  if [ $out -ne 0 ]; then
+    ViashDockerBuild $@
+  fi
+}
+
+# ViashDockerSetup: create a Docker image, according to specified docker setup strategy
+#
+# $1          : image identifier with format `[registry/]image[:tag]`
+# $2          : docker setup strategy, see DockerSetupStrategy.scala
+# examples:
+#   ViashDockerSetup mynewcomponent alwaysbuild
+function ViashDockerSetup {
+  local image_id="$1"
+  local setup_strategy="$2"
+  if [ "$setup_strategy" == "alwaysbuild" -o "$setup_strategy" == "build" -o "$setup_strategy" == "b" ]; then
+    ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+  elif [ "$setup_strategy" == "alwayspull" -o "$setup_strategy" == "pull" -o "$setup_strategy" == "p" ]; then
+    ViashDockerPull $image_id
+  elif [ "$setup_strategy" == "alwayspullelsebuild" -o "$setup_strategy" == "pullelsebuild" ]; then
+    ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+  elif [ "$setup_strategy" == "alwayspullelsecachedbuild" -o "$setup_strategy" == "pullelsecachedbuild" ]; then
+    ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+  elif [ "$setup_strategy" == "alwayscachedbuild" -o "$setup_strategy" == "cachedbuild" -o "$setup_strategy" == "cb" ]; then
+    ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+  elif [[ "$setup_strategy" =~ ^ifneedbe ]]; then
+    local save=$-; set +e
+    ViashDockerLocalTagCheck $image_id
+    local outCheck=$?
+    [[ $save =~ e ]] && set -e
+    if [ $outCheck -eq 0 ]; then
+      ViashInfo "Image $image_id already exists"
+    elif [ "$setup_strategy" == "ifneedbebuild" ]; then
+      ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+    elif [ "$setup_strategy" == "ifneedbecachedbuild" ]; then
+      ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+    elif [ "$setup_strategy" == "ifneedbepull" ]; then
+      ViashDockerPull $image_id
+    elif [ "$setup_strategy" == "ifneedbepullelsebuild" ]; then
+      ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+    elif [ "$setup_strategy" == "ifneedbepullelsecachedbuild" ]; then
+      ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+    else
+      ViashError "Unrecognised Docker strategy: $setup_strategy"
+      exit 1
+    fi
+  elif [ "$setup_strategy" == "push" -o "$setup_strategy" == "forcepush" -o "$setup_strategy" == "alwayspush" ]; then
+    ViashDockerPush "$image_id"
+  elif [ "$setup_strategy" == "pushifnotpresent" -o "$setup_strategy" == "gentlepush" -o "$setup_strategy" == "maybepush" ]; then
+    local save=$-; set +e
+    ViashDockerRemoteTagCheck $image_id
+    local outCheck=$?
+    [[ $save =~ e ]] && set -e
+    if [ $outCheck -eq 0 ]; then
+      ViashNotice "Container '$image_id' exists, doing nothing."
+    else
+      ViashNotice "Container '$image_id' does not yet exist."
+      ViashDockerPush "$image_id"
+    fi
+  elif [ "$setup_strategy" == "donothing" -o "$setup_strategy" == "meh" ]; then
+    ViashNotice "Skipping setup."
+  else
+    ViashError "Unrecognised Docker strategy: $setup_strategy"
+    exit 1
+  fi
+}
+
+# ViashDockerCheckCommands: Check whether a docker container has the required commands
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# $@                  : commands to verify being present
+# examples:
+#   ViashDockerCheckCommands bash:4.0 bash ps foo
+function ViashDockerCheckCommands {
+  local image_id="$1"
+  shift 1
+  local commands="$@"
+  local save=$-; set +e
+  local missing # mark 'missing' as local in advance, otherwise the exit code of the command will be missing and always be '0'
+  missing=$(docker run --rm --entrypoint=sh "$image_id" -c "for command in $commands; do command -v \$command >/dev/null 2>&1; if [ \$? -ne 0 ]; then echo \$command; exit 1; fi; done")
+  local outCheck=$?
+  [[ $save =~ e ]] && set -e
+  if [ $outCheck -ne 0 ]; then
+  	ViashError "Docker container '$image_id' does not contain command '$missing'."
+  	exit 1
+  fi
+}
+
+# ViashDockerBuild: build a docker image
+# $1                               : image identifier with format `[registry/]image[:tag]`
+# $...                             : additional arguments to pass to docker build
+# $VIASH_META_TEMP_DIR             : temporary directory to store dockerfile & optional resources in
+# $VIASH_META_NAME                 : name of the component
+# $VIASH_META_RESOURCES_DIR        : directory containing the resources
+# $VIASH_VERBOSITY                 : verbosity level
+# exit code $?                     : whether or not the image was built successfully
+function ViashDockerBuild {
+  local image_id="$1"
+  shift 1
+
+  # create temporary directory to store dockerfile & optional resources in
+  local tmpdir=$(mktemp -d "$VIASH_META_TEMP_DIR/dockerbuild-$VIASH_META_NAME-XXXXXX")
+  local dockerfile="$tmpdir/Dockerfile"
+  function clean_up {
+    rm -rf "$tmpdir"
+  }
+  trap clean_up EXIT
+
+  # store dockerfile and resources
+  ViashDockerfile "$VIASH_ENGINE_ID" > "$dockerfile"
+
+  # generate the build command
+  local docker_build_cmd="docker build -t '$image_id' $@ '$VIASH_META_RESOURCES_DIR' -f '$dockerfile'"
+
+  # build the container
+  ViashNotice "Building container '$image_id' with Dockerfile"
+  ViashInfo "$docker_build_cmd"
+  local save=$-; set +e
+  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
+    eval $docker_build_cmd
+  else
+    eval $docker_build_cmd &> "$tmpdir/docker_build.log"
+  fi
+
+  # check exit code
+  local out=$?
+  [[ $save =~ e ]] && set -e
+  if [ $out -ne 0 ]; then
+    ViashError "Error occurred while building container '$image_id'"
+    if [ $VIASH_VERBOSITY -lt $VIASH_LOGCODE_INFO ]; then
+      ViashError "Transcript: --------------------------------"
+      cat "$tmpdir/docker_build.log"
+      ViashError "End of transcript --------------------------"
+    fi
+    exit 1
+  fi
+}
+
+######## End of helper functions for setting up Docker images for viash ########
+
+# ViashDockerFile: print the dockerfile to stdout
+# $1    : engine identifier
+# return : dockerfile required to run this component
+# examples:
+#   ViashDockerFile
+function ViashDockerfile {
+  local engine_id="$1"
+
+  if [[ "$engine_id" == "docker" ]]; then
+    cat << 'VIASHDOCKER'
+FROM python:3.12
+ENTRYPOINT []
+RUN pip install --upgrade pip && \
+  pip install --upgrade --no-cache-dir "cutadapt"
+
+RUN cutadapt --version | sed 's/\(.*\)/cutadapt: "\1"/' > /var/software_versions.txt
+
+LABEL org.opencontainers.image.authors="Toni Verbeiren"
+LABEL org.opencontainers.image.description="Companion container for running component cutadapt"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:35Z"
+LABEL org.opencontainers.image.source="https://github.com/marcelm/cutadapt"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+LABEL org.opencontainers.image.version="main"
+
+VIASHDOCKER
+  fi
+}
+
+# ViashDockerBuildArgs: return the arguments to pass to docker build
+# $1    : engine identifier
+# return : arguments to pass to docker build
+function ViashDockerBuildArgs {
+  local engine_id="$1"
+
+  if [[ "$engine_id" == "docker" ]]; then
+    echo ""
+  fi
+}
+
+# ViashAbsolutePath: generate absolute path from relative path
+# borrowed from https://stackoverflow.com/a/21951256
+# $1     : relative filename
+# return : absolute path
+# examples:
+#   ViashAbsolutePath some_file.txt   # returns /path/to/some_file.txt
+#   ViashAbsolutePath /foo/bar/..     # returns /foo
+function ViashAbsolutePath {
+  local thePath
+  local parr
+  local outp
+  local len
+  if [[ ! "$1" =~ ^/ ]]; then
+    thePath="$PWD/$1"
+  else
+    thePath="$1"
+  fi
+  echo "$thePath" | (
+    IFS=/
+    read -a parr
+    declare -a outp
+    for i in "${parr[@]}"; do
+      case "$i" in
+      ''|.) continue ;;
+      ..)
+        len=${#outp[@]}
+        if ((len==0)); then
+          continue
+        else
+          unset outp[$((len-1))]
+        fi
+        ;;
+      *)
+        len=${#outp[@]}
+        outp[$len]="$i"
+      ;;
+      esac
+    done
+    echo /"${outp[*]}"
+  )
+}
+# ViashDockerAutodetectMount: auto configuring docker mounts from parameters
+# $1                             : The parameter value
+# returns                        : New parameter
+# $VIASH_DIRECTORY_MOUNTS        : Added another parameter to be passed to docker
+# $VIASH_DOCKER_AUTOMOUNT_PREFIX : The prefix to be used for the automounts
+# examples:
+#   ViashDockerAutodetectMount /path/to/bar      # returns '/viash_automount/path/to/bar'
+#   ViashDockerAutodetectMountArg /path/to/bar   # returns '--volume="/path/to:/viash_automount/path/to"'
+function ViashDockerAutodetectMount {
+  local abs_path=$(ViashAbsolutePath "$1")
+  local mount_source
+  local base_name
+  if [ -d "$abs_path" ]; then
+    mount_source="$abs_path"
+    base_name=""
+  else
+    mount_source=`dirname "$abs_path"`
+    base_name=`basename "$abs_path"`
+  fi
+  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
+  if [ -z "$base_name" ]; then
+    echo "$mount_target"
+  else
+    echo "$mount_target/$base_name"
+  fi
+}
+function ViashDockerAutodetectMountArg {
+  local abs_path=$(ViashAbsolutePath "$1")
+  local mount_source
+  local base_name
+  if [ -d "$abs_path" ]; then
+    mount_source="$abs_path"
+    base_name=""
+  else
+    mount_source=`dirname "$abs_path"`
+    base_name=`basename "$abs_path"`
+  fi
+  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
+  ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target"
+  echo "--volume=\"$mount_source:$mount_target\""
+}
+function ViashDockerStripAutomount {
+  local abs_path=$(ViashAbsolutePath "$1")
+  echo "${abs_path#$VIASH_DOCKER_AUTOMOUNT_PREFIX}"
+}
+# initialise variables
+VIASH_DIRECTORY_MOUNTS=()
+
+# configure default docker automount prefix if it is unset
+if [ -z "${VIASH_DOCKER_AUTOMOUNT_PREFIX+x}" ]; then
+  VIASH_DOCKER_AUTOMOUNT_PREFIX="/viash_automount"
+fi
+
+# initialise docker variables
+VIASH_DOCKER_RUN_ARGS=(-i --rm)
+
+
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
   echo "cutadapt main"
@@ -547,407 +948,32 @@ function ViashHelp {
   echo "    --debug"
   echo "        type: boolean_true"
   echo "        Print debug information"
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
 }
 
-# initialise variables
-VIASH_MODE='run'
-VIASH_ENGINE_ID='docker'
-
-######## Helper functions for setting up Docker images for viash ########
-# expects: ViashDockerBuild
-
-# ViashDockerInstallationCheck: check whether Docker is installed correctly
-#
-# examples:
-#   ViashDockerInstallationCheck
-function ViashDockerInstallationCheck {
-  ViashDebug "Checking whether Docker is installed"
-  if [ ! command -v docker &> /dev/null ]; then
-    ViashCritical "Docker doesn't seem to be installed. See 'https://docs.docker.com/get-docker/' for instructions."
-    exit 1
-  fi
-
-  ViashDebug "Checking whether the Docker daemon is running"
-  local save=$-; set +e
-  local docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
-  local out=$?
-  [[ $save =~ e ]] && set -e
-  if [ $out -ne 0 ]; then
-    ViashCritical "Docker daemon does not seem to be running. Try one of the following:"
-    ViashCritical "- Try running 'dockerd' in the command line"
-    ViashCritical "- See https://docs.docker.com/config/daemon/"
-    exit 1
-  fi
-}
-
-# ViashDockerRemoteTagCheck: check whether a Docker image is available 
-# on a remote. Assumes `docker login` has been performed, if relevant.
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   ViashDockerRemoteTagCheck python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerRemoteTagCheck sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerRemoteTagCheck {
-  docker manifest inspect $1 > /dev/null 2> /dev/null
-}
-
-# ViashDockerLocalTagCheck: check whether a Docker image is available locally
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   docker pull python:latest
-#   ViashDockerLocalTagCheck python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerLocalTagCheck sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerLocalTagCheck {
-  [ -n "$(docker images -q $1)" ]
-}
-
-# ViashDockerPull: pull a Docker image
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   ViashDockerPull python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerPull sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerPull {
-  ViashNotice "Checking if Docker image is available at '$1'"
-  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
-    docker pull $1 && return 0 || return 1
-  else
-    local save=$-; set +e
-    docker pull $1 2> /dev/null > /dev/null
-    local out=$?
-    [[ $save =~ e ]] && set -e
-    if [ $out -ne 0 ]; then
-      ViashWarning "Could not pull from '$1'. Docker image doesn't exist or is not accessible."
-    fi
-    return $out
-  fi
-}
-
-# ViashDockerPush: push a Docker image
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   ViashDockerPush python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerPush sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerPush {
-  ViashNotice "Pushing image to '$1'"
-  local save=$-; set +e
-  local out
-  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
-    docker push $1
-    out=$?
-  else
-    docker push $1 2> /dev/null > /dev/null
-    out=$?
-  fi
-  [[ $save =~ e ]] && set -e
-  if [ $out -eq 0 ]; then
-    ViashNotice "Container '$1' push succeeded."
-  else
-    ViashError "Container '$1' push errored. You might not be logged in or have the necessary permissions."
-  fi
-  return $out
-}
-
-# ViashDockerPullElseBuild: pull a Docker image, else build it
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# ViashDockerBuild    : a Bash function which builds a docker image, takes image identifier as argument.
-# examples:
-#   ViashDockerPullElseBuild mynewcomponent
-function ViashDockerPullElseBuild {
-  local save=$-; set +e
-  ViashDockerPull $1
-  local out=$?
-  [[ $save =~ e ]] && set -e
-  if [ $out -ne 0 ]; then
-    ViashDockerBuild $@
-  fi
-}
-
-# ViashDockerSetup: create a Docker image, according to specified docker setup strategy
-#
-# $1          : image identifier with format `[registry/]image[:tag]`
-# $2          : docker setup strategy, see DockerSetupStrategy.scala
-# examples:
-#   ViashDockerSetup mynewcomponent alwaysbuild
-function ViashDockerSetup {
-  local image_id="$1"
-  local setup_strategy="$2"
-  if [ "$setup_strategy" == "alwaysbuild" -o "$setup_strategy" == "build" -o "$setup_strategy" == "b" ]; then
-    ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-  elif [ "$setup_strategy" == "alwayspull" -o "$setup_strategy" == "pull" -o "$setup_strategy" == "p" ]; then
-    ViashDockerPull $image_id
-  elif [ "$setup_strategy" == "alwayspullelsebuild" -o "$setup_strategy" == "pullelsebuild" ]; then
-    ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-  elif [ "$setup_strategy" == "alwayspullelsecachedbuild" -o "$setup_strategy" == "pullelsecachedbuild" ]; then
-    ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-  elif [ "$setup_strategy" == "alwayscachedbuild" -o "$setup_strategy" == "cachedbuild" -o "$setup_strategy" == "cb" ]; then
-    ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-  elif [[ "$setup_strategy" =~ ^ifneedbe ]]; then
-    local save=$-; set +e
-    ViashDockerLocalTagCheck $image_id
-    local outCheck=$?
-    [[ $save =~ e ]] && set -e
-    if [ $outCheck -eq 0 ]; then
-      ViashInfo "Image $image_id already exists"
-    elif [ "$setup_strategy" == "ifneedbebuild" ]; then
-      ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-    elif [ "$setup_strategy" == "ifneedbecachedbuild" ]; then
-      ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-    elif [ "$setup_strategy" == "ifneedbepull" ]; then
-      ViashDockerPull $image_id
-    elif [ "$setup_strategy" == "ifneedbepullelsebuild" ]; then
-      ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-    elif [ "$setup_strategy" == "ifneedbepullelsecachedbuild" ]; then
-      ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-    else
-      ViashError "Unrecognised Docker strategy: $setup_strategy"
-      exit 1
-    fi
-  elif [ "$setup_strategy" == "push" -o "$setup_strategy" == "forcepush" -o "$setup_strategy" == "alwayspush" ]; then
-    ViashDockerPush "$image_id"
-  elif [ "$setup_strategy" == "pushifnotpresent" -o "$setup_strategy" == "gentlepush" -o "$setup_strategy" == "maybepush" ]; then
-    local save=$-; set +e
-    ViashDockerRemoteTagCheck $image_id
-    local outCheck=$?
-    [[ $save =~ e ]] && set -e
-    if [ $outCheck -eq 0 ]; then
-      ViashNotice "Container '$image_id' exists, doing nothing."
-    else
-      ViashNotice "Container '$image_id' does not yet exist."
-      ViashDockerPush "$image_id"
-    fi
-  elif [ "$setup_strategy" == "donothing" -o "$setup_strategy" == "meh" ]; then
-    ViashNotice "Skipping setup."
-  else
-    ViashError "Unrecognised Docker strategy: $setup_strategy"
-    exit 1
-  fi
-}
-
-# ViashDockerCheckCommands: Check whether a docker container has the required commands
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# $@                  : commands to verify being present
-# examples:
-#   ViashDockerCheckCommands bash:4.0 bash ps foo
-function ViashDockerCheckCommands {
-  local image_id="$1"
-  shift 1
-  local commands="$@"
-  local save=$-; set +e
-  local missing # mark 'missing' as local in advance, otherwise the exit code of the command will be missing and always be '0'
-  missing=$(docker run --rm --entrypoint=sh "$image_id" -c "for command in $commands; do command -v \$command >/dev/null 2>&1; if [ \$? -ne 0 ]; then echo \$command; exit 1; fi; done")
-  local outCheck=$?
-  [[ $save =~ e ]] && set -e
-  if [ $outCheck -ne 0 ]; then
-  	ViashError "Docker container '$image_id' does not contain command '$missing'."
-  	exit 1
-  fi
-}
-
-# ViashDockerBuild: build a docker image
-# $1                               : image identifier with format `[registry/]image[:tag]`
-# $...                             : additional arguments to pass to docker build
-# $VIASH_META_TEMP_DIR             : temporary directory to store dockerfile & optional resources in
-# $VIASH_META_NAME                 : name of the component
-# $VIASH_META_RESOURCES_DIR        : directory containing the resources
-# $VIASH_VERBOSITY                 : verbosity level
-# exit code $?                     : whether or not the image was built successfully
-function ViashDockerBuild {
-  local image_id="$1"
-  shift 1
-
-  # create temporary directory to store dockerfile & optional resources in
-  local tmpdir=$(mktemp -d "$VIASH_META_TEMP_DIR/dockerbuild-$VIASH_META_NAME-XXXXXX")
-  local dockerfile="$tmpdir/Dockerfile"
-  function clean_up {
-    rm -rf "$tmpdir"
-  }
-  trap clean_up EXIT
-
-  # store dockerfile and resources
-  ViashDockerfile "$VIASH_ENGINE_ID" > "$dockerfile"
-
-  # generate the build command
-  local docker_build_cmd="docker build -t '$image_id' $@ '$VIASH_META_RESOURCES_DIR' -f '$dockerfile'"
-
-  # build the container
-  ViashNotice "Building container '$image_id' with Dockerfile"
-  ViashInfo "$docker_build_cmd"
-  local save=$-; set +e
-  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
-    eval $docker_build_cmd
-  else
-    eval $docker_build_cmd &> "$tmpdir/docker_build.log"
-  fi
-
-  # check exit code
-  local out=$?
-  [[ $save =~ e ]] && set -e
-  if [ $out -ne 0 ]; then
-    ViashError "Error occurred while building container '$image_id'"
-    if [ $VIASH_VERBOSITY -lt $VIASH_LOGCODE_INFO ]; then
-      ViashError "Transcript: --------------------------------"
-      cat "$tmpdir/docker_build.log"
-      ViashError "End of transcript --------------------------"
-    fi
-    exit 1
-  fi
-}
-
-######## End of helper functions for setting up Docker images for viash ########
-
-# ViashDockerFile: print the dockerfile to stdout
-# $1    : engine identifier
-# return : dockerfile required to run this component
-# examples:
-#   ViashDockerFile
-function ViashDockerfile {
-  local engine_id="$1"
-
-  if [[ "$engine_id" == "docker" ]]; then
-    cat << 'VIASHDOCKER'
-FROM python:3.12
-ENTRYPOINT []
-RUN pip install --upgrade pip && \
-  pip install --upgrade --no-cache-dir "cutadapt"
-
-RUN cutadapt --version | sed 's/\(.*\)/cutadapt: "\1"/' > /var/software_versions.txt
-
-LABEL org.opencontainers.image.authors="Toni Verbeiren"
-LABEL org.opencontainers.image.description="Companion container for running component cutadapt"
-LABEL org.opencontainers.image.created="2024-12-03T10:33:56Z"
-LABEL org.opencontainers.image.source="https://github.com/marcelm/cutadapt"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-LABEL org.opencontainers.image.version="main"
-
-VIASHDOCKER
-  fi
-}
-
-# ViashDockerBuildArgs: return the arguments to pass to docker build
-# $1    : engine identifier
-# return : arguments to pass to docker build
-function ViashDockerBuildArgs {
-  local engine_id="$1"
-
-  if [[ "$engine_id" == "docker" ]]; then
-    echo ""
-  fi
-}
-
-# ViashAbsolutePath: generate absolute path from relative path
-# borrowed from https://stackoverflow.com/a/21951256
-# $1     : relative filename
-# return : absolute path
-# examples:
-#   ViashAbsolutePath some_file.txt   # returns /path/to/some_file.txt
-#   ViashAbsolutePath /foo/bar/..     # returns /foo
-function ViashAbsolutePath {
-  local thePath
-  local parr
-  local outp
-  local len
-  if [[ ! "$1" =~ ^/ ]]; then
-    thePath="$PWD/$1"
-  else
-    thePath="$1"
-  fi
-  echo "$thePath" | (
-    IFS=/
-    read -a parr
-    declare -a outp
-    for i in "${parr[@]}"; do
-      case "$i" in
-      ''|.) continue ;;
-      ..)
-        len=${#outp[@]}
-        if ((len==0)); then
-          continue
-        else
-          unset outp[$((len-1))]
-        fi
-        ;;
-      *)
-        len=${#outp[@]}
-        outp[$len]="$i"
-      ;;
-      esac
-    done
-    echo /"${outp[*]}"
-  )
-}
-# ViashDockerAutodetectMount: auto configuring docker mounts from parameters
-# $1                             : The parameter value
-# returns                        : New parameter
-# $VIASH_DIRECTORY_MOUNTS        : Added another parameter to be passed to docker
-# $VIASH_DOCKER_AUTOMOUNT_PREFIX : The prefix to be used for the automounts
-# examples:
-#   ViashDockerAutodetectMount /path/to/bar      # returns '/viash_automount/path/to/bar'
-#   ViashDockerAutodetectMountArg /path/to/bar   # returns '--volume="/path/to:/viash_automount/path/to"'
-function ViashDockerAutodetectMount {
-  local abs_path=$(ViashAbsolutePath "$1")
-  local mount_source
-  local base_name
-  if [ -d "$abs_path" ]; then
-    mount_source="$abs_path"
-    base_name=""
-  else
-    mount_source=`dirname "$abs_path"`
-    base_name=`basename "$abs_path"`
-  fi
-  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
-  if [ -z "$base_name" ]; then
-    echo "$mount_target"
-  else
-    echo "$mount_target/$base_name"
-  fi
-}
-function ViashDockerAutodetectMountArg {
-  local abs_path=$(ViashAbsolutePath "$1")
-  local mount_source
-  local base_name
-  if [ -d "$abs_path" ]; then
-    mount_source="$abs_path"
-    base_name=""
-  else
-    mount_source=`dirname "$abs_path"`
-    base_name=`basename "$abs_path"`
-  fi
-  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
-  ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target"
-  echo "--volume=\"$mount_source:$mount_target\""
-}
-function ViashDockerStripAutomount {
-  local abs_path=$(ViashAbsolutePath "$1")
-  echo "${abs_path#$VIASH_DOCKER_AUTOMOUNT_PREFIX}"
-}
-# initialise variables
-VIASH_DIRECTORY_MOUNTS=()
-
-# configure default docker automount prefix if it is unset
-if [ -z "${VIASH_DOCKER_AUTOMOUNT_PREFIX+x}" ]; then
-  VIASH_DOCKER_AUTOMOUNT_PREFIX="/viash_automount"
-fi
-
-# initialise docker variables
-VIASH_DOCKER_RUN_ARGS=(-i --rm)
-
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/falco/.config.vsh.yaml b/target/executable/falco/.config.vsh.yaml
index bf8cbe6b..8ef28831 100644
--- a/target/executable/falco/.config.vsh.yaml
+++ b/target/executable/falco/.config.vsh.yaml
@@ -203,6 +203,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -316,16 +319,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/falco"
   executable: "target/executable/falco/falco"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/falco/falco b/target/executable/falco/falco
index c9a3dd6f..24635cb2 100755
--- a/target/executable/falco/falco
+++ b/target/executable/falco/falco
@@ -2,7 +2,7 @@
 
 # falco main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,131 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "falco main"
-  echo ""
-  echo "A C++ drop-in replacement of FastQC to assess the quality of sequence read data"
-  echo ""
-  echo "Input arguments:"
-  echo "    --input"
-  echo "        type: file, required parameter, multiple values allowed, file must exist"
-  echo "        example: input1.fastq;input2.fastq"
-  echo "        input fastq files"
-  echo ""
-  echo "Run arguments:"
-  echo "    --nogroup"
-  echo "        type: boolean_true"
-  echo "        Disable grouping of bases for reads >50bp."
-  echo "        All reports will show data for every base in"
-  echo "        the read. WARNING: When using this option,"
-  echo "        your plots may end up a ridiculous size. You"
-  echo "        have been warned!"
-  echo ""
-  echo "    --contaminents"
-  echo "        type: file, file must exist"
-  echo "        Specifies a non-default file which contains"
-  echo "        the list of contaminants to screen"
-  echo "        overrepresented sequences against. The file"
-  echo "        must contain sets of named contaminants in"
-  echo "        the form name[tab]sequence. Lines prefixed"
-  echo "        with a hash will be ignored. Default:"
-  echo "       "
-  echo "https://github.com/smithlabcode/falco/blob/v1.2.2/Configuration/contaminant_list.txt"
-  echo ""
-  echo "    --adapters"
-  echo "        type: file, file must exist"
-  echo "        Specifies a non-default file which contains"
-  echo "        the list of adapter sequences which will be"
-  echo "        explicity searched against the library. The"
-  echo "        file must contain sets of named adapters in"
-  echo "        the form name[tab]sequence. Lines prefixed"
-  echo "        with a hash will be ignored. Default:"
-  echo "       "
-  echo "https://github.com/smithlabcode/falco/blob/v1.2.2/Configuration/adapter_list.txt"
-  echo ""
-  echo "    --limits"
-  echo "        type: file, file must exist"
-  echo "        Specifies a non-default file which contains"
-  echo "        a set of criteria which will be used to"
-  echo "        determine the warn/error limits for the"
-  echo "        various modules. This file can also be used"
-  echo "        to selectively remove some modules from the"
-  echo "        output all together. The format needs to"
-  echo "        mirror the default limits.txt file found in"
-  echo "        the Configuration folder. Default:"
-  echo "       "
-  echo "https://github.com/smithlabcode/falco/blob/v1.2.2/Configuration/limits.txt"
-  echo ""
-  echo "    -s, --subsample"
-  echo "        type: integer"
-  echo "        example: 10"
-  echo "        [Falco only] makes falco faster (but"
-  echo "        possibly less accurate) by only processing"
-  echo "        reads that are a multiple of this value (using"
-  echo "        0-based indexing to number reads)."
-  echo ""
-  echo "    -b, --bisulfite"
-  echo "        type: boolean_true"
-  echo "        [Falco only] reads are whole genome"
-  echo "        bisulfite sequencing, and more Ts and fewer"
-  echo "        Cs are therefore expected and will be"
-  echo "        accounted for in base content."
-  echo ""
-  echo "    -r, --reverse_complement"
-  echo "        type: boolean_true"
-  echo "        [Falco only] The input is a"
-  echo "        reverse-complement. All modules will be"
-  echo "        tested by swapping A/T and C/G"
-  echo ""
-  echo "Output arguments:"
-  echo "    -o, --outdir"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        example: output"
-  echo "        Create all output files in the specified"
-  echo "        output directory. FALCO-SPECIFIC: If the"
-  echo "        directory does not exists, the program will"
-  echo "        create it."
-  echo ""
-  echo "    -f, --format"
-  echo "        type: string"
-  echo "        choices: [ bam, sam, bam_mapped, sam_mapped, fastq, fq, fastq.gz, fq.gz"
-  echo "]"
-  echo "        Bypasses the normal sequence file format"
-  echo "        detection and forces the program to use the"
-  echo "        specified format. Validformats are bam, sam,"
-  echo "        bam_mapped, sam_mapped, fastq, fq, fastq.gz"
-  echo "        or fq.gz."
-  echo ""
-  echo "    -D, --data_filename"
-  echo "        type: file, output, file must exist"
-  echo "        [Falco only] Specify filename for FastQC"
-  echo "        data output (TXT). If not specified, it will"
-  echo "        be called fastq_data.txt in either the input"
-  echo "        file's directory or the one specified in the"
-  echo "        --output flag. Only available when running"
-  echo "        falco with a single input."
-  echo ""
-  echo "    -R, --report_filename"
-  echo "        type: file, output, file must exist"
-  echo "        [Falco only] Specify filename for FastQC"
-  echo "        report output (HTML). If not specified, it"
-  echo "        will be called fastq_report.html in either"
-  echo "        the input file's directory or the one"
-  echo "        specified in the --output flag. Only"
-  echo "        available when running falco with a single"
-  echo "        input."
-  echo ""
-  echo "    -S, --summary_filename"
-  echo "        type: file, output, file must exist"
-  echo "        [Falco only] Specify filename for the short"
-  echo "        summary output (TXT). If not specified, it"
-  echo "        will be called fastq_report.html in either"
-  echo "        the input file's directory or the one"
-  echo "        specified in the --output flag. Only"
-  echo "        available when running falco with a single"
-  echo "        input."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -589,9 +464,9 @@ RUN echo "falco: \"$(falco -v | sed -n 's/^falco //p')\"" > /var/software_versio
 
 LABEL org.opencontainers.image.authors="Toni Verbeiren"
 LABEL org.opencontainers.image.description="Companion container for running component falco"
-LABEL org.opencontainers.image.created="2024-12-03T10:33:53Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:42Z"
 LABEL org.opencontainers.image.source="https://github.com/smithlabcode/falco"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -706,6 +581,157 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "falco main"
+  echo ""
+  echo "A C++ drop-in replacement of FastQC to assess the quality of sequence read data"
+  echo ""
+  echo "Input arguments:"
+  echo "    --input"
+  echo "        type: file, required parameter, multiple values allowed, file must exist"
+  echo "        example: input1.fastq;input2.fastq"
+  echo "        input fastq files"
+  echo ""
+  echo "Run arguments:"
+  echo "    --nogroup"
+  echo "        type: boolean_true"
+  echo "        Disable grouping of bases for reads >50bp."
+  echo "        All reports will show data for every base in"
+  echo "        the read. WARNING: When using this option,"
+  echo "        your plots may end up a ridiculous size. You"
+  echo "        have been warned!"
+  echo ""
+  echo "    --contaminents"
+  echo "        type: file, file must exist"
+  echo "        Specifies a non-default file which contains"
+  echo "        the list of contaminants to screen"
+  echo "        overrepresented sequences against. The file"
+  echo "        must contain sets of named contaminants in"
+  echo "        the form name[tab]sequence. Lines prefixed"
+  echo "        with a hash will be ignored. Default:"
+  echo "       "
+  echo "https://github.com/smithlabcode/falco/blob/v1.2.2/Configuration/contaminant_list.txt"
+  echo ""
+  echo "    --adapters"
+  echo "        type: file, file must exist"
+  echo "        Specifies a non-default file which contains"
+  echo "        the list of adapter sequences which will be"
+  echo "        explicity searched against the library. The"
+  echo "        file must contain sets of named adapters in"
+  echo "        the form name[tab]sequence. Lines prefixed"
+  echo "        with a hash will be ignored. Default:"
+  echo "       "
+  echo "https://github.com/smithlabcode/falco/blob/v1.2.2/Configuration/adapter_list.txt"
+  echo ""
+  echo "    --limits"
+  echo "        type: file, file must exist"
+  echo "        Specifies a non-default file which contains"
+  echo "        a set of criteria which will be used to"
+  echo "        determine the warn/error limits for the"
+  echo "        various modules. This file can also be used"
+  echo "        to selectively remove some modules from the"
+  echo "        output all together. The format needs to"
+  echo "        mirror the default limits.txt file found in"
+  echo "        the Configuration folder. Default:"
+  echo "       "
+  echo "https://github.com/smithlabcode/falco/blob/v1.2.2/Configuration/limits.txt"
+  echo ""
+  echo "    -s, --subsample"
+  echo "        type: integer"
+  echo "        example: 10"
+  echo "        [Falco only] makes falco faster (but"
+  echo "        possibly less accurate) by only processing"
+  echo "        reads that are a multiple of this value (using"
+  echo "        0-based indexing to number reads)."
+  echo ""
+  echo "    -b, --bisulfite"
+  echo "        type: boolean_true"
+  echo "        [Falco only] reads are whole genome"
+  echo "        bisulfite sequencing, and more Ts and fewer"
+  echo "        Cs are therefore expected and will be"
+  echo "        accounted for in base content."
+  echo ""
+  echo "    -r, --reverse_complement"
+  echo "        type: boolean_true"
+  echo "        [Falco only] The input is a"
+  echo "        reverse-complement. All modules will be"
+  echo "        tested by swapping A/T and C/G"
+  echo ""
+  echo "Output arguments:"
+  echo "    -o, --outdir"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        example: output"
+  echo "        Create all output files in the specified"
+  echo "        output directory. FALCO-SPECIFIC: If the"
+  echo "        directory does not exists, the program will"
+  echo "        create it."
+  echo ""
+  echo "    -f, --format"
+  echo "        type: string"
+  echo "        choices: [ bam, sam, bam_mapped, sam_mapped, fastq, fq, fastq.gz, fq.gz"
+  echo "]"
+  echo "        Bypasses the normal sequence file format"
+  echo "        detection and forces the program to use the"
+  echo "        specified format. Validformats are bam, sam,"
+  echo "        bam_mapped, sam_mapped, fastq, fq, fastq.gz"
+  echo "        or fq.gz."
+  echo ""
+  echo "    -D, --data_filename"
+  echo "        type: file, output, file must exist"
+  echo "        [Falco only] Specify filename for FastQC"
+  echo "        data output (TXT). If not specified, it will"
+  echo "        be called fastq_data.txt in either the input"
+  echo "        file's directory or the one specified in the"
+  echo "        --output flag. Only available when running"
+  echo "        falco with a single input."
+  echo ""
+  echo "    -R, --report_filename"
+  echo "        type: file, output, file must exist"
+  echo "        [Falco only] Specify filename for FastQC"
+  echo "        report output (HTML). If not specified, it"
+  echo "        will be called fastq_report.html in either"
+  echo "        the input file's directory or the one"
+  echo "        specified in the --output flag. Only"
+  echo "        available when running falco with a single"
+  echo "        input."
+  echo ""
+  echo "    -S, --summary_filename"
+  echo "        type: file, output, file must exist"
+  echo "        [Falco only] Specify filename for the short"
+  echo "        summary output (TXT). If not specified, it"
+  echo "        will be called fastq_report.html in either"
+  echo "        the input file's directory or the one"
+  echo "        specified in the --output flag. Only"
+  echo "        available when running falco with a single"
+  echo "        input."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/fastp/.config.vsh.yaml b/target/executable/fastp/.config.vsh.yaml
index 2ed2f08c..23ee81e8 100644
--- a/target/executable/fastp/.config.vsh.yaml
+++ b/target/executable/fastp/.config.vsh.yaml
@@ -982,6 +982,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -1082,16 +1085,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/fastp"
   executable: "target/executable/fastp/fastp"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/fastp/fastp b/target/executable/fastp/fastp
index aec9e4e9..cc8d95de 100755
--- a/target/executable/fastp/fastp
+++ b/target/executable/fastp/fastp
@@ -2,7 +2,7 @@
 
 # fastp main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,6 +172,404 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
+
+# initialise variables
+VIASH_MODE='run'
+VIASH_ENGINE_ID='docker'
+
+######## Helper functions for setting up Docker images for viash ########
+# expects: ViashDockerBuild
+
+# ViashDockerInstallationCheck: check whether Docker is installed correctly
+#
+# examples:
+#   ViashDockerInstallationCheck
+function ViashDockerInstallationCheck {
+  ViashDebug "Checking whether Docker is installed"
+  if [ ! command -v docker &> /dev/null ]; then
+    ViashCritical "Docker doesn't seem to be installed. See 'https://docs.docker.com/get-docker/' for instructions."
+    exit 1
+  fi
+
+  ViashDebug "Checking whether the Docker daemon is running"
+  local save=$-; set +e
+  local docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
+  local out=$?
+  [[ $save =~ e ]] && set -e
+  if [ $out -ne 0 ]; then
+    ViashCritical "Docker daemon does not seem to be running. Try one of the following:"
+    ViashCritical "- Try running 'dockerd' in the command line"
+    ViashCritical "- See https://docs.docker.com/config/daemon/"
+    exit 1
+  fi
+}
+
+# ViashDockerRemoteTagCheck: check whether a Docker image is available 
+# on a remote. Assumes `docker login` has been performed, if relevant.
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   ViashDockerRemoteTagCheck python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerRemoteTagCheck sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerRemoteTagCheck {
+  docker manifest inspect $1 > /dev/null 2> /dev/null
+}
+
+# ViashDockerLocalTagCheck: check whether a Docker image is available locally
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   docker pull python:latest
+#   ViashDockerLocalTagCheck python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerLocalTagCheck sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerLocalTagCheck {
+  [ -n "$(docker images -q $1)" ]
+}
+
+# ViashDockerPull: pull a Docker image
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   ViashDockerPull python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerPull sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerPull {
+  ViashNotice "Checking if Docker image is available at '$1'"
+  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
+    docker pull $1 && return 0 || return 1
+  else
+    local save=$-; set +e
+    docker pull $1 2> /dev/null > /dev/null
+    local out=$?
+    [[ $save =~ e ]] && set -e
+    if [ $out -ne 0 ]; then
+      ViashWarning "Could not pull from '$1'. Docker image doesn't exist or is not accessible."
+    fi
+    return $out
+  fi
+}
+
+# ViashDockerPush: push a Docker image
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   ViashDockerPush python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerPush sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerPush {
+  ViashNotice "Pushing image to '$1'"
+  local save=$-; set +e
+  local out
+  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
+    docker push $1
+    out=$?
+  else
+    docker push $1 2> /dev/null > /dev/null
+    out=$?
+  fi
+  [[ $save =~ e ]] && set -e
+  if [ $out -eq 0 ]; then
+    ViashNotice "Container '$1' push succeeded."
+  else
+    ViashError "Container '$1' push errored. You might not be logged in or have the necessary permissions."
+  fi
+  return $out
+}
+
+# ViashDockerPullElseBuild: pull a Docker image, else build it
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# ViashDockerBuild    : a Bash function which builds a docker image, takes image identifier as argument.
+# examples:
+#   ViashDockerPullElseBuild mynewcomponent
+function ViashDockerPullElseBuild {
+  local save=$-; set +e
+  ViashDockerPull $1
+  local out=$?
+  [[ $save =~ e ]] && set -e
+  if [ $out -ne 0 ]; then
+    ViashDockerBuild $@
+  fi
+}
+
+# ViashDockerSetup: create a Docker image, according to specified docker setup strategy
+#
+# $1          : image identifier with format `[registry/]image[:tag]`
+# $2          : docker setup strategy, see DockerSetupStrategy.scala
+# examples:
+#   ViashDockerSetup mynewcomponent alwaysbuild
+function ViashDockerSetup {
+  local image_id="$1"
+  local setup_strategy="$2"
+  if [ "$setup_strategy" == "alwaysbuild" -o "$setup_strategy" == "build" -o "$setup_strategy" == "b" ]; then
+    ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+  elif [ "$setup_strategy" == "alwayspull" -o "$setup_strategy" == "pull" -o "$setup_strategy" == "p" ]; then
+    ViashDockerPull $image_id
+  elif [ "$setup_strategy" == "alwayspullelsebuild" -o "$setup_strategy" == "pullelsebuild" ]; then
+    ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+  elif [ "$setup_strategy" == "alwayspullelsecachedbuild" -o "$setup_strategy" == "pullelsecachedbuild" ]; then
+    ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+  elif [ "$setup_strategy" == "alwayscachedbuild" -o "$setup_strategy" == "cachedbuild" -o "$setup_strategy" == "cb" ]; then
+    ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+  elif [[ "$setup_strategy" =~ ^ifneedbe ]]; then
+    local save=$-; set +e
+    ViashDockerLocalTagCheck $image_id
+    local outCheck=$?
+    [[ $save =~ e ]] && set -e
+    if [ $outCheck -eq 0 ]; then
+      ViashInfo "Image $image_id already exists"
+    elif [ "$setup_strategy" == "ifneedbebuild" ]; then
+      ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+    elif [ "$setup_strategy" == "ifneedbecachedbuild" ]; then
+      ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+    elif [ "$setup_strategy" == "ifneedbepull" ]; then
+      ViashDockerPull $image_id
+    elif [ "$setup_strategy" == "ifneedbepullelsebuild" ]; then
+      ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+    elif [ "$setup_strategy" == "ifneedbepullelsecachedbuild" ]; then
+      ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+    else
+      ViashError "Unrecognised Docker strategy: $setup_strategy"
+      exit 1
+    fi
+  elif [ "$setup_strategy" == "push" -o "$setup_strategy" == "forcepush" -o "$setup_strategy" == "alwayspush" ]; then
+    ViashDockerPush "$image_id"
+  elif [ "$setup_strategy" == "pushifnotpresent" -o "$setup_strategy" == "gentlepush" -o "$setup_strategy" == "maybepush" ]; then
+    local save=$-; set +e
+    ViashDockerRemoteTagCheck $image_id
+    local outCheck=$?
+    [[ $save =~ e ]] && set -e
+    if [ $outCheck -eq 0 ]; then
+      ViashNotice "Container '$image_id' exists, doing nothing."
+    else
+      ViashNotice "Container '$image_id' does not yet exist."
+      ViashDockerPush "$image_id"
+    fi
+  elif [ "$setup_strategy" == "donothing" -o "$setup_strategy" == "meh" ]; then
+    ViashNotice "Skipping setup."
+  else
+    ViashError "Unrecognised Docker strategy: $setup_strategy"
+    exit 1
+  fi
+}
+
+# ViashDockerCheckCommands: Check whether a docker container has the required commands
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# $@                  : commands to verify being present
+# examples:
+#   ViashDockerCheckCommands bash:4.0 bash ps foo
+function ViashDockerCheckCommands {
+  local image_id="$1"
+  shift 1
+  local commands="$@"
+  local save=$-; set +e
+  local missing # mark 'missing' as local in advance, otherwise the exit code of the command will be missing and always be '0'
+  missing=$(docker run --rm --entrypoint=sh "$image_id" -c "for command in $commands; do command -v \$command >/dev/null 2>&1; if [ \$? -ne 0 ]; then echo \$command; exit 1; fi; done")
+  local outCheck=$?
+  [[ $save =~ e ]] && set -e
+  if [ $outCheck -ne 0 ]; then
+  	ViashError "Docker container '$image_id' does not contain command '$missing'."
+  	exit 1
+  fi
+}
+
+# ViashDockerBuild: build a docker image
+# $1                               : image identifier with format `[registry/]image[:tag]`
+# $...                             : additional arguments to pass to docker build
+# $VIASH_META_TEMP_DIR             : temporary directory to store dockerfile & optional resources in
+# $VIASH_META_NAME                 : name of the component
+# $VIASH_META_RESOURCES_DIR        : directory containing the resources
+# $VIASH_VERBOSITY                 : verbosity level
+# exit code $?                     : whether or not the image was built successfully
+function ViashDockerBuild {
+  local image_id="$1"
+  shift 1
+
+  # create temporary directory to store dockerfile & optional resources in
+  local tmpdir=$(mktemp -d "$VIASH_META_TEMP_DIR/dockerbuild-$VIASH_META_NAME-XXXXXX")
+  local dockerfile="$tmpdir/Dockerfile"
+  function clean_up {
+    rm -rf "$tmpdir"
+  }
+  trap clean_up EXIT
+
+  # store dockerfile and resources
+  ViashDockerfile "$VIASH_ENGINE_ID" > "$dockerfile"
+
+  # generate the build command
+  local docker_build_cmd="docker build -t '$image_id' $@ '$VIASH_META_RESOURCES_DIR' -f '$dockerfile'"
+
+  # build the container
+  ViashNotice "Building container '$image_id' with Dockerfile"
+  ViashInfo "$docker_build_cmd"
+  local save=$-; set +e
+  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
+    eval $docker_build_cmd
+  else
+    eval $docker_build_cmd &> "$tmpdir/docker_build.log"
+  fi
+
+  # check exit code
+  local out=$?
+  [[ $save =~ e ]] && set -e
+  if [ $out -ne 0 ]; then
+    ViashError "Error occurred while building container '$image_id'"
+    if [ $VIASH_VERBOSITY -lt $VIASH_LOGCODE_INFO ]; then
+      ViashError "Transcript: --------------------------------"
+      cat "$tmpdir/docker_build.log"
+      ViashError "End of transcript --------------------------"
+    fi
+    exit 1
+  fi
+}
+
+######## End of helper functions for setting up Docker images for viash ########
+
+# ViashDockerFile: print the dockerfile to stdout
+# $1    : engine identifier
+# return : dockerfile required to run this component
+# examples:
+#   ViashDockerFile
+function ViashDockerfile {
+  local engine_id="$1"
+
+  if [[ "$engine_id" == "docker" ]]; then
+    cat << 'VIASHDOCKER'
+FROM quay.io/biocontainers/fastp:0.23.4--hadf994f_2
+ENTRYPOINT []
+RUN fastp --version 2>&1 | sed 's# #: "#;s#$#"#' > /var/software_versions.txt
+
+LABEL org.opencontainers.image.authors="Robrecht Cannoodt"
+LABEL org.opencontainers.image.description="Companion container for running component fastp"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:40Z"
+LABEL org.opencontainers.image.source="https://github.com/OpenGene/fastp"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+LABEL org.opencontainers.image.version="main"
+
+VIASHDOCKER
+  fi
+}
+
+# ViashDockerBuildArgs: return the arguments to pass to docker build
+# $1    : engine identifier
+# return : arguments to pass to docker build
+function ViashDockerBuildArgs {
+  local engine_id="$1"
+
+  if [[ "$engine_id" == "docker" ]]; then
+    echo ""
+  fi
+}
+
+# ViashAbsolutePath: generate absolute path from relative path
+# borrowed from https://stackoverflow.com/a/21951256
+# $1     : relative filename
+# return : absolute path
+# examples:
+#   ViashAbsolutePath some_file.txt   # returns /path/to/some_file.txt
+#   ViashAbsolutePath /foo/bar/..     # returns /foo
+function ViashAbsolutePath {
+  local thePath
+  local parr
+  local outp
+  local len
+  if [[ ! "$1" =~ ^/ ]]; then
+    thePath="$PWD/$1"
+  else
+    thePath="$1"
+  fi
+  echo "$thePath" | (
+    IFS=/
+    read -a parr
+    declare -a outp
+    for i in "${parr[@]}"; do
+      case "$i" in
+      ''|.) continue ;;
+      ..)
+        len=${#outp[@]}
+        if ((len==0)); then
+          continue
+        else
+          unset outp[$((len-1))]
+        fi
+        ;;
+      *)
+        len=${#outp[@]}
+        outp[$len]="$i"
+      ;;
+      esac
+    done
+    echo /"${outp[*]}"
+  )
+}
+# ViashDockerAutodetectMount: auto configuring docker mounts from parameters
+# $1                             : The parameter value
+# returns                        : New parameter
+# $VIASH_DIRECTORY_MOUNTS        : Added another parameter to be passed to docker
+# $VIASH_DOCKER_AUTOMOUNT_PREFIX : The prefix to be used for the automounts
+# examples:
+#   ViashDockerAutodetectMount /path/to/bar      # returns '/viash_automount/path/to/bar'
+#   ViashDockerAutodetectMountArg /path/to/bar   # returns '--volume="/path/to:/viash_automount/path/to"'
+function ViashDockerAutodetectMount {
+  local abs_path=$(ViashAbsolutePath "$1")
+  local mount_source
+  local base_name
+  if [ -d "$abs_path" ]; then
+    mount_source="$abs_path"
+    base_name=""
+  else
+    mount_source=`dirname "$abs_path"`
+    base_name=`basename "$abs_path"`
+  fi
+  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
+  if [ -z "$base_name" ]; then
+    echo "$mount_target"
+  else
+    echo "$mount_target/$base_name"
+  fi
+}
+function ViashDockerAutodetectMountArg {
+  local abs_path=$(ViashAbsolutePath "$1")
+  local mount_source
+  local base_name
+  if [ -d "$abs_path" ]; then
+    mount_source="$abs_path"
+    base_name=""
+  else
+    mount_source=`dirname "$abs_path"`
+    base_name=`basename "$abs_path"`
+  fi
+  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
+  ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target"
+  echo "--volume=\"$mount_source:$mount_target\""
+}
+function ViashDockerStripAutomount {
+  local abs_path=$(ViashAbsolutePath "$1")
+  echo "${abs_path#$VIASH_DOCKER_AUTOMOUNT_PREFIX}"
+}
+# initialise variables
+VIASH_DIRECTORY_MOUNTS=()
+
+# configure default docker automount prefix if it is unset
+if [ -z "${VIASH_DOCKER_AUTOMOUNT_PREFIX+x}" ]; then
+  VIASH_DOCKER_AUTOMOUNT_PREFIX="/viash_automount"
+fi
+
+# initialise docker variables
+VIASH_DOCKER_RUN_ARGS=(-i --rm)
+
+
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
   echo "fastp main"
@@ -747,404 +1145,32 @@ function ViashHelp {
   echo "        min: 1"
   echo "        One in (--overrepresentation_sampling) reads will be computed for"
   echo "        overrepresentation analysis (1~10000), smaller is slower, default is 20."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
 }
 
-# initialise variables
-VIASH_MODE='run'
-VIASH_ENGINE_ID='docker'
-
-######## Helper functions for setting up Docker images for viash ########
-# expects: ViashDockerBuild
-
-# ViashDockerInstallationCheck: check whether Docker is installed correctly
-#
-# examples:
-#   ViashDockerInstallationCheck
-function ViashDockerInstallationCheck {
-  ViashDebug "Checking whether Docker is installed"
-  if [ ! command -v docker &> /dev/null ]; then
-    ViashCritical "Docker doesn't seem to be installed. See 'https://docs.docker.com/get-docker/' for instructions."
-    exit 1
-  fi
-
-  ViashDebug "Checking whether the Docker daemon is running"
-  local save=$-; set +e
-  local docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
-  local out=$?
-  [[ $save =~ e ]] && set -e
-  if [ $out -ne 0 ]; then
-    ViashCritical "Docker daemon does not seem to be running. Try one of the following:"
-    ViashCritical "- Try running 'dockerd' in the command line"
-    ViashCritical "- See https://docs.docker.com/config/daemon/"
-    exit 1
-  fi
-}
-
-# ViashDockerRemoteTagCheck: check whether a Docker image is available 
-# on a remote. Assumes `docker login` has been performed, if relevant.
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   ViashDockerRemoteTagCheck python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerRemoteTagCheck sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerRemoteTagCheck {
-  docker manifest inspect $1 > /dev/null 2> /dev/null
-}
-
-# ViashDockerLocalTagCheck: check whether a Docker image is available locally
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   docker pull python:latest
-#   ViashDockerLocalTagCheck python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerLocalTagCheck sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerLocalTagCheck {
-  [ -n "$(docker images -q $1)" ]
-}
-
-# ViashDockerPull: pull a Docker image
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   ViashDockerPull python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerPull sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerPull {
-  ViashNotice "Checking if Docker image is available at '$1'"
-  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
-    docker pull $1 && return 0 || return 1
-  else
-    local save=$-; set +e
-    docker pull $1 2> /dev/null > /dev/null
-    local out=$?
-    [[ $save =~ e ]] && set -e
-    if [ $out -ne 0 ]; then
-      ViashWarning "Could not pull from '$1'. Docker image doesn't exist or is not accessible."
-    fi
-    return $out
-  fi
-}
-
-# ViashDockerPush: push a Docker image
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   ViashDockerPush python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerPush sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerPush {
-  ViashNotice "Pushing image to '$1'"
-  local save=$-; set +e
-  local out
-  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
-    docker push $1
-    out=$?
-  else
-    docker push $1 2> /dev/null > /dev/null
-    out=$?
-  fi
-  [[ $save =~ e ]] && set -e
-  if [ $out -eq 0 ]; then
-    ViashNotice "Container '$1' push succeeded."
-  else
-    ViashError "Container '$1' push errored. You might not be logged in or have the necessary permissions."
-  fi
-  return $out
-}
-
-# ViashDockerPullElseBuild: pull a Docker image, else build it
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# ViashDockerBuild    : a Bash function which builds a docker image, takes image identifier as argument.
-# examples:
-#   ViashDockerPullElseBuild mynewcomponent
-function ViashDockerPullElseBuild {
-  local save=$-; set +e
-  ViashDockerPull $1
-  local out=$?
-  [[ $save =~ e ]] && set -e
-  if [ $out -ne 0 ]; then
-    ViashDockerBuild $@
-  fi
-}
-
-# ViashDockerSetup: create a Docker image, according to specified docker setup strategy
-#
-# $1          : image identifier with format `[registry/]image[:tag]`
-# $2          : docker setup strategy, see DockerSetupStrategy.scala
-# examples:
-#   ViashDockerSetup mynewcomponent alwaysbuild
-function ViashDockerSetup {
-  local image_id="$1"
-  local setup_strategy="$2"
-  if [ "$setup_strategy" == "alwaysbuild" -o "$setup_strategy" == "build" -o "$setup_strategy" == "b" ]; then
-    ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-  elif [ "$setup_strategy" == "alwayspull" -o "$setup_strategy" == "pull" -o "$setup_strategy" == "p" ]; then
-    ViashDockerPull $image_id
-  elif [ "$setup_strategy" == "alwayspullelsebuild" -o "$setup_strategy" == "pullelsebuild" ]; then
-    ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-  elif [ "$setup_strategy" == "alwayspullelsecachedbuild" -o "$setup_strategy" == "pullelsecachedbuild" ]; then
-    ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-  elif [ "$setup_strategy" == "alwayscachedbuild" -o "$setup_strategy" == "cachedbuild" -o "$setup_strategy" == "cb" ]; then
-    ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-  elif [[ "$setup_strategy" =~ ^ifneedbe ]]; then
-    local save=$-; set +e
-    ViashDockerLocalTagCheck $image_id
-    local outCheck=$?
-    [[ $save =~ e ]] && set -e
-    if [ $outCheck -eq 0 ]; then
-      ViashInfo "Image $image_id already exists"
-    elif [ "$setup_strategy" == "ifneedbebuild" ]; then
-      ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-    elif [ "$setup_strategy" == "ifneedbecachedbuild" ]; then
-      ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-    elif [ "$setup_strategy" == "ifneedbepull" ]; then
-      ViashDockerPull $image_id
-    elif [ "$setup_strategy" == "ifneedbepullelsebuild" ]; then
-      ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-    elif [ "$setup_strategy" == "ifneedbepullelsecachedbuild" ]; then
-      ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-    else
-      ViashError "Unrecognised Docker strategy: $setup_strategy"
-      exit 1
-    fi
-  elif [ "$setup_strategy" == "push" -o "$setup_strategy" == "forcepush" -o "$setup_strategy" == "alwayspush" ]; then
-    ViashDockerPush "$image_id"
-  elif [ "$setup_strategy" == "pushifnotpresent" -o "$setup_strategy" == "gentlepush" -o "$setup_strategy" == "maybepush" ]; then
-    local save=$-; set +e
-    ViashDockerRemoteTagCheck $image_id
-    local outCheck=$?
-    [[ $save =~ e ]] && set -e
-    if [ $outCheck -eq 0 ]; then
-      ViashNotice "Container '$image_id' exists, doing nothing."
-    else
-      ViashNotice "Container '$image_id' does not yet exist."
-      ViashDockerPush "$image_id"
-    fi
-  elif [ "$setup_strategy" == "donothing" -o "$setup_strategy" == "meh" ]; then
-    ViashNotice "Skipping setup."
-  else
-    ViashError "Unrecognised Docker strategy: $setup_strategy"
-    exit 1
-  fi
-}
-
-# ViashDockerCheckCommands: Check whether a docker container has the required commands
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# $@                  : commands to verify being present
-# examples:
-#   ViashDockerCheckCommands bash:4.0 bash ps foo
-function ViashDockerCheckCommands {
-  local image_id="$1"
-  shift 1
-  local commands="$@"
-  local save=$-; set +e
-  local missing # mark 'missing' as local in advance, otherwise the exit code of the command will be missing and always be '0'
-  missing=$(docker run --rm --entrypoint=sh "$image_id" -c "for command in $commands; do command -v \$command >/dev/null 2>&1; if [ \$? -ne 0 ]; then echo \$command; exit 1; fi; done")
-  local outCheck=$?
-  [[ $save =~ e ]] && set -e
-  if [ $outCheck -ne 0 ]; then
-  	ViashError "Docker container '$image_id' does not contain command '$missing'."
-  	exit 1
-  fi
-}
-
-# ViashDockerBuild: build a docker image
-# $1                               : image identifier with format `[registry/]image[:tag]`
-# $...                             : additional arguments to pass to docker build
-# $VIASH_META_TEMP_DIR             : temporary directory to store dockerfile & optional resources in
-# $VIASH_META_NAME                 : name of the component
-# $VIASH_META_RESOURCES_DIR        : directory containing the resources
-# $VIASH_VERBOSITY                 : verbosity level
-# exit code $?                     : whether or not the image was built successfully
-function ViashDockerBuild {
-  local image_id="$1"
-  shift 1
-
-  # create temporary directory to store dockerfile & optional resources in
-  local tmpdir=$(mktemp -d "$VIASH_META_TEMP_DIR/dockerbuild-$VIASH_META_NAME-XXXXXX")
-  local dockerfile="$tmpdir/Dockerfile"
-  function clean_up {
-    rm -rf "$tmpdir"
-  }
-  trap clean_up EXIT
-
-  # store dockerfile and resources
-  ViashDockerfile "$VIASH_ENGINE_ID" > "$dockerfile"
-
-  # generate the build command
-  local docker_build_cmd="docker build -t '$image_id' $@ '$VIASH_META_RESOURCES_DIR' -f '$dockerfile'"
-
-  # build the container
-  ViashNotice "Building container '$image_id' with Dockerfile"
-  ViashInfo "$docker_build_cmd"
-  local save=$-; set +e
-  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
-    eval $docker_build_cmd
-  else
-    eval $docker_build_cmd &> "$tmpdir/docker_build.log"
-  fi
-
-  # check exit code
-  local out=$?
-  [[ $save =~ e ]] && set -e
-  if [ $out -ne 0 ]; then
-    ViashError "Error occurred while building container '$image_id'"
-    if [ $VIASH_VERBOSITY -lt $VIASH_LOGCODE_INFO ]; then
-      ViashError "Transcript: --------------------------------"
-      cat "$tmpdir/docker_build.log"
-      ViashError "End of transcript --------------------------"
-    fi
-    exit 1
-  fi
-}
-
-######## End of helper functions for setting up Docker images for viash ########
-
-# ViashDockerFile: print the dockerfile to stdout
-# $1    : engine identifier
-# return : dockerfile required to run this component
-# examples:
-#   ViashDockerFile
-function ViashDockerfile {
-  local engine_id="$1"
-
-  if [[ "$engine_id" == "docker" ]]; then
-    cat << 'VIASHDOCKER'
-FROM quay.io/biocontainers/fastp:0.23.4--hadf994f_2
-ENTRYPOINT []
-RUN fastp --version 2>&1 | sed 's# #: "#;s#$#"#' > /var/software_versions.txt
-
-LABEL org.opencontainers.image.authors="Robrecht Cannoodt"
-LABEL org.opencontainers.image.description="Companion container for running component fastp"
-LABEL org.opencontainers.image.created="2024-12-03T10:34:04Z"
-LABEL org.opencontainers.image.source="https://github.com/OpenGene/fastp"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-LABEL org.opencontainers.image.version="main"
-
-VIASHDOCKER
-  fi
-}
-
-# ViashDockerBuildArgs: return the arguments to pass to docker build
-# $1    : engine identifier
-# return : arguments to pass to docker build
-function ViashDockerBuildArgs {
-  local engine_id="$1"
-
-  if [[ "$engine_id" == "docker" ]]; then
-    echo ""
-  fi
-}
-
-# ViashAbsolutePath: generate absolute path from relative path
-# borrowed from https://stackoverflow.com/a/21951256
-# $1     : relative filename
-# return : absolute path
-# examples:
-#   ViashAbsolutePath some_file.txt   # returns /path/to/some_file.txt
-#   ViashAbsolutePath /foo/bar/..     # returns /foo
-function ViashAbsolutePath {
-  local thePath
-  local parr
-  local outp
-  local len
-  if [[ ! "$1" =~ ^/ ]]; then
-    thePath="$PWD/$1"
-  else
-    thePath="$1"
-  fi
-  echo "$thePath" | (
-    IFS=/
-    read -a parr
-    declare -a outp
-    for i in "${parr[@]}"; do
-      case "$i" in
-      ''|.) continue ;;
-      ..)
-        len=${#outp[@]}
-        if ((len==0)); then
-          continue
-        else
-          unset outp[$((len-1))]
-        fi
-        ;;
-      *)
-        len=${#outp[@]}
-        outp[$len]="$i"
-      ;;
-      esac
-    done
-    echo /"${outp[*]}"
-  )
-}
-# ViashDockerAutodetectMount: auto configuring docker mounts from parameters
-# $1                             : The parameter value
-# returns                        : New parameter
-# $VIASH_DIRECTORY_MOUNTS        : Added another parameter to be passed to docker
-# $VIASH_DOCKER_AUTOMOUNT_PREFIX : The prefix to be used for the automounts
-# examples:
-#   ViashDockerAutodetectMount /path/to/bar      # returns '/viash_automount/path/to/bar'
-#   ViashDockerAutodetectMountArg /path/to/bar   # returns '--volume="/path/to:/viash_automount/path/to"'
-function ViashDockerAutodetectMount {
-  local abs_path=$(ViashAbsolutePath "$1")
-  local mount_source
-  local base_name
-  if [ -d "$abs_path" ]; then
-    mount_source="$abs_path"
-    base_name=""
-  else
-    mount_source=`dirname "$abs_path"`
-    base_name=`basename "$abs_path"`
-  fi
-  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
-  if [ -z "$base_name" ]; then
-    echo "$mount_target"
-  else
-    echo "$mount_target/$base_name"
-  fi
-}
-function ViashDockerAutodetectMountArg {
-  local abs_path=$(ViashAbsolutePath "$1")
-  local mount_source
-  local base_name
-  if [ -d "$abs_path" ]; then
-    mount_source="$abs_path"
-    base_name=""
-  else
-    mount_source=`dirname "$abs_path"`
-    base_name=`basename "$abs_path"`
-  fi
-  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
-  ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target"
-  echo "--volume=\"$mount_source:$mount_target\""
-}
-function ViashDockerStripAutomount {
-  local abs_path=$(ViashAbsolutePath "$1")
-  echo "${abs_path#$VIASH_DOCKER_AUTOMOUNT_PREFIX}"
-}
-# initialise variables
-VIASH_DIRECTORY_MOUNTS=()
-
-# configure default docker automount prefix if it is unset
-if [ -z "${VIASH_DOCKER_AUTOMOUNT_PREFIX+x}" ]; then
-  VIASH_DOCKER_AUTOMOUNT_PREFIX="/viash_automount"
-fi
-
-# initialise docker variables
-VIASH_DOCKER_RUN_ARGS=(-i --rm)
-
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/fastqc/.config.vsh.yaml b/target/executable/fastqc/.config.vsh.yaml
index b2e14f8a..43ae634a 100644
--- a/target/executable/fastqc/.config.vsh.yaml
+++ b/target/executable/fastqc/.config.vsh.yaml
@@ -239,6 +239,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -339,16 +342,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/fastqc"
   executable: "target/executable/fastqc/fastqc"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/fastqc/fastqc b/target/executable/fastqc/fastqc
index aba1d846..d8b185ba 100755
--- a/target/executable/fastqc/fastqc
+++ b/target/executable/fastqc/fastqc
@@ -2,7 +2,7 @@
 
 # fastqc main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,155 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "fastqc main"
-  echo ""
-  echo "FastQC - A high throughput sequence QC analysis tool."
-  echo ""
-  echo "Inputs:"
-  echo "    --input"
-  echo "        type: file, required parameter, multiple values allowed, file must exist"
-  echo "        example: input.fq"
-  echo "        FASTQ file(s) to be analyzed."
-  echo ""
-  echo "Outputs:"
-  echo "    At least one of the output options (--html, --zip, --summary, --data) must"
-  echo "    be used."
-  echo ""
-  echo "    --html"
-  echo "        type: file, multiple values allowed, output, file must exist"
-  echo "        example: *.html"
-  echo "        Create the HTML report of the results."
-  echo "        '*' wild card must be provided in the output file name."
-  echo "        Wild card will be replaced by the input file basename."
-  echo "        e.g."
-  echo "          --input \"sample_1.fq\""
-  echo "          --html \"*.html\""
-  echo "          would create an output html file named sample_1.html"
-  echo ""
-  echo "    --zip"
-  echo "        type: file, multiple values allowed, output, file must exist"
-  echo "        example: *.zip"
-  echo "        Create the zip file(s) containing: html report, data, images, icons,"
-  echo "        summary, etc."
-  echo "        '*' wild card must be provided in the output file name."
-  echo "        Wild card will be replaced by the input basename."
-  echo "        e.g."
-  echo "          --input \"sample_1.fq\""
-  echo "          --html \"*.zip\""
-  echo "          would create an output zip file named sample_1.zip"
-  echo ""
-  echo "    --summary"
-  echo "        type: file, multiple values allowed, output, file must exist"
-  echo "        example: *_summary.txt"
-  echo "        Create the summary file(s)."
-  echo "        '*' wild card must be provided in the output file name."
-  echo "        Wild card will be replaced by the input basename."
-  echo "        e.g."
-  echo "          --input \"sample_1.fq\""
-  echo "          --summary \"*_summary.txt\""
-  echo "          would create an output summary.txt file named sample_1_summary.txt"
-  echo ""
-  echo "    --data"
-  echo "        type: file, multiple values allowed, output, file must exist"
-  echo "        example: *_data.txt"
-  echo "        Create the data file(s)."
-  echo "        '*' wild card must be provided in the output file name."
-  echo "        Wild card will be replaced by the input basename."
-  echo "        e.g."
-  echo "          --input \"sample_1.fq\""
-  echo "          --summary \"*_data.txt\""
-  echo "          would create an output data.txt file named sample_1_data.txt"
-  echo ""
-  echo "Options:"
-  echo "    --casava"
-  echo "        type: boolean_true"
-  echo "        Files come from raw casava output. Files in the same sample"
-  echo "        group (differing only by the group number) will be analysed"
-  echo "        as a set rather than individually. Sequences with the filter"
-  echo "        flag set in the header will be excluded from the analysis."
-  echo "        Files must have the same names given to them by casava"
-  echo "        (including being gzipped and ending with .gz) otherwise they"
-  echo "        won't be grouped together correctly."
-  echo ""
-  echo "    --nano"
-  echo "        type: boolean_true"
-  echo "        Files come from nanopore sequences and are in fast5 format. In"
-  echo "        this mode you can pass in directories to process and the program"
-  echo "        will take in all fast5 files within those directories and produce"
-  echo "        a single output file from the sequences found in all files."
-  echo ""
-  echo "    --nofilter"
-  echo "        type: boolean_true"
-  echo "        If running with --casava then don't remove read flagged by"
-  echo "        casava as poor quality when performing the QC analysis."
-  echo ""
-  echo "    --nogroup"
-  echo "        type: boolean_true"
-  echo "        Disable grouping of bases for reads >50bp."
-  echo "        All reports will show data for every base in the read."
-  echo "        WARNING: Using this option will cause fastqc to crash"
-  echo "        and burn if you use it on really long reads, and your"
-  echo "        plots may end up a ridiculous size. You have been warned!"
-  echo ""
-  echo "    --min_length"
-  echo "        type: integer"
-  echo "        example: 0"
-  echo "        Sets an artificial lower limit on the length of the"
-  echo "        sequence to be shown in the report. As long as you"
-  echo "        set this to a value greater or equal to your longest"
-  echo "        read length then this will be the sequence length used"
-  echo "        to create your read groups. This can be useful for making"
-  echo "        directly comparable statistics from datasets with somewhat"
-  echo "        variable read lengths."
-  echo ""
-  echo "    -f, --format"
-  echo "        type: string"
-  echo "        example: bam"
-  echo "        Bypasses the normal sequence file format detection and"
-  echo "        forces the program to use the specified format."
-  echo "        Valid formats are bam, sam, bam_mapped, sam_mapped, and fastq."
-  echo ""
-  echo "    -c, --contaminants"
-  echo "        type: file, file must exist"
-  echo "        example: contaminants.txt"
-  echo "        Specifies a non-default file which contains the list"
-  echo "        of contaminants to screen overrepresented sequences against."
-  echo "        The file must contain sets of named contaminants in the form"
-  echo "        name[tab]sequence. Lines prefixed with a hash will be ignored."
-  echo ""
-  echo "    -a, --adapters"
-  echo "        type: file, file must exist"
-  echo "        example: adapters.txt"
-  echo "        Specifies a non-default file which contains the list of"
-  echo "        adapter sequences which will be explicitly searched against"
-  echo "        the library. The file must contain sets of named adapters"
-  echo "        in the form name[tab]sequence. Lines prefixed with a hash will be"
-  echo "        ignored."
-  echo ""
-  echo "    -l, --limits"
-  echo "        type: file, file must exist"
-  echo "        example: limits.txt"
-  echo "        Specifies a non-default file which contains"
-  echo "        a set of criteria which will be used to determine"
-  echo "        the warn/error limits for the various modules."
-  echo "        This file can also be used to selectively remove"
-  echo "        some modules from the output altogether. The format"
-  echo "        needs to mirror the default limits.txt file found in"
-  echo "        the Configuration folder."
-  echo ""
-  echo "    -k, --kmers"
-  echo "        type: integer"
-  echo "        example: 7"
-  echo "        Specifies the length of Kmer to look for in the Kmer"
-  echo "        content module. Specified Kmer length must be between"
-  echo "        2 and 10. Default length is 7 if not specified."
-  echo ""
-  echo "    -q, --quiet"
-  echo "        type: boolean_true"
-  echo "        Suppress all progress messages on stdout and only report errors."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -601,9 +452,9 @@ RUN echo "fastqc: $(fastqc --version | sed -n 's/^FastQC //p')" > /var/software_
 
 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component fastqc"
-LABEL org.opencontainers.image.created="2024-12-03T10:34:06Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:44Z"
 LABEL org.opencontainers.image.source="https://github.com/s-andrews/FastQC"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -718,6 +569,181 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "fastqc main"
+  echo ""
+  echo "FastQC - A high throughput sequence QC analysis tool."
+  echo ""
+  echo "Inputs:"
+  echo "    --input"
+  echo "        type: file, required parameter, multiple values allowed, file must exist"
+  echo "        example: input.fq"
+  echo "        FASTQ file(s) to be analyzed."
+  echo ""
+  echo "Outputs:"
+  echo "    At least one of the output options (--html, --zip, --summary, --data) must"
+  echo "    be used."
+  echo ""
+  echo "    --html"
+  echo "        type: file, multiple values allowed, output, file must exist"
+  echo "        example: *.html"
+  echo "        Create the HTML report of the results."
+  echo "        '*' wild card must be provided in the output file name."
+  echo "        Wild card will be replaced by the input file basename."
+  echo "        e.g."
+  echo "          --input \"sample_1.fq\""
+  echo "          --html \"*.html\""
+  echo "          would create an output html file named sample_1.html"
+  echo ""
+  echo "    --zip"
+  echo "        type: file, multiple values allowed, output, file must exist"
+  echo "        example: *.zip"
+  echo "        Create the zip file(s) containing: html report, data, images, icons,"
+  echo "        summary, etc."
+  echo "        '*' wild card must be provided in the output file name."
+  echo "        Wild card will be replaced by the input basename."
+  echo "        e.g."
+  echo "          --input \"sample_1.fq\""
+  echo "          --html \"*.zip\""
+  echo "          would create an output zip file named sample_1.zip"
+  echo ""
+  echo "    --summary"
+  echo "        type: file, multiple values allowed, output, file must exist"
+  echo "        example: *_summary.txt"
+  echo "        Create the summary file(s)."
+  echo "        '*' wild card must be provided in the output file name."
+  echo "        Wild card will be replaced by the input basename."
+  echo "        e.g."
+  echo "          --input \"sample_1.fq\""
+  echo "          --summary \"*_summary.txt\""
+  echo "          would create an output summary.txt file named sample_1_summary.txt"
+  echo ""
+  echo "    --data"
+  echo "        type: file, multiple values allowed, output, file must exist"
+  echo "        example: *_data.txt"
+  echo "        Create the data file(s)."
+  echo "        '*' wild card must be provided in the output file name."
+  echo "        Wild card will be replaced by the input basename."
+  echo "        e.g."
+  echo "          --input \"sample_1.fq\""
+  echo "          --summary \"*_data.txt\""
+  echo "          would create an output data.txt file named sample_1_data.txt"
+  echo ""
+  echo "Options:"
+  echo "    --casava"
+  echo "        type: boolean_true"
+  echo "        Files come from raw casava output. Files in the same sample"
+  echo "        group (differing only by the group number) will be analysed"
+  echo "        as a set rather than individually. Sequences with the filter"
+  echo "        flag set in the header will be excluded from the analysis."
+  echo "        Files must have the same names given to them by casava"
+  echo "        (including being gzipped and ending with .gz) otherwise they"
+  echo "        won't be grouped together correctly."
+  echo ""
+  echo "    --nano"
+  echo "        type: boolean_true"
+  echo "        Files come from nanopore sequences and are in fast5 format. In"
+  echo "        this mode you can pass in directories to process and the program"
+  echo "        will take in all fast5 files within those directories and produce"
+  echo "        a single output file from the sequences found in all files."
+  echo ""
+  echo "    --nofilter"
+  echo "        type: boolean_true"
+  echo "        If running with --casava then don't remove read flagged by"
+  echo "        casava as poor quality when performing the QC analysis."
+  echo ""
+  echo "    --nogroup"
+  echo "        type: boolean_true"
+  echo "        Disable grouping of bases for reads >50bp."
+  echo "        All reports will show data for every base in the read."
+  echo "        WARNING: Using this option will cause fastqc to crash"
+  echo "        and burn if you use it on really long reads, and your"
+  echo "        plots may end up a ridiculous size. You have been warned!"
+  echo ""
+  echo "    --min_length"
+  echo "        type: integer"
+  echo "        example: 0"
+  echo "        Sets an artificial lower limit on the length of the"
+  echo "        sequence to be shown in the report. As long as you"
+  echo "        set this to a value greater or equal to your longest"
+  echo "        read length then this will be the sequence length used"
+  echo "        to create your read groups. This can be useful for making"
+  echo "        directly comparable statistics from datasets with somewhat"
+  echo "        variable read lengths."
+  echo ""
+  echo "    -f, --format"
+  echo "        type: string"
+  echo "        example: bam"
+  echo "        Bypasses the normal sequence file format detection and"
+  echo "        forces the program to use the specified format."
+  echo "        Valid formats are bam, sam, bam_mapped, sam_mapped, and fastq."
+  echo ""
+  echo "    -c, --contaminants"
+  echo "        type: file, file must exist"
+  echo "        example: contaminants.txt"
+  echo "        Specifies a non-default file which contains the list"
+  echo "        of contaminants to screen overrepresented sequences against."
+  echo "        The file must contain sets of named contaminants in the form"
+  echo "        name[tab]sequence. Lines prefixed with a hash will be ignored."
+  echo ""
+  echo "    -a, --adapters"
+  echo "        type: file, file must exist"
+  echo "        example: adapters.txt"
+  echo "        Specifies a non-default file which contains the list of"
+  echo "        adapter sequences which will be explicitly searched against"
+  echo "        the library. The file must contain sets of named adapters"
+  echo "        in the form name[tab]sequence. Lines prefixed with a hash will be"
+  echo "        ignored."
+  echo ""
+  echo "    -l, --limits"
+  echo "        type: file, file must exist"
+  echo "        example: limits.txt"
+  echo "        Specifies a non-default file which contains"
+  echo "        a set of criteria which will be used to determine"
+  echo "        the warn/error limits for the various modules."
+  echo "        This file can also be used to selectively remove"
+  echo "        some modules from the output altogether. The format"
+  echo "        needs to mirror the default limits.txt file found in"
+  echo "        the Configuration folder."
+  echo ""
+  echo "    -k, --kmers"
+  echo "        type: integer"
+  echo "        example: 7"
+  echo "        Specifies the length of Kmer to look for in the Kmer"
+  echo "        content module. Specified Kmer length must be between"
+  echo "        2 and 10. Default length is 7 if not specified."
+  echo ""
+  echo "    -q, --quiet"
+  echo "        type: boolean_true"
+  echo "        Suppress all progress messages on stdout and only report errors."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/featurecounts/.config.vsh.yaml b/target/executable/featurecounts/.config.vsh.yaml
index b8c2cfcd..ebac86cd 100644
--- a/target/executable/featurecounts/.config.vsh.yaml
+++ b/target/executable/featurecounts/.config.vsh.yaml
@@ -543,6 +543,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -644,16 +647,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/featurecounts"
   executable: "target/executable/featurecounts/featurecounts"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/featurecounts/featurecounts b/target/executable/featurecounts/featurecounts
index 3d0983b9..0980c026 100755
--- a/target/executable/featurecounts/featurecounts
+++ b/target/executable/featurecounts/featurecounts
@@ -2,7 +2,7 @@
 
 # featurecounts main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,6 +172,404 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
+
+# initialise variables
+VIASH_MODE='run'
+VIASH_ENGINE_ID='docker'
+
+######## Helper functions for setting up Docker images for viash ########
+# expects: ViashDockerBuild
+
+# ViashDockerInstallationCheck: check whether Docker is installed correctly
+#
+# examples:
+#   ViashDockerInstallationCheck
+function ViashDockerInstallationCheck {
+  ViashDebug "Checking whether Docker is installed"
+  if [ ! command -v docker &> /dev/null ]; then
+    ViashCritical "Docker doesn't seem to be installed. See 'https://docs.docker.com/get-docker/' for instructions."
+    exit 1
+  fi
+
+  ViashDebug "Checking whether the Docker daemon is running"
+  local save=$-; set +e
+  local docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
+  local out=$?
+  [[ $save =~ e ]] && set -e
+  if [ $out -ne 0 ]; then
+    ViashCritical "Docker daemon does not seem to be running. Try one of the following:"
+    ViashCritical "- Try running 'dockerd' in the command line"
+    ViashCritical "- See https://docs.docker.com/config/daemon/"
+    exit 1
+  fi
+}
+
+# ViashDockerRemoteTagCheck: check whether a Docker image is available 
+# on a remote. Assumes `docker login` has been performed, if relevant.
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   ViashDockerRemoteTagCheck python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerRemoteTagCheck sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerRemoteTagCheck {
+  docker manifest inspect $1 > /dev/null 2> /dev/null
+}
+
+# ViashDockerLocalTagCheck: check whether a Docker image is available locally
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   docker pull python:latest
+#   ViashDockerLocalTagCheck python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerLocalTagCheck sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerLocalTagCheck {
+  [ -n "$(docker images -q $1)" ]
+}
+
+# ViashDockerPull: pull a Docker image
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   ViashDockerPull python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerPull sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerPull {
+  ViashNotice "Checking if Docker image is available at '$1'"
+  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
+    docker pull $1 && return 0 || return 1
+  else
+    local save=$-; set +e
+    docker pull $1 2> /dev/null > /dev/null
+    local out=$?
+    [[ $save =~ e ]] && set -e
+    if [ $out -ne 0 ]; then
+      ViashWarning "Could not pull from '$1'. Docker image doesn't exist or is not accessible."
+    fi
+    return $out
+  fi
+}
+
+# ViashDockerPush: push a Docker image
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   ViashDockerPush python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerPush sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerPush {
+  ViashNotice "Pushing image to '$1'"
+  local save=$-; set +e
+  local out
+  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
+    docker push $1
+    out=$?
+  else
+    docker push $1 2> /dev/null > /dev/null
+    out=$?
+  fi
+  [[ $save =~ e ]] && set -e
+  if [ $out -eq 0 ]; then
+    ViashNotice "Container '$1' push succeeded."
+  else
+    ViashError "Container '$1' push errored. You might not be logged in or have the necessary permissions."
+  fi
+  return $out
+}
+
+# ViashDockerPullElseBuild: pull a Docker image, else build it
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# ViashDockerBuild    : a Bash function which builds a docker image, takes image identifier as argument.
+# examples:
+#   ViashDockerPullElseBuild mynewcomponent
+function ViashDockerPullElseBuild {
+  local save=$-; set +e
+  ViashDockerPull $1
+  local out=$?
+  [[ $save =~ e ]] && set -e
+  if [ $out -ne 0 ]; then
+    ViashDockerBuild $@
+  fi
+}
+
+# ViashDockerSetup: create a Docker image, according to specified docker setup strategy
+#
+# $1          : image identifier with format `[registry/]image[:tag]`
+# $2          : docker setup strategy, see DockerSetupStrategy.scala
+# examples:
+#   ViashDockerSetup mynewcomponent alwaysbuild
+function ViashDockerSetup {
+  local image_id="$1"
+  local setup_strategy="$2"
+  if [ "$setup_strategy" == "alwaysbuild" -o "$setup_strategy" == "build" -o "$setup_strategy" == "b" ]; then
+    ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+  elif [ "$setup_strategy" == "alwayspull" -o "$setup_strategy" == "pull" -o "$setup_strategy" == "p" ]; then
+    ViashDockerPull $image_id
+  elif [ "$setup_strategy" == "alwayspullelsebuild" -o "$setup_strategy" == "pullelsebuild" ]; then
+    ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+  elif [ "$setup_strategy" == "alwayspullelsecachedbuild" -o "$setup_strategy" == "pullelsecachedbuild" ]; then
+    ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+  elif [ "$setup_strategy" == "alwayscachedbuild" -o "$setup_strategy" == "cachedbuild" -o "$setup_strategy" == "cb" ]; then
+    ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+  elif [[ "$setup_strategy" =~ ^ifneedbe ]]; then
+    local save=$-; set +e
+    ViashDockerLocalTagCheck $image_id
+    local outCheck=$?
+    [[ $save =~ e ]] && set -e
+    if [ $outCheck -eq 0 ]; then
+      ViashInfo "Image $image_id already exists"
+    elif [ "$setup_strategy" == "ifneedbebuild" ]; then
+      ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+    elif [ "$setup_strategy" == "ifneedbecachedbuild" ]; then
+      ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+    elif [ "$setup_strategy" == "ifneedbepull" ]; then
+      ViashDockerPull $image_id
+    elif [ "$setup_strategy" == "ifneedbepullelsebuild" ]; then
+      ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+    elif [ "$setup_strategy" == "ifneedbepullelsecachedbuild" ]; then
+      ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+    else
+      ViashError "Unrecognised Docker strategy: $setup_strategy"
+      exit 1
+    fi
+  elif [ "$setup_strategy" == "push" -o "$setup_strategy" == "forcepush" -o "$setup_strategy" == "alwayspush" ]; then
+    ViashDockerPush "$image_id"
+  elif [ "$setup_strategy" == "pushifnotpresent" -o "$setup_strategy" == "gentlepush" -o "$setup_strategy" == "maybepush" ]; then
+    local save=$-; set +e
+    ViashDockerRemoteTagCheck $image_id
+    local outCheck=$?
+    [[ $save =~ e ]] && set -e
+    if [ $outCheck -eq 0 ]; then
+      ViashNotice "Container '$image_id' exists, doing nothing."
+    else
+      ViashNotice "Container '$image_id' does not yet exist."
+      ViashDockerPush "$image_id"
+    fi
+  elif [ "$setup_strategy" == "donothing" -o "$setup_strategy" == "meh" ]; then
+    ViashNotice "Skipping setup."
+  else
+    ViashError "Unrecognised Docker strategy: $setup_strategy"
+    exit 1
+  fi
+}
+
+# ViashDockerCheckCommands: Check whether a docker container has the required commands
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# $@                  : commands to verify being present
+# examples:
+#   ViashDockerCheckCommands bash:4.0 bash ps foo
+function ViashDockerCheckCommands {
+  local image_id="$1"
+  shift 1
+  local commands="$@"
+  local save=$-; set +e
+  local missing # mark 'missing' as local in advance, otherwise the exit code of the command will be missing and always be '0'
+  missing=$(docker run --rm --entrypoint=sh "$image_id" -c "for command in $commands; do command -v \$command >/dev/null 2>&1; if [ \$? -ne 0 ]; then echo \$command; exit 1; fi; done")
+  local outCheck=$?
+  [[ $save =~ e ]] && set -e
+  if [ $outCheck -ne 0 ]; then
+  	ViashError "Docker container '$image_id' does not contain command '$missing'."
+  	exit 1
+  fi
+}
+
+# ViashDockerBuild: build a docker image
+# $1                               : image identifier with format `[registry/]image[:tag]`
+# $...                             : additional arguments to pass to docker build
+# $VIASH_META_TEMP_DIR             : temporary directory to store dockerfile & optional resources in
+# $VIASH_META_NAME                 : name of the component
+# $VIASH_META_RESOURCES_DIR        : directory containing the resources
+# $VIASH_VERBOSITY                 : verbosity level
+# exit code $?                     : whether or not the image was built successfully
+function ViashDockerBuild {
+  local image_id="$1"
+  shift 1
+
+  # create temporary directory to store dockerfile & optional resources in
+  local tmpdir=$(mktemp -d "$VIASH_META_TEMP_DIR/dockerbuild-$VIASH_META_NAME-XXXXXX")
+  local dockerfile="$tmpdir/Dockerfile"
+  function clean_up {
+    rm -rf "$tmpdir"
+  }
+  trap clean_up EXIT
+
+  # store dockerfile and resources
+  ViashDockerfile "$VIASH_ENGINE_ID" > "$dockerfile"
+
+  # generate the build command
+  local docker_build_cmd="docker build -t '$image_id' $@ '$VIASH_META_RESOURCES_DIR' -f '$dockerfile'"
+
+  # build the container
+  ViashNotice "Building container '$image_id' with Dockerfile"
+  ViashInfo "$docker_build_cmd"
+  local save=$-; set +e
+  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
+    eval $docker_build_cmd
+  else
+    eval $docker_build_cmd &> "$tmpdir/docker_build.log"
+  fi
+
+  # check exit code
+  local out=$?
+  [[ $save =~ e ]] && set -e
+  if [ $out -ne 0 ]; then
+    ViashError "Error occurred while building container '$image_id'"
+    if [ $VIASH_VERBOSITY -lt $VIASH_LOGCODE_INFO ]; then
+      ViashError "Transcript: --------------------------------"
+      cat "$tmpdir/docker_build.log"
+      ViashError "End of transcript --------------------------"
+    fi
+    exit 1
+  fi
+}
+
+######## End of helper functions for setting up Docker images for viash ########
+
+# ViashDockerFile: print the dockerfile to stdout
+# $1    : engine identifier
+# return : dockerfile required to run this component
+# examples:
+#   ViashDockerFile
+function ViashDockerfile {
+  local engine_id="$1"
+
+  if [[ "$engine_id" == "docker" ]]; then
+    cat << 'VIASHDOCKER'
+FROM quay.io/biocontainers/subread:2.0.6--he4a0461_0
+ENTRYPOINT []
+RUN featureCounts -v 2>&1 | sed 's/featureCounts v\([0-9.]*\)/featureCounts: \1/' > /var/software_versions.txt
+
+LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
+LABEL org.opencontainers.image.description="Companion container for running component featurecounts"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:35Z"
+LABEL org.opencontainers.image.source="https://github.com/ShiLab-Bioinformatics/subread"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+LABEL org.opencontainers.image.version="main"
+
+VIASHDOCKER
+  fi
+}
+
+# ViashDockerBuildArgs: return the arguments to pass to docker build
+# $1    : engine identifier
+# return : arguments to pass to docker build
+function ViashDockerBuildArgs {
+  local engine_id="$1"
+
+  if [[ "$engine_id" == "docker" ]]; then
+    echo ""
+  fi
+}
+
+# ViashAbsolutePath: generate absolute path from relative path
+# borrowed from https://stackoverflow.com/a/21951256
+# $1     : relative filename
+# return : absolute path
+# examples:
+#   ViashAbsolutePath some_file.txt   # returns /path/to/some_file.txt
+#   ViashAbsolutePath /foo/bar/..     # returns /foo
+function ViashAbsolutePath {
+  local thePath
+  local parr
+  local outp
+  local len
+  if [[ ! "$1" =~ ^/ ]]; then
+    thePath="$PWD/$1"
+  else
+    thePath="$1"
+  fi
+  echo "$thePath" | (
+    IFS=/
+    read -a parr
+    declare -a outp
+    for i in "${parr[@]}"; do
+      case "$i" in
+      ''|.) continue ;;
+      ..)
+        len=${#outp[@]}
+        if ((len==0)); then
+          continue
+        else
+          unset outp[$((len-1))]
+        fi
+        ;;
+      *)
+        len=${#outp[@]}
+        outp[$len]="$i"
+      ;;
+      esac
+    done
+    echo /"${outp[*]}"
+  )
+}
+# ViashDockerAutodetectMount: auto configuring docker mounts from parameters
+# $1                             : The parameter value
+# returns                        : New parameter
+# $VIASH_DIRECTORY_MOUNTS        : Added another parameter to be passed to docker
+# $VIASH_DOCKER_AUTOMOUNT_PREFIX : The prefix to be used for the automounts
+# examples:
+#   ViashDockerAutodetectMount /path/to/bar      # returns '/viash_automount/path/to/bar'
+#   ViashDockerAutodetectMountArg /path/to/bar   # returns '--volume="/path/to:/viash_automount/path/to"'
+function ViashDockerAutodetectMount {
+  local abs_path=$(ViashAbsolutePath "$1")
+  local mount_source
+  local base_name
+  if [ -d "$abs_path" ]; then
+    mount_source="$abs_path"
+    base_name=""
+  else
+    mount_source=`dirname "$abs_path"`
+    base_name=`basename "$abs_path"`
+  fi
+  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
+  if [ -z "$base_name" ]; then
+    echo "$mount_target"
+  else
+    echo "$mount_target/$base_name"
+  fi
+}
+function ViashDockerAutodetectMountArg {
+  local abs_path=$(ViashAbsolutePath "$1")
+  local mount_source
+  local base_name
+  if [ -d "$abs_path" ]; then
+    mount_source="$abs_path"
+    base_name=""
+  else
+    mount_source=`dirname "$abs_path"`
+    base_name=`basename "$abs_path"`
+  fi
+  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
+  ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target"
+  echo "--volume=\"$mount_source:$mount_target\""
+}
+function ViashDockerStripAutomount {
+  local abs_path=$(ViashAbsolutePath "$1")
+  echo "${abs_path#$VIASH_DOCKER_AUTOMOUNT_PREFIX}"
+}
+# initialise variables
+VIASH_DIRECTORY_MOUNTS=()
+
+# configure default docker automount prefix if it is unset
+if [ -z "${VIASH_DOCKER_AUTOMOUNT_PREFIX+x}" ]; then
+  VIASH_DOCKER_AUTOMOUNT_PREFIX="/viash_automount"
+fi
+
+# initialise docker variables
+VIASH_DOCKER_RUN_ARGS=(-i --rm)
+
+
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
   echo "featurecounts main"
@@ -473,404 +871,32 @@ function ViashHelp {
   echo "        type: boolean_true"
   echo "        Output verbose information for debugging, such as un-matched"
   echo "        chromosome/contig names."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
 }
 
-# initialise variables
-VIASH_MODE='run'
-VIASH_ENGINE_ID='docker'
-
-######## Helper functions for setting up Docker images for viash ########
-# expects: ViashDockerBuild
-
-# ViashDockerInstallationCheck: check whether Docker is installed correctly
-#
-# examples:
-#   ViashDockerInstallationCheck
-function ViashDockerInstallationCheck {
-  ViashDebug "Checking whether Docker is installed"
-  if [ ! command -v docker &> /dev/null ]; then
-    ViashCritical "Docker doesn't seem to be installed. See 'https://docs.docker.com/get-docker/' for instructions."
-    exit 1
-  fi
-
-  ViashDebug "Checking whether the Docker daemon is running"
-  local save=$-; set +e
-  local docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
-  local out=$?
-  [[ $save =~ e ]] && set -e
-  if [ $out -ne 0 ]; then
-    ViashCritical "Docker daemon does not seem to be running. Try one of the following:"
-    ViashCritical "- Try running 'dockerd' in the command line"
-    ViashCritical "- See https://docs.docker.com/config/daemon/"
-    exit 1
-  fi
-}
-
-# ViashDockerRemoteTagCheck: check whether a Docker image is available 
-# on a remote. Assumes `docker login` has been performed, if relevant.
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   ViashDockerRemoteTagCheck python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerRemoteTagCheck sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerRemoteTagCheck {
-  docker manifest inspect $1 > /dev/null 2> /dev/null
-}
-
-# ViashDockerLocalTagCheck: check whether a Docker image is available locally
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   docker pull python:latest
-#   ViashDockerLocalTagCheck python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerLocalTagCheck sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerLocalTagCheck {
-  [ -n "$(docker images -q $1)" ]
-}
-
-# ViashDockerPull: pull a Docker image
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   ViashDockerPull python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerPull sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerPull {
-  ViashNotice "Checking if Docker image is available at '$1'"
-  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
-    docker pull $1 && return 0 || return 1
-  else
-    local save=$-; set +e
-    docker pull $1 2> /dev/null > /dev/null
-    local out=$?
-    [[ $save =~ e ]] && set -e
-    if [ $out -ne 0 ]; then
-      ViashWarning "Could not pull from '$1'. Docker image doesn't exist or is not accessible."
-    fi
-    return $out
-  fi
-}
-
-# ViashDockerPush: push a Docker image
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   ViashDockerPush python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerPush sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerPush {
-  ViashNotice "Pushing image to '$1'"
-  local save=$-; set +e
-  local out
-  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
-    docker push $1
-    out=$?
-  else
-    docker push $1 2> /dev/null > /dev/null
-    out=$?
-  fi
-  [[ $save =~ e ]] && set -e
-  if [ $out -eq 0 ]; then
-    ViashNotice "Container '$1' push succeeded."
-  else
-    ViashError "Container '$1' push errored. You might not be logged in or have the necessary permissions."
-  fi
-  return $out
-}
-
-# ViashDockerPullElseBuild: pull a Docker image, else build it
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# ViashDockerBuild    : a Bash function which builds a docker image, takes image identifier as argument.
-# examples:
-#   ViashDockerPullElseBuild mynewcomponent
-function ViashDockerPullElseBuild {
-  local save=$-; set +e
-  ViashDockerPull $1
-  local out=$?
-  [[ $save =~ e ]] && set -e
-  if [ $out -ne 0 ]; then
-    ViashDockerBuild $@
-  fi
-}
-
-# ViashDockerSetup: create a Docker image, according to specified docker setup strategy
-#
-# $1          : image identifier with format `[registry/]image[:tag]`
-# $2          : docker setup strategy, see DockerSetupStrategy.scala
-# examples:
-#   ViashDockerSetup mynewcomponent alwaysbuild
-function ViashDockerSetup {
-  local image_id="$1"
-  local setup_strategy="$2"
-  if [ "$setup_strategy" == "alwaysbuild" -o "$setup_strategy" == "build" -o "$setup_strategy" == "b" ]; then
-    ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-  elif [ "$setup_strategy" == "alwayspull" -o "$setup_strategy" == "pull" -o "$setup_strategy" == "p" ]; then
-    ViashDockerPull $image_id
-  elif [ "$setup_strategy" == "alwayspullelsebuild" -o "$setup_strategy" == "pullelsebuild" ]; then
-    ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-  elif [ "$setup_strategy" == "alwayspullelsecachedbuild" -o "$setup_strategy" == "pullelsecachedbuild" ]; then
-    ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-  elif [ "$setup_strategy" == "alwayscachedbuild" -o "$setup_strategy" == "cachedbuild" -o "$setup_strategy" == "cb" ]; then
-    ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-  elif [[ "$setup_strategy" =~ ^ifneedbe ]]; then
-    local save=$-; set +e
-    ViashDockerLocalTagCheck $image_id
-    local outCheck=$?
-    [[ $save =~ e ]] && set -e
-    if [ $outCheck -eq 0 ]; then
-      ViashInfo "Image $image_id already exists"
-    elif [ "$setup_strategy" == "ifneedbebuild" ]; then
-      ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-    elif [ "$setup_strategy" == "ifneedbecachedbuild" ]; then
-      ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-    elif [ "$setup_strategy" == "ifneedbepull" ]; then
-      ViashDockerPull $image_id
-    elif [ "$setup_strategy" == "ifneedbepullelsebuild" ]; then
-      ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-    elif [ "$setup_strategy" == "ifneedbepullelsecachedbuild" ]; then
-      ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-    else
-      ViashError "Unrecognised Docker strategy: $setup_strategy"
-      exit 1
-    fi
-  elif [ "$setup_strategy" == "push" -o "$setup_strategy" == "forcepush" -o "$setup_strategy" == "alwayspush" ]; then
-    ViashDockerPush "$image_id"
-  elif [ "$setup_strategy" == "pushifnotpresent" -o "$setup_strategy" == "gentlepush" -o "$setup_strategy" == "maybepush" ]; then
-    local save=$-; set +e
-    ViashDockerRemoteTagCheck $image_id
-    local outCheck=$?
-    [[ $save =~ e ]] && set -e
-    if [ $outCheck -eq 0 ]; then
-      ViashNotice "Container '$image_id' exists, doing nothing."
-    else
-      ViashNotice "Container '$image_id' does not yet exist."
-      ViashDockerPush "$image_id"
-    fi
-  elif [ "$setup_strategy" == "donothing" -o "$setup_strategy" == "meh" ]; then
-    ViashNotice "Skipping setup."
-  else
-    ViashError "Unrecognised Docker strategy: $setup_strategy"
-    exit 1
-  fi
-}
-
-# ViashDockerCheckCommands: Check whether a docker container has the required commands
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# $@                  : commands to verify being present
-# examples:
-#   ViashDockerCheckCommands bash:4.0 bash ps foo
-function ViashDockerCheckCommands {
-  local image_id="$1"
-  shift 1
-  local commands="$@"
-  local save=$-; set +e
-  local missing # mark 'missing' as local in advance, otherwise the exit code of the command will be missing and always be '0'
-  missing=$(docker run --rm --entrypoint=sh "$image_id" -c "for command in $commands; do command -v \$command >/dev/null 2>&1; if [ \$? -ne 0 ]; then echo \$command; exit 1; fi; done")
-  local outCheck=$?
-  [[ $save =~ e ]] && set -e
-  if [ $outCheck -ne 0 ]; then
-  	ViashError "Docker container '$image_id' does not contain command '$missing'."
-  	exit 1
-  fi
-}
-
-# ViashDockerBuild: build a docker image
-# $1                               : image identifier with format `[registry/]image[:tag]`
-# $...                             : additional arguments to pass to docker build
-# $VIASH_META_TEMP_DIR             : temporary directory to store dockerfile & optional resources in
-# $VIASH_META_NAME                 : name of the component
-# $VIASH_META_RESOURCES_DIR        : directory containing the resources
-# $VIASH_VERBOSITY                 : verbosity level
-# exit code $?                     : whether or not the image was built successfully
-function ViashDockerBuild {
-  local image_id="$1"
-  shift 1
-
-  # create temporary directory to store dockerfile & optional resources in
-  local tmpdir=$(mktemp -d "$VIASH_META_TEMP_DIR/dockerbuild-$VIASH_META_NAME-XXXXXX")
-  local dockerfile="$tmpdir/Dockerfile"
-  function clean_up {
-    rm -rf "$tmpdir"
-  }
-  trap clean_up EXIT
-
-  # store dockerfile and resources
-  ViashDockerfile "$VIASH_ENGINE_ID" > "$dockerfile"
-
-  # generate the build command
-  local docker_build_cmd="docker build -t '$image_id' $@ '$VIASH_META_RESOURCES_DIR' -f '$dockerfile'"
-
-  # build the container
-  ViashNotice "Building container '$image_id' with Dockerfile"
-  ViashInfo "$docker_build_cmd"
-  local save=$-; set +e
-  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
-    eval $docker_build_cmd
-  else
-    eval $docker_build_cmd &> "$tmpdir/docker_build.log"
-  fi
-
-  # check exit code
-  local out=$?
-  [[ $save =~ e ]] && set -e
-  if [ $out -ne 0 ]; then
-    ViashError "Error occurred while building container '$image_id'"
-    if [ $VIASH_VERBOSITY -lt $VIASH_LOGCODE_INFO ]; then
-      ViashError "Transcript: --------------------------------"
-      cat "$tmpdir/docker_build.log"
-      ViashError "End of transcript --------------------------"
-    fi
-    exit 1
-  fi
-}
-
-######## End of helper functions for setting up Docker images for viash ########
-
-# ViashDockerFile: print the dockerfile to stdout
-# $1    : engine identifier
-# return : dockerfile required to run this component
-# examples:
-#   ViashDockerFile
-function ViashDockerfile {
-  local engine_id="$1"
-
-  if [[ "$engine_id" == "docker" ]]; then
-    cat << 'VIASHDOCKER'
-FROM quay.io/biocontainers/subread:2.0.6--he4a0461_0
-ENTRYPOINT []
-RUN featureCounts -v 2>&1 | sed 's/featureCounts v\([0-9.]*\)/featureCounts: \1/' > /var/software_versions.txt
-
-LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
-LABEL org.opencontainers.image.description="Companion container for running component featurecounts"
-LABEL org.opencontainers.image.created="2024-12-03T10:33:51Z"
-LABEL org.opencontainers.image.source="https://github.com/ShiLab-Bioinformatics/subread"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-LABEL org.opencontainers.image.version="main"
-
-VIASHDOCKER
-  fi
-}
-
-# ViashDockerBuildArgs: return the arguments to pass to docker build
-# $1    : engine identifier
-# return : arguments to pass to docker build
-function ViashDockerBuildArgs {
-  local engine_id="$1"
-
-  if [[ "$engine_id" == "docker" ]]; then
-    echo ""
-  fi
-}
-
-# ViashAbsolutePath: generate absolute path from relative path
-# borrowed from https://stackoverflow.com/a/21951256
-# $1     : relative filename
-# return : absolute path
-# examples:
-#   ViashAbsolutePath some_file.txt   # returns /path/to/some_file.txt
-#   ViashAbsolutePath /foo/bar/..     # returns /foo
-function ViashAbsolutePath {
-  local thePath
-  local parr
-  local outp
-  local len
-  if [[ ! "$1" =~ ^/ ]]; then
-    thePath="$PWD/$1"
-  else
-    thePath="$1"
-  fi
-  echo "$thePath" | (
-    IFS=/
-    read -a parr
-    declare -a outp
-    for i in "${parr[@]}"; do
-      case "$i" in
-      ''|.) continue ;;
-      ..)
-        len=${#outp[@]}
-        if ((len==0)); then
-          continue
-        else
-          unset outp[$((len-1))]
-        fi
-        ;;
-      *)
-        len=${#outp[@]}
-        outp[$len]="$i"
-      ;;
-      esac
-    done
-    echo /"${outp[*]}"
-  )
-}
-# ViashDockerAutodetectMount: auto configuring docker mounts from parameters
-# $1                             : The parameter value
-# returns                        : New parameter
-# $VIASH_DIRECTORY_MOUNTS        : Added another parameter to be passed to docker
-# $VIASH_DOCKER_AUTOMOUNT_PREFIX : The prefix to be used for the automounts
-# examples:
-#   ViashDockerAutodetectMount /path/to/bar      # returns '/viash_automount/path/to/bar'
-#   ViashDockerAutodetectMountArg /path/to/bar   # returns '--volume="/path/to:/viash_automount/path/to"'
-function ViashDockerAutodetectMount {
-  local abs_path=$(ViashAbsolutePath "$1")
-  local mount_source
-  local base_name
-  if [ -d "$abs_path" ]; then
-    mount_source="$abs_path"
-    base_name=""
-  else
-    mount_source=`dirname "$abs_path"`
-    base_name=`basename "$abs_path"`
-  fi
-  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
-  if [ -z "$base_name" ]; then
-    echo "$mount_target"
-  else
-    echo "$mount_target/$base_name"
-  fi
-}
-function ViashDockerAutodetectMountArg {
-  local abs_path=$(ViashAbsolutePath "$1")
-  local mount_source
-  local base_name
-  if [ -d "$abs_path" ]; then
-    mount_source="$abs_path"
-    base_name=""
-  else
-    mount_source=`dirname "$abs_path"`
-    base_name=`basename "$abs_path"`
-  fi
-  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
-  ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target"
-  echo "--volume=\"$mount_source:$mount_target\""
-}
-function ViashDockerStripAutomount {
-  local abs_path=$(ViashAbsolutePath "$1")
-  echo "${abs_path#$VIASH_DOCKER_AUTOMOUNT_PREFIX}"
-}
-# initialise variables
-VIASH_DIRECTORY_MOUNTS=()
-
-# configure default docker automount prefix if it is unset
-if [ -z "${VIASH_DOCKER_AUTOMOUNT_PREFIX+x}" ]; then
-  VIASH_DOCKER_AUTOMOUNT_PREFIX="/viash_automount"
-fi
-
-# initialise docker variables
-VIASH_DOCKER_RUN_ARGS=(-i --rm)
-
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/fq_subsample/.config.vsh.yaml b/target/executable/fq_subsample/.config.vsh.yaml
index ef40cbf3..e432c498 100644
--- a/target/executable/fq_subsample/.config.vsh.yaml
+++ b/target/executable/fq_subsample/.config.vsh.yaml
@@ -88,6 +88,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -189,16 +192,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/fq_subsample"
   executable: "target/executable/fq_subsample/fq_subsample"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/fq_subsample/fq_subsample b/target/executable/fq_subsample/fq_subsample
index 9c0de661..9c3264ec 100755
--- a/target/executable/fq_subsample/fq_subsample
+++ b/target/executable/fq_subsample/fq_subsample
@@ -2,7 +2,7 @@
 
 # fq_subsample main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -169,46 +169,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "fq_subsample main"
-  echo ""
-  echo "fq subsample outputs a subset of records from single or paired FASTQ files."
-  echo ""
-  echo "Input:"
-  echo "    --input_1"
-  echo "        type: file, required parameter, file must exist"
-  echo "        First input fastq file to subsample. Accepts both raw and gzipped FASTQ"
-  echo "        inputs."
-  echo ""
-  echo "    --input_2"
-  echo "        type: file, file must exist"
-  echo "        Second input fastq files to subsample. Accepts both raw and gzipped"
-  echo "        FASTQ inputs."
-  echo ""
-  echo "Output:"
-  echo "    --output_1"
-  echo "        type: file, output, file must exist"
-  echo "        Sampled read 1 fastq files. Output will be gzipped if ends in \`.gz\`."
-  echo ""
-  echo "    --output_2"
-  echo "        type: file, output, file must exist"
-  echo "        Sampled read 2 fastq files. Output will be gzipped if ends in \`.gz\`."
-  echo ""
-  echo "Options:"
-  echo "    --probability"
-  echo "        type: double"
-  echo "        The probability a record is kept, as a percentage (0.0, 1.0). Cannot be"
-  echo "        used with \`record-count\`"
-  echo ""
-  echo "    --record_count"
-  echo "        type: integer"
-  echo "        The exact number of records to keep. Cannot be used with \`probability\`"
-  echo ""
-  echo "    --seed"
-  echo "        type: integer"
-  echo "        Seed to use for the random number generator"
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -493,9 +453,9 @@ mv target/release/fq /usr/local/bin/ && \
 cd / && rm -rf /fq
 
 LABEL org.opencontainers.image.description="Companion container for running component fq_subsample"
-LABEL org.opencontainers.image.created="2024-12-03T10:33:59Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:44Z"
 LABEL org.opencontainers.image.source="https://github.com/stjude-rust-labs/fq"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -610,6 +570,72 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "fq_subsample main"
+  echo ""
+  echo "fq subsample outputs a subset of records from single or paired FASTQ files."
+  echo ""
+  echo "Input:"
+  echo "    --input_1"
+  echo "        type: file, required parameter, file must exist"
+  echo "        First input fastq file to subsample. Accepts both raw and gzipped FASTQ"
+  echo "        inputs."
+  echo ""
+  echo "    --input_2"
+  echo "        type: file, file must exist"
+  echo "        Second input fastq files to subsample. Accepts both raw and gzipped"
+  echo "        FASTQ inputs."
+  echo ""
+  echo "Output:"
+  echo "    --output_1"
+  echo "        type: file, output, file must exist"
+  echo "        Sampled read 1 fastq files. Output will be gzipped if ends in \`.gz\`."
+  echo ""
+  echo "    --output_2"
+  echo "        type: file, output, file must exist"
+  echo "        Sampled read 2 fastq files. Output will be gzipped if ends in \`.gz\`."
+  echo ""
+  echo "Options:"
+  echo "    --probability"
+  echo "        type: double"
+  echo "        The probability a record is kept, as a percentage (0.0, 1.0). Cannot be"
+  echo "        used with \`record-count\`"
+  echo ""
+  echo "    --record_count"
+  echo "        type: integer"
+  echo "        The exact number of records to keep. Cannot be used with \`probability\`"
+  echo ""
+  echo "    --seed"
+  echo "        type: integer"
+  echo "        Seed to use for the random number generator"
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/gffread/.config.vsh.yaml b/target/executable/gffread/.config.vsh.yaml
index 6f7ecbfe..8329026d 100644
--- a/target/executable/gffread/.config.vsh.yaml
+++ b/target/executable/gffread/.config.vsh.yaml
@@ -582,6 +582,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -684,16 +687,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/gffread"
   executable: "target/executable/gffread/gffread"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/gffread/gffread b/target/executable/gffread/gffread
index bedae97f..b23177a7 100755
--- a/target/executable/gffread/gffread
+++ b/target/executable/gffread/gffread
@@ -2,7 +2,7 @@
 
 # gffread main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,6 +172,404 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
+
+# initialise variables
+VIASH_MODE='run'
+VIASH_ENGINE_ID='docker'
+
+######## Helper functions for setting up Docker images for viash ########
+# expects: ViashDockerBuild
+
+# ViashDockerInstallationCheck: check whether Docker is installed correctly
+#
+# examples:
+#   ViashDockerInstallationCheck
+function ViashDockerInstallationCheck {
+  ViashDebug "Checking whether Docker is installed"
+  if [ ! command -v docker &> /dev/null ]; then
+    ViashCritical "Docker doesn't seem to be installed. See 'https://docs.docker.com/get-docker/' for instructions."
+    exit 1
+  fi
+
+  ViashDebug "Checking whether the Docker daemon is running"
+  local save=$-; set +e
+  local docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
+  local out=$?
+  [[ $save =~ e ]] && set -e
+  if [ $out -ne 0 ]; then
+    ViashCritical "Docker daemon does not seem to be running. Try one of the following:"
+    ViashCritical "- Try running 'dockerd' in the command line"
+    ViashCritical "- See https://docs.docker.com/config/daemon/"
+    exit 1
+  fi
+}
+
+# ViashDockerRemoteTagCheck: check whether a Docker image is available 
+# on a remote. Assumes `docker login` has been performed, if relevant.
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   ViashDockerRemoteTagCheck python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerRemoteTagCheck sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerRemoteTagCheck {
+  docker manifest inspect $1 > /dev/null 2> /dev/null
+}
+
+# ViashDockerLocalTagCheck: check whether a Docker image is available locally
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   docker pull python:latest
+#   ViashDockerLocalTagCheck python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerLocalTagCheck sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerLocalTagCheck {
+  [ -n "$(docker images -q $1)" ]
+}
+
+# ViashDockerPull: pull a Docker image
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   ViashDockerPull python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerPull sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerPull {
+  ViashNotice "Checking if Docker image is available at '$1'"
+  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
+    docker pull $1 && return 0 || return 1
+  else
+    local save=$-; set +e
+    docker pull $1 2> /dev/null > /dev/null
+    local out=$?
+    [[ $save =~ e ]] && set -e
+    if [ $out -ne 0 ]; then
+      ViashWarning "Could not pull from '$1'. Docker image doesn't exist or is not accessible."
+    fi
+    return $out
+  fi
+}
+
+# ViashDockerPush: push a Docker image
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   ViashDockerPush python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerPush sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerPush {
+  ViashNotice "Pushing image to '$1'"
+  local save=$-; set +e
+  local out
+  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
+    docker push $1
+    out=$?
+  else
+    docker push $1 2> /dev/null > /dev/null
+    out=$?
+  fi
+  [[ $save =~ e ]] && set -e
+  if [ $out -eq 0 ]; then
+    ViashNotice "Container '$1' push succeeded."
+  else
+    ViashError "Container '$1' push errored. You might not be logged in or have the necessary permissions."
+  fi
+  return $out
+}
+
+# ViashDockerPullElseBuild: pull a Docker image, else build it
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# ViashDockerBuild    : a Bash function which builds a docker image, takes image identifier as argument.
+# examples:
+#   ViashDockerPullElseBuild mynewcomponent
+function ViashDockerPullElseBuild {
+  local save=$-; set +e
+  ViashDockerPull $1
+  local out=$?
+  [[ $save =~ e ]] && set -e
+  if [ $out -ne 0 ]; then
+    ViashDockerBuild $@
+  fi
+}
+
+# ViashDockerSetup: create a Docker image, according to specified docker setup strategy
+#
+# $1          : image identifier with format `[registry/]image[:tag]`
+# $2          : docker setup strategy, see DockerSetupStrategy.scala
+# examples:
+#   ViashDockerSetup mynewcomponent alwaysbuild
+function ViashDockerSetup {
+  local image_id="$1"
+  local setup_strategy="$2"
+  if [ "$setup_strategy" == "alwaysbuild" -o "$setup_strategy" == "build" -o "$setup_strategy" == "b" ]; then
+    ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+  elif [ "$setup_strategy" == "alwayspull" -o "$setup_strategy" == "pull" -o "$setup_strategy" == "p" ]; then
+    ViashDockerPull $image_id
+  elif [ "$setup_strategy" == "alwayspullelsebuild" -o "$setup_strategy" == "pullelsebuild" ]; then
+    ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+  elif [ "$setup_strategy" == "alwayspullelsecachedbuild" -o "$setup_strategy" == "pullelsecachedbuild" ]; then
+    ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+  elif [ "$setup_strategy" == "alwayscachedbuild" -o "$setup_strategy" == "cachedbuild" -o "$setup_strategy" == "cb" ]; then
+    ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+  elif [[ "$setup_strategy" =~ ^ifneedbe ]]; then
+    local save=$-; set +e
+    ViashDockerLocalTagCheck $image_id
+    local outCheck=$?
+    [[ $save =~ e ]] && set -e
+    if [ $outCheck -eq 0 ]; then
+      ViashInfo "Image $image_id already exists"
+    elif [ "$setup_strategy" == "ifneedbebuild" ]; then
+      ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+    elif [ "$setup_strategy" == "ifneedbecachedbuild" ]; then
+      ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+    elif [ "$setup_strategy" == "ifneedbepull" ]; then
+      ViashDockerPull $image_id
+    elif [ "$setup_strategy" == "ifneedbepullelsebuild" ]; then
+      ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+    elif [ "$setup_strategy" == "ifneedbepullelsecachedbuild" ]; then
+      ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+    else
+      ViashError "Unrecognised Docker strategy: $setup_strategy"
+      exit 1
+    fi
+  elif [ "$setup_strategy" == "push" -o "$setup_strategy" == "forcepush" -o "$setup_strategy" == "alwayspush" ]; then
+    ViashDockerPush "$image_id"
+  elif [ "$setup_strategy" == "pushifnotpresent" -o "$setup_strategy" == "gentlepush" -o "$setup_strategy" == "maybepush" ]; then
+    local save=$-; set +e
+    ViashDockerRemoteTagCheck $image_id
+    local outCheck=$?
+    [[ $save =~ e ]] && set -e
+    if [ $outCheck -eq 0 ]; then
+      ViashNotice "Container '$image_id' exists, doing nothing."
+    else
+      ViashNotice "Container '$image_id' does not yet exist."
+      ViashDockerPush "$image_id"
+    fi
+  elif [ "$setup_strategy" == "donothing" -o "$setup_strategy" == "meh" ]; then
+    ViashNotice "Skipping setup."
+  else
+    ViashError "Unrecognised Docker strategy: $setup_strategy"
+    exit 1
+  fi
+}
+
+# ViashDockerCheckCommands: Check whether a docker container has the required commands
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# $@                  : commands to verify being present
+# examples:
+#   ViashDockerCheckCommands bash:4.0 bash ps foo
+function ViashDockerCheckCommands {
+  local image_id="$1"
+  shift 1
+  local commands="$@"
+  local save=$-; set +e
+  local missing # mark 'missing' as local in advance, otherwise the exit code of the command will be missing and always be '0'
+  missing=$(docker run --rm --entrypoint=sh "$image_id" -c "for command in $commands; do command -v \$command >/dev/null 2>&1; if [ \$? -ne 0 ]; then echo \$command; exit 1; fi; done")
+  local outCheck=$?
+  [[ $save =~ e ]] && set -e
+  if [ $outCheck -ne 0 ]; then
+  	ViashError "Docker container '$image_id' does not contain command '$missing'."
+  	exit 1
+  fi
+}
+
+# ViashDockerBuild: build a docker image
+# $1                               : image identifier with format `[registry/]image[:tag]`
+# $...                             : additional arguments to pass to docker build
+# $VIASH_META_TEMP_DIR             : temporary directory to store dockerfile & optional resources in
+# $VIASH_META_NAME                 : name of the component
+# $VIASH_META_RESOURCES_DIR        : directory containing the resources
+# $VIASH_VERBOSITY                 : verbosity level
+# exit code $?                     : whether or not the image was built successfully
+function ViashDockerBuild {
+  local image_id="$1"
+  shift 1
+
+  # create temporary directory to store dockerfile & optional resources in
+  local tmpdir=$(mktemp -d "$VIASH_META_TEMP_DIR/dockerbuild-$VIASH_META_NAME-XXXXXX")
+  local dockerfile="$tmpdir/Dockerfile"
+  function clean_up {
+    rm -rf "$tmpdir"
+  }
+  trap clean_up EXIT
+
+  # store dockerfile and resources
+  ViashDockerfile "$VIASH_ENGINE_ID" > "$dockerfile"
+
+  # generate the build command
+  local docker_build_cmd="docker build -t '$image_id' $@ '$VIASH_META_RESOURCES_DIR' -f '$dockerfile'"
+
+  # build the container
+  ViashNotice "Building container '$image_id' with Dockerfile"
+  ViashInfo "$docker_build_cmd"
+  local save=$-; set +e
+  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
+    eval $docker_build_cmd
+  else
+    eval $docker_build_cmd &> "$tmpdir/docker_build.log"
+  fi
+
+  # check exit code
+  local out=$?
+  [[ $save =~ e ]] && set -e
+  if [ $out -ne 0 ]; then
+    ViashError "Error occurred while building container '$image_id'"
+    if [ $VIASH_VERBOSITY -lt $VIASH_LOGCODE_INFO ]; then
+      ViashError "Transcript: --------------------------------"
+      cat "$tmpdir/docker_build.log"
+      ViashError "End of transcript --------------------------"
+    fi
+    exit 1
+  fi
+}
+
+######## End of helper functions for setting up Docker images for viash ########
+
+# ViashDockerFile: print the dockerfile to stdout
+# $1    : engine identifier
+# return : dockerfile required to run this component
+# examples:
+#   ViashDockerFile
+function ViashDockerfile {
+  local engine_id="$1"
+
+  if [[ "$engine_id" == "docker" ]]; then
+    cat << 'VIASHDOCKER'
+FROM quay.io/biocontainers/gffread:0.12.7--hdcf5f25_3
+ENTRYPOINT []
+RUN echo "gffread: \"$(gffread --version 2>&1)\"" > /var/software_versions.txt
+
+LABEL org.opencontainers.image.authors="Emma Rousseau"
+LABEL org.opencontainers.image.description="Companion container for running component gffread"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:42Z"
+LABEL org.opencontainers.image.source="https://github.com/gpertea/gffread"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+LABEL org.opencontainers.image.version="main"
+
+VIASHDOCKER
+  fi
+}
+
+# ViashDockerBuildArgs: return the arguments to pass to docker build
+# $1    : engine identifier
+# return : arguments to pass to docker build
+function ViashDockerBuildArgs {
+  local engine_id="$1"
+
+  if [[ "$engine_id" == "docker" ]]; then
+    echo ""
+  fi
+}
+
+# ViashAbsolutePath: generate absolute path from relative path
+# borrowed from https://stackoverflow.com/a/21951256
+# $1     : relative filename
+# return : absolute path
+# examples:
+#   ViashAbsolutePath some_file.txt   # returns /path/to/some_file.txt
+#   ViashAbsolutePath /foo/bar/..     # returns /foo
+function ViashAbsolutePath {
+  local thePath
+  local parr
+  local outp
+  local len
+  if [[ ! "$1" =~ ^/ ]]; then
+    thePath="$PWD/$1"
+  else
+    thePath="$1"
+  fi
+  echo "$thePath" | (
+    IFS=/
+    read -a parr
+    declare -a outp
+    for i in "${parr[@]}"; do
+      case "$i" in
+      ''|.) continue ;;
+      ..)
+        len=${#outp[@]}
+        if ((len==0)); then
+          continue
+        else
+          unset outp[$((len-1))]
+        fi
+        ;;
+      *)
+        len=${#outp[@]}
+        outp[$len]="$i"
+      ;;
+      esac
+    done
+    echo /"${outp[*]}"
+  )
+}
+# ViashDockerAutodetectMount: auto configuring docker mounts from parameters
+# $1                             : The parameter value
+# returns                        : New parameter
+# $VIASH_DIRECTORY_MOUNTS        : Added another parameter to be passed to docker
+# $VIASH_DOCKER_AUTOMOUNT_PREFIX : The prefix to be used for the automounts
+# examples:
+#   ViashDockerAutodetectMount /path/to/bar      # returns '/viash_automount/path/to/bar'
+#   ViashDockerAutodetectMountArg /path/to/bar   # returns '--volume="/path/to:/viash_automount/path/to"'
+function ViashDockerAutodetectMount {
+  local abs_path=$(ViashAbsolutePath "$1")
+  local mount_source
+  local base_name
+  if [ -d "$abs_path" ]; then
+    mount_source="$abs_path"
+    base_name=""
+  else
+    mount_source=`dirname "$abs_path"`
+    base_name=`basename "$abs_path"`
+  fi
+  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
+  if [ -z "$base_name" ]; then
+    echo "$mount_target"
+  else
+    echo "$mount_target/$base_name"
+  fi
+}
+function ViashDockerAutodetectMountArg {
+  local abs_path=$(ViashAbsolutePath "$1")
+  local mount_source
+  local base_name
+  if [ -d "$abs_path" ]; then
+    mount_source="$abs_path"
+    base_name=""
+  else
+    mount_source=`dirname "$abs_path"`
+    base_name=`basename "$abs_path"`
+  fi
+  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
+  ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target"
+  echo "--volume=\"$mount_source:$mount_target\""
+}
+function ViashDockerStripAutomount {
+  local abs_path=$(ViashAbsolutePath "$1")
+  echo "${abs_path#$VIASH_DOCKER_AUTOMOUNT_PREFIX}"
+}
+# initialise variables
+VIASH_DIRECTORY_MOUNTS=()
+
+# configure default docker automount prefix if it is unset
+if [ -z "${VIASH_DOCKER_AUTOMOUNT_PREFIX+x}" ]; then
+  VIASH_DOCKER_AUTOMOUNT_PREFIX="/viash_automount"
+fi
+
+# initialise docker variables
+VIASH_DOCKER_RUN_ARGS=(-i --rm)
+
+
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
   echo "gffread main"
@@ -526,404 +924,32 @@ function ViashHelp {
   echo "        For --merge option, enforce --no_boundary but also discard overlapping"
   echo "        single-exon transcripts,"
   echo "        even on the opposite strand (can be combined with --rm_redudant)."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
 }
 
-# initialise variables
-VIASH_MODE='run'
-VIASH_ENGINE_ID='docker'
-
-######## Helper functions for setting up Docker images for viash ########
-# expects: ViashDockerBuild
-
-# ViashDockerInstallationCheck: check whether Docker is installed correctly
-#
-# examples:
-#   ViashDockerInstallationCheck
-function ViashDockerInstallationCheck {
-  ViashDebug "Checking whether Docker is installed"
-  if [ ! command -v docker &> /dev/null ]; then
-    ViashCritical "Docker doesn't seem to be installed. See 'https://docs.docker.com/get-docker/' for instructions."
-    exit 1
-  fi
-
-  ViashDebug "Checking whether the Docker daemon is running"
-  local save=$-; set +e
-  local docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
-  local out=$?
-  [[ $save =~ e ]] && set -e
-  if [ $out -ne 0 ]; then
-    ViashCritical "Docker daemon does not seem to be running. Try one of the following:"
-    ViashCritical "- Try running 'dockerd' in the command line"
-    ViashCritical "- See https://docs.docker.com/config/daemon/"
-    exit 1
-  fi
-}
-
-# ViashDockerRemoteTagCheck: check whether a Docker image is available 
-# on a remote. Assumes `docker login` has been performed, if relevant.
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   ViashDockerRemoteTagCheck python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerRemoteTagCheck sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerRemoteTagCheck {
-  docker manifest inspect $1 > /dev/null 2> /dev/null
-}
-
-# ViashDockerLocalTagCheck: check whether a Docker image is available locally
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   docker pull python:latest
-#   ViashDockerLocalTagCheck python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerLocalTagCheck sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerLocalTagCheck {
-  [ -n "$(docker images -q $1)" ]
-}
-
-# ViashDockerPull: pull a Docker image
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   ViashDockerPull python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerPull sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerPull {
-  ViashNotice "Checking if Docker image is available at '$1'"
-  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
-    docker pull $1 && return 0 || return 1
-  else
-    local save=$-; set +e
-    docker pull $1 2> /dev/null > /dev/null
-    local out=$?
-    [[ $save =~ e ]] && set -e
-    if [ $out -ne 0 ]; then
-      ViashWarning "Could not pull from '$1'. Docker image doesn't exist or is not accessible."
-    fi
-    return $out
-  fi
-}
-
-# ViashDockerPush: push a Docker image
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   ViashDockerPush python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerPush sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerPush {
-  ViashNotice "Pushing image to '$1'"
-  local save=$-; set +e
-  local out
-  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
-    docker push $1
-    out=$?
-  else
-    docker push $1 2> /dev/null > /dev/null
-    out=$?
-  fi
-  [[ $save =~ e ]] && set -e
-  if [ $out -eq 0 ]; then
-    ViashNotice "Container '$1' push succeeded."
-  else
-    ViashError "Container '$1' push errored. You might not be logged in or have the necessary permissions."
-  fi
-  return $out
-}
-
-# ViashDockerPullElseBuild: pull a Docker image, else build it
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# ViashDockerBuild    : a Bash function which builds a docker image, takes image identifier as argument.
-# examples:
-#   ViashDockerPullElseBuild mynewcomponent
-function ViashDockerPullElseBuild {
-  local save=$-; set +e
-  ViashDockerPull $1
-  local out=$?
-  [[ $save =~ e ]] && set -e
-  if [ $out -ne 0 ]; then
-    ViashDockerBuild $@
-  fi
-}
-
-# ViashDockerSetup: create a Docker image, according to specified docker setup strategy
-#
-# $1          : image identifier with format `[registry/]image[:tag]`
-# $2          : docker setup strategy, see DockerSetupStrategy.scala
-# examples:
-#   ViashDockerSetup mynewcomponent alwaysbuild
-function ViashDockerSetup {
-  local image_id="$1"
-  local setup_strategy="$2"
-  if [ "$setup_strategy" == "alwaysbuild" -o "$setup_strategy" == "build" -o "$setup_strategy" == "b" ]; then
-    ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-  elif [ "$setup_strategy" == "alwayspull" -o "$setup_strategy" == "pull" -o "$setup_strategy" == "p" ]; then
-    ViashDockerPull $image_id
-  elif [ "$setup_strategy" == "alwayspullelsebuild" -o "$setup_strategy" == "pullelsebuild" ]; then
-    ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-  elif [ "$setup_strategy" == "alwayspullelsecachedbuild" -o "$setup_strategy" == "pullelsecachedbuild" ]; then
-    ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-  elif [ "$setup_strategy" == "alwayscachedbuild" -o "$setup_strategy" == "cachedbuild" -o "$setup_strategy" == "cb" ]; then
-    ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-  elif [[ "$setup_strategy" =~ ^ifneedbe ]]; then
-    local save=$-; set +e
-    ViashDockerLocalTagCheck $image_id
-    local outCheck=$?
-    [[ $save =~ e ]] && set -e
-    if [ $outCheck -eq 0 ]; then
-      ViashInfo "Image $image_id already exists"
-    elif [ "$setup_strategy" == "ifneedbebuild" ]; then
-      ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-    elif [ "$setup_strategy" == "ifneedbecachedbuild" ]; then
-      ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-    elif [ "$setup_strategy" == "ifneedbepull" ]; then
-      ViashDockerPull $image_id
-    elif [ "$setup_strategy" == "ifneedbepullelsebuild" ]; then
-      ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-    elif [ "$setup_strategy" == "ifneedbepullelsecachedbuild" ]; then
-      ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-    else
-      ViashError "Unrecognised Docker strategy: $setup_strategy"
-      exit 1
-    fi
-  elif [ "$setup_strategy" == "push" -o "$setup_strategy" == "forcepush" -o "$setup_strategy" == "alwayspush" ]; then
-    ViashDockerPush "$image_id"
-  elif [ "$setup_strategy" == "pushifnotpresent" -o "$setup_strategy" == "gentlepush" -o "$setup_strategy" == "maybepush" ]; then
-    local save=$-; set +e
-    ViashDockerRemoteTagCheck $image_id
-    local outCheck=$?
-    [[ $save =~ e ]] && set -e
-    if [ $outCheck -eq 0 ]; then
-      ViashNotice "Container '$image_id' exists, doing nothing."
-    else
-      ViashNotice "Container '$image_id' does not yet exist."
-      ViashDockerPush "$image_id"
-    fi
-  elif [ "$setup_strategy" == "donothing" -o "$setup_strategy" == "meh" ]; then
-    ViashNotice "Skipping setup."
-  else
-    ViashError "Unrecognised Docker strategy: $setup_strategy"
-    exit 1
-  fi
-}
-
-# ViashDockerCheckCommands: Check whether a docker container has the required commands
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# $@                  : commands to verify being present
-# examples:
-#   ViashDockerCheckCommands bash:4.0 bash ps foo
-function ViashDockerCheckCommands {
-  local image_id="$1"
-  shift 1
-  local commands="$@"
-  local save=$-; set +e
-  local missing # mark 'missing' as local in advance, otherwise the exit code of the command will be missing and always be '0'
-  missing=$(docker run --rm --entrypoint=sh "$image_id" -c "for command in $commands; do command -v \$command >/dev/null 2>&1; if [ \$? -ne 0 ]; then echo \$command; exit 1; fi; done")
-  local outCheck=$?
-  [[ $save =~ e ]] && set -e
-  if [ $outCheck -ne 0 ]; then
-  	ViashError "Docker container '$image_id' does not contain command '$missing'."
-  	exit 1
-  fi
-}
-
-# ViashDockerBuild: build a docker image
-# $1                               : image identifier with format `[registry/]image[:tag]`
-# $...                             : additional arguments to pass to docker build
-# $VIASH_META_TEMP_DIR             : temporary directory to store dockerfile & optional resources in
-# $VIASH_META_NAME                 : name of the component
-# $VIASH_META_RESOURCES_DIR        : directory containing the resources
-# $VIASH_VERBOSITY                 : verbosity level
-# exit code $?                     : whether or not the image was built successfully
-function ViashDockerBuild {
-  local image_id="$1"
-  shift 1
-
-  # create temporary directory to store dockerfile & optional resources in
-  local tmpdir=$(mktemp -d "$VIASH_META_TEMP_DIR/dockerbuild-$VIASH_META_NAME-XXXXXX")
-  local dockerfile="$tmpdir/Dockerfile"
-  function clean_up {
-    rm -rf "$tmpdir"
-  }
-  trap clean_up EXIT
-
-  # store dockerfile and resources
-  ViashDockerfile "$VIASH_ENGINE_ID" > "$dockerfile"
-
-  # generate the build command
-  local docker_build_cmd="docker build -t '$image_id' $@ '$VIASH_META_RESOURCES_DIR' -f '$dockerfile'"
-
-  # build the container
-  ViashNotice "Building container '$image_id' with Dockerfile"
-  ViashInfo "$docker_build_cmd"
-  local save=$-; set +e
-  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
-    eval $docker_build_cmd
-  else
-    eval $docker_build_cmd &> "$tmpdir/docker_build.log"
-  fi
-
-  # check exit code
-  local out=$?
-  [[ $save =~ e ]] && set -e
-  if [ $out -ne 0 ]; then
-    ViashError "Error occurred while building container '$image_id'"
-    if [ $VIASH_VERBOSITY -lt $VIASH_LOGCODE_INFO ]; then
-      ViashError "Transcript: --------------------------------"
-      cat "$tmpdir/docker_build.log"
-      ViashError "End of transcript --------------------------"
-    fi
-    exit 1
-  fi
-}
-
-######## End of helper functions for setting up Docker images for viash ########
-
-# ViashDockerFile: print the dockerfile to stdout
-# $1    : engine identifier
-# return : dockerfile required to run this component
-# examples:
-#   ViashDockerFile
-function ViashDockerfile {
-  local engine_id="$1"
-
-  if [[ "$engine_id" == "docker" ]]; then
-    cat << 'VIASHDOCKER'
-FROM quay.io/biocontainers/gffread:0.12.7--hdcf5f25_3
-ENTRYPOINT []
-RUN echo "gffread: \"$(gffread --version 2>&1)\"" > /var/software_versions.txt
-
-LABEL org.opencontainers.image.authors="Emma Rousseau"
-LABEL org.opencontainers.image.description="Companion container for running component gffread"
-LABEL org.opencontainers.image.created="2024-12-03T10:33:54Z"
-LABEL org.opencontainers.image.source="https://github.com/gpertea/gffread"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-LABEL org.opencontainers.image.version="main"
-
-VIASHDOCKER
-  fi
-}
-
-# ViashDockerBuildArgs: return the arguments to pass to docker build
-# $1    : engine identifier
-# return : arguments to pass to docker build
-function ViashDockerBuildArgs {
-  local engine_id="$1"
-
-  if [[ "$engine_id" == "docker" ]]; then
-    echo ""
-  fi
-}
-
-# ViashAbsolutePath: generate absolute path from relative path
-# borrowed from https://stackoverflow.com/a/21951256
-# $1     : relative filename
-# return : absolute path
-# examples:
-#   ViashAbsolutePath some_file.txt   # returns /path/to/some_file.txt
-#   ViashAbsolutePath /foo/bar/..     # returns /foo
-function ViashAbsolutePath {
-  local thePath
-  local parr
-  local outp
-  local len
-  if [[ ! "$1" =~ ^/ ]]; then
-    thePath="$PWD/$1"
-  else
-    thePath="$1"
-  fi
-  echo "$thePath" | (
-    IFS=/
-    read -a parr
-    declare -a outp
-    for i in "${parr[@]}"; do
-      case "$i" in
-      ''|.) continue ;;
-      ..)
-        len=${#outp[@]}
-        if ((len==0)); then
-          continue
-        else
-          unset outp[$((len-1))]
-        fi
-        ;;
-      *)
-        len=${#outp[@]}
-        outp[$len]="$i"
-      ;;
-      esac
-    done
-    echo /"${outp[*]}"
-  )
-}
-# ViashDockerAutodetectMount: auto configuring docker mounts from parameters
-# $1                             : The parameter value
-# returns                        : New parameter
-# $VIASH_DIRECTORY_MOUNTS        : Added another parameter to be passed to docker
-# $VIASH_DOCKER_AUTOMOUNT_PREFIX : The prefix to be used for the automounts
-# examples:
-#   ViashDockerAutodetectMount /path/to/bar      # returns '/viash_automount/path/to/bar'
-#   ViashDockerAutodetectMountArg /path/to/bar   # returns '--volume="/path/to:/viash_automount/path/to"'
-function ViashDockerAutodetectMount {
-  local abs_path=$(ViashAbsolutePath "$1")
-  local mount_source
-  local base_name
-  if [ -d "$abs_path" ]; then
-    mount_source="$abs_path"
-    base_name=""
-  else
-    mount_source=`dirname "$abs_path"`
-    base_name=`basename "$abs_path"`
-  fi
-  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
-  if [ -z "$base_name" ]; then
-    echo "$mount_target"
-  else
-    echo "$mount_target/$base_name"
-  fi
-}
-function ViashDockerAutodetectMountArg {
-  local abs_path=$(ViashAbsolutePath "$1")
-  local mount_source
-  local base_name
-  if [ -d "$abs_path" ]; then
-    mount_source="$abs_path"
-    base_name=""
-  else
-    mount_source=`dirname "$abs_path"`
-    base_name=`basename "$abs_path"`
-  fi
-  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
-  ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target"
-  echo "--volume=\"$mount_source:$mount_target\""
-}
-function ViashDockerStripAutomount {
-  local abs_path=$(ViashAbsolutePath "$1")
-  echo "${abs_path#$VIASH_DOCKER_AUTOMOUNT_PREFIX}"
-}
-# initialise variables
-VIASH_DIRECTORY_MOUNTS=()
-
-# configure default docker automount prefix if it is unset
-if [ -z "${VIASH_DOCKER_AUTOMOUNT_PREFIX+x}" ]; then
-  VIASH_DOCKER_AUTOMOUNT_PREFIX="/viash_automount"
-fi
-
-# initialise docker variables
-VIASH_DOCKER_RUN_ARGS=(-i --rm)
-
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/kallisto/kallisto_index/.config.vsh.yaml b/target/executable/kallisto/kallisto_index/.config.vsh.yaml
index 702b8703..8f7e7725 100644
--- a/target/executable/kallisto/kallisto_index/.config.vsh.yaml
+++ b/target/executable/kallisto/kallisto_index/.config.vsh.yaml
@@ -113,6 +113,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -217,16 +220,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/kallisto/kallisto_index"
   executable: "target/executable/kallisto/kallisto_index/kallisto_index"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/kallisto/kallisto_index/kallisto_index b/target/executable/kallisto/kallisto_index/kallisto_index
index 838ec13f..13e01f32 100755
--- a/target/executable/kallisto/kallisto_index/kallisto_index
+++ b/target/executable/kallisto/kallisto_index/kallisto_index
@@ -2,7 +2,7 @@
 
 # kallisto_index main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -169,60 +169,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "kallisto_index main"
-  echo ""
-  echo "Build a Kallisto index for the transcriptome to use Kallisto in the"
-  echo "mapping-based mode."
-  echo ""
-  echo "Input:"
-  echo "    --input"
-  echo "        type: file, required parameter, file must exist"
-  echo "        Path to a FASTA-file containing the transcriptome sequences, either in"
-  echo "        plain text or"
-  echo "        compressed (.gz) format."
-  echo ""
-  echo "    --d_list"
-  echo "        type: file, file must exist"
-  echo "        Path to a FASTA-file containing sequences to mask from quantification."
-  echo ""
-  echo "Output:"
-  echo "    --index"
-  echo "        type: file, output, file must exist"
-  echo "        example: Kallisto_index"
-  echo ""
-  echo "Options:"
-  echo "    --kmer_size"
-  echo "        type: integer"
-  echo "        example: 31"
-  echo "        Kmer length passed to indexing step of pseudoaligners (default: '31')."
-  echo ""
-  echo "    --make_unique"
-  echo "        type: boolean_true"
-  echo "        Replace repeated target names with unique names."
-  echo ""
-  echo "    --aa"
-  echo "        type: boolean_true"
-  echo "        Generate index from a FASTA-file containing amino acid sequences."
-  echo ""
-  echo "    --distiguish"
-  echo "        type: boolean_true"
-  echo "        Generate index where sequences are distinguished by the sequence names."
-  echo ""
-  echo "    -m, --min_size"
-  echo "        type: integer"
-  echo "        Length of minimizers (default: automatically chosen)."
-  echo ""
-  echo "    -e, --ec_max_size"
-  echo "        type: integer"
-  echo "        Maximum number of targets in an equivalence class (default: no maximum)."
-  echo ""
-  echo "    -T, --tmp"
-  echo "        type: string"
-  echo "        example: tmp"
-  echo "        Path to a directory for temporary files."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -506,9 +452,9 @@ tar -xzf kallisto_linux-v0.50.1.tar.gz && \
 mv kallisto/kallisto /usr/local/bin/
 
 LABEL org.opencontainers.image.description="Companion container for running component kallisto kallisto_index"
-LABEL org.opencontainers.image.created="2024-12-03T10:33:53Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:45Z"
 LABEL org.opencontainers.image.source="https://github.com/pachterlab/kallisto"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -623,6 +569,86 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "kallisto_index main"
+  echo ""
+  echo "Build a Kallisto index for the transcriptome to use Kallisto in the"
+  echo "mapping-based mode."
+  echo ""
+  echo "Input:"
+  echo "    --input"
+  echo "        type: file, required parameter, file must exist"
+  echo "        Path to a FASTA-file containing the transcriptome sequences, either in"
+  echo "        plain text or"
+  echo "        compressed (.gz) format."
+  echo ""
+  echo "    --d_list"
+  echo "        type: file, file must exist"
+  echo "        Path to a FASTA-file containing sequences to mask from quantification."
+  echo ""
+  echo "Output:"
+  echo "    --index"
+  echo "        type: file, output, file must exist"
+  echo "        example: Kallisto_index"
+  echo ""
+  echo "Options:"
+  echo "    --kmer_size"
+  echo "        type: integer"
+  echo "        example: 31"
+  echo "        Kmer length passed to indexing step of pseudoaligners (default: '31')."
+  echo ""
+  echo "    --make_unique"
+  echo "        type: boolean_true"
+  echo "        Replace repeated target names with unique names."
+  echo ""
+  echo "    --aa"
+  echo "        type: boolean_true"
+  echo "        Generate index from a FASTA-file containing amino acid sequences."
+  echo ""
+  echo "    --distiguish"
+  echo "        type: boolean_true"
+  echo "        Generate index where sequences are distinguished by the sequence names."
+  echo ""
+  echo "    -m, --min_size"
+  echo "        type: integer"
+  echo "        Length of minimizers (default: automatically chosen)."
+  echo ""
+  echo "    -e, --ec_max_size"
+  echo "        type: integer"
+  echo "        Maximum number of targets in an equivalence class (default: no maximum)."
+  echo ""
+  echo "    -T, --tmp"
+  echo "        type: string"
+  echo "        example: tmp"
+  echo "        Path to a directory for temporary files."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/kallisto/kallisto_quant/.config.vsh.yaml b/target/executable/kallisto/kallisto_quant/.config.vsh.yaml
index 9e8d6ab2..a7905ede 100644
--- a/target/executable/kallisto/kallisto_quant/.config.vsh.yaml
+++ b/target/executable/kallisto/kallisto_quant/.config.vsh.yaml
@@ -137,6 +137,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -245,16 +248,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/kallisto/kallisto_quant"
   executable: "target/executable/kallisto/kallisto_quant/kallisto_quant"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/kallisto/kallisto_quant/kallisto_quant b/target/executable/kallisto/kallisto_quant/kallisto_quant
index 46f7605e..49416512 100755
--- a/target/executable/kallisto/kallisto_quant/kallisto_quant
+++ b/target/executable/kallisto/kallisto_quant/kallisto_quant
@@ -2,7 +2,7 @@
 
 # kallisto_quant main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -169,74 +169,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "kallisto_quant main"
-  echo ""
-  echo "Quantifying abundances of transcripts from RNA-Seq data, or more generally of"
-  echo "target sequences using high-throughput sequencing reads."
-  echo ""
-  echo "Input:"
-  echo "    --input"
-  echo "        type: file, required parameter, multiple values allowed, file must exist"
-  echo "        List of input FastQ files of size 1 and 2 for single-end and paired-end"
-  echo "        data, respectively."
-  echo ""
-  echo "    -i, --index"
-  echo "        type: file, required parameter, file must exist"
-  echo "        Kallisto genome index."
-  echo ""
-  echo "Output:"
-  echo "    -o, --output_dir"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        Directory to write output to."
-  echo ""
-  echo "    --log"
-  echo "        type: file, output, file must exist"
-  echo "        File containing log information from running kallisto quant"
-  echo ""
-  echo "Options:"
-  echo "    --single"
-  echo "        type: boolean_true"
-  echo "        Single end mode."
-  echo ""
-  echo "    --single_overhang"
-  echo "        type: boolean_true"
-  echo "        Include reads where unobserved rest of fragment is predicted to lie"
-  echo "        outside a transcript."
-  echo ""
-  echo "    --fr_stranded"
-  echo "        type: boolean_true"
-  echo "        Strand specific reads, first read forward."
-  echo ""
-  echo "    --rf_stranded"
-  echo "        type: boolean_true"
-  echo "        Strand specific reads, first read reverse."
-  echo ""
-  echo "    -l, --fragment_length"
-  echo "        type: double"
-  echo "        The estimated average fragment length."
-  echo ""
-  echo "    -s, --sd"
-  echo "        type: double"
-  echo "        The estimated standard deviation of the fragment length (default: -l, -s"
-  echo "        values are estimated"
-  echo "        from paired end data, but are required when using --single)."
-  echo ""
-  echo "    --plaintext"
-  echo "        type: boolean_true"
-  echo "        Output plaintext instead of HDF5."
-  echo ""
-  echo "    -b, --bootstrap_samples"
-  echo "        type: integer"
-  echo "        example: 0"
-  echo "        Number of bootstrap samples to draw. Default: '0'"
-  echo ""
-  echo "    --seed"
-  echo "        type: integer"
-  echo "        example: 42"
-  echo "        Random seed for bootstrap. Default: '42'"
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -522,9 +454,9 @@ mv kallisto/kallisto /usr/local/bin/
 RUN echo "kallisto: $(kallisto version | sed 's/kallisto, version //')" > /var/software_versions.txt
 
 LABEL org.opencontainers.image.description="Companion container for running component kallisto kallisto_quant"
-LABEL org.opencontainers.image.created="2024-12-03T10:33:54Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:44Z"
 LABEL org.opencontainers.image.source="https://github.com/pachterlab/kallisto"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -639,6 +571,100 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "kallisto_quant main"
+  echo ""
+  echo "Quantifying abundances of transcripts from RNA-Seq data, or more generally of"
+  echo "target sequences using high-throughput sequencing reads."
+  echo ""
+  echo "Input:"
+  echo "    --input"
+  echo "        type: file, required parameter, multiple values allowed, file must exist"
+  echo "        List of input FastQ files of size 1 and 2 for single-end and paired-end"
+  echo "        data, respectively."
+  echo ""
+  echo "    -i, --index"
+  echo "        type: file, required parameter, file must exist"
+  echo "        Kallisto genome index."
+  echo ""
+  echo "Output:"
+  echo "    -o, --output_dir"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        Directory to write output to."
+  echo ""
+  echo "    --log"
+  echo "        type: file, output, file must exist"
+  echo "        File containing log information from running kallisto quant"
+  echo ""
+  echo "Options:"
+  echo "    --single"
+  echo "        type: boolean_true"
+  echo "        Single end mode."
+  echo ""
+  echo "    --single_overhang"
+  echo "        type: boolean_true"
+  echo "        Include reads where unobserved rest of fragment is predicted to lie"
+  echo "        outside a transcript."
+  echo ""
+  echo "    --fr_stranded"
+  echo "        type: boolean_true"
+  echo "        Strand specific reads, first read forward."
+  echo ""
+  echo "    --rf_stranded"
+  echo "        type: boolean_true"
+  echo "        Strand specific reads, first read reverse."
+  echo ""
+  echo "    -l, --fragment_length"
+  echo "        type: double"
+  echo "        The estimated average fragment length."
+  echo ""
+  echo "    -s, --sd"
+  echo "        type: double"
+  echo "        The estimated standard deviation of the fragment length (default: -l, -s"
+  echo "        values are estimated"
+  echo "        from paired end data, but are required when using --single)."
+  echo ""
+  echo "    --plaintext"
+  echo "        type: boolean_true"
+  echo "        Output plaintext instead of HDF5."
+  echo ""
+  echo "    -b, --bootstrap_samples"
+  echo "        type: integer"
+  echo "        example: 0"
+  echo "        Number of bootstrap samples to draw. Default: '0'"
+  echo ""
+  echo "    --seed"
+  echo "        type: integer"
+  echo "        example: 42"
+  echo "        Random seed for bootstrap. Default: '42'"
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/lofreq/lofreq_call/.config.vsh.yaml b/target/executable/lofreq/lofreq_call/.config.vsh.yaml
index 13dc43f8..6b60791a 100644
--- a/target/executable/lofreq/lofreq_call/.config.vsh.yaml
+++ b/target/executable/lofreq/lofreq_call/.config.vsh.yaml
@@ -403,6 +403,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -506,16 +509,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/lofreq/lofreq_call"
   executable: "target/executable/lofreq/lofreq_call/lofreq_call"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/lofreq/lofreq_call/lofreq_call b/target/executable/lofreq/lofreq_call/lofreq_call
index a7b4e890..5520d8aa 100755
--- a/target/executable/lofreq/lofreq_call/lofreq_call
+++ b/target/executable/lofreq/lofreq_call/lofreq_call
@@ -2,7 +2,7 @@
 
 # lofreq_call main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,209 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "lofreq_call main"
-  echo ""
-  echo "Call variants from a BAM file."
-  echo ""
-  echo "LoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for"
-  echo "inferring SNVs and indels from next-generation sequencing data. It makes full"
-  echo "use of base-call qualities and other sources of errors inherent in sequencing"
-  echo "(e.g. mapping or base/indel alignment uncertainty), which are usually ignored by"
-  echo "other methods or only used for filtering."
-  echo ""
-  echo "LoFreq* can run on almost any type of aligned sequencing data (e.g. Illumina,"
-  echo "IonTorrent or Pacbio) since no machine- or sequencing-technology dependent"
-  echo "thresholds are used. It automatically adapts to changes in coverage and"
-  echo "sequencing quality and can therefore be applied to a variety of data-sets e.g."
-  echo "viral/quasispecies, bacterial, metagenomics or somatic data."
-  echo ""
-  echo "LoFreq* is very sensitive; most notably, it is able to predict variants below"
-  echo "the average base-call quality (i.e. sequencing error rate). Each variant call is"
-  echo "assigned a p-value which allows for rigorous false positive control. Even though"
-  echo "it uses no approximations or heuristics, it is very efficient due to several"
-  echo "runtime optimizations and also provides a (pseudo-)parallel implementation."
-  echo "LoFreq* is generic and fast enough to be applied to high-coverage data and large"
-  echo "genomes. On a single processor it takes a minute to analyze Dengue genome"
-  echo "sequencing data with nearly 4000X coverage, roughly one hour to call SNVs on a"
-  echo "600X coverage E.coli genome and also roughly an hour to run on a 100X coverage"
-  echo "human exome dataset."
-  echo ""
-  echo "Inputs:"
-  echo "    --input"
-  echo "        type: file, required parameter, file must exist"
-  echo "        example: normal.bam"
-  echo "        Input BAM file."
-  echo ""
-  echo "    --input_bai"
-  echo "        type: file, required parameter, file must exist"
-  echo "        example: normal.bai"
-  echo "        Index file for the input BAM file."
-  echo ""
-  echo "    -f, --ref"
-  echo "        type: file, required parameter, file must exist"
-  echo "        example: reference.fasta"
-  echo "        Indexed reference fasta file (gzip supported). Default: none."
-  echo ""
-  echo "Outputs:"
-  echo "    -o, --out"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        example: output.vcf"
-  echo "        Vcf output file. Default: stdout."
-  echo ""
-  echo "Arguments:"
-  echo "    -r, --region"
-  echo "        type: string"
-  echo "        example: chr1:1000-2000"
-  echo "        Limit calls to this region (chrom:start-end). Default: none."
-  echo ""
-  echo "    -l, --bed"
-  echo "        type: file, file must exist"
-  echo "        example: regions.bed"
-  echo "        List of positions (chr pos) or regions (BED). Default: none."
-  echo ""
-  echo "    -q, --min_bq"
-  echo "        type: integer"
-  echo "        example: 6"
-  echo "        Skip any base with baseQ smaller than INT. Default: 6."
-  echo ""
-  echo "    -Q, --min_alt_bq"
-  echo "        type: integer"
-  echo "        example: 6"
-  echo "        Skip alternate bases with baseQ smaller than INT. Default: 6."
-  echo ""
-  echo "    -R, --def_alt_bq"
-  echo "        type: integer"
-  echo "        example: 0"
-  echo "        Overwrite baseQs of alternate bases (that passed bq filter) with this"
-  echo "        value (-1: use median ref-bq; 0: keep). Default: 0."
-  echo ""
-  echo "    -j, --min_jq"
-  echo "        type: integer"
-  echo "        example: 0"
-  echo "        Skip any base with joinedQ smaller than INT. Default: 0."
-  echo ""
-  echo "    -J, --min_alt_jq"
-  echo "        type: integer"
-  echo "        example: 0"
-  echo "        Skip alternate bases with joinedQ smaller than INT. Default: 0."
-  echo ""
-  echo "    -K, --def_alt_jq"
-  echo "        type: integer"
-  echo "        example: 0"
-  echo "        Overwrite joinedQs of alternate bases (that passed jq filter) with this"
-  echo "        value (-1: use median ref-bq; 0: keep). Default: 0."
-  echo ""
-  echo "    -B, --no_baq"
-  echo "        type: boolean_true"
-  echo "        Disable use of base-alignment quality (BAQ)."
-  echo ""
-  echo "    -A, --no_idaq"
-  echo "        type: boolean_true"
-  echo "        Don't use IDAQ values (NOT recommended under ANY circumstances other"
-  echo "        than debugging)."
-  echo ""
-  echo "    -D, --del_baq"
-  echo "        type: boolean_true"
-  echo "        Delete pre-existing BAQ values, i.e. compute even if already present in"
-  echo "        BAM."
-  echo ""
-  echo "    -e, --no_ext_baq"
-  echo "        type: boolean_true"
-  echo "        Use 'normal' BAQ (samtools default) instead of extended BAQ (both"
-  echo "        computed on the fly if not already present in lb tag)."
-  echo ""
-  echo "    -m, --min_mq"
-  echo "        type: integer"
-  echo "        example: 0"
-  echo "        Skip reads with mapping quality smaller than INT. Default: 0."
-  echo ""
-  echo "    -M, --max_mq"
-  echo "        type: integer"
-  echo "        example: 255"
-  echo "        Cap mapping quality at INT. Default: 255."
-  echo ""
-  echo "    -N, --no_mq"
-  echo "        type: boolean_true"
-  echo "        Don't merge mapping quality in LoFreq's model."
-  echo ""
-  echo "    --call_indels"
-  echo "        type: boolean_true"
-  echo "        Enable indel calls (note: preprocess your file to include indel"
-  echo "        alignment qualities!)."
-  echo ""
-  echo "    --only_indels"
-  echo "        type: boolean_true"
-  echo "        Only call indels; no SNVs."
-  echo ""
-  echo "    -s, --src_qual"
-  echo "        type: boolean_true"
-  echo "        Enable computation of source quality."
-  echo ""
-  echo "    -S, --ign_vcf"
-  echo "        type: file, file must exist"
-  echo "        example: variants.vcf"
-  echo "        Ignore variants in this vcf file for source quality computation."
-  echo "        Multiple files can be given separated by commas."
-  echo ""
-  echo "    -T, --def_nm_q"
-  echo "        type: integer"
-  echo "        example: -1"
-  echo "        If >= 0, then replace non-match base qualities with this default value."
-  echo "        Default: -1."
-  echo ""
-  echo "    -a, --sig"
-  echo "        type: double"
-  echo "        example: 0.01"
-  echo "        P-Value cutoff / significance level. Default: 0.010000."
-  echo ""
-  echo "    -b, --bonf"
-  echo "        type: string"
-  echo "        example: dynamic"
-  echo "        Bonferroni factor. 'dynamic' (increase per actually performed test) or"
-  echo "        INT. Default: Dynamic."
-  echo ""
-  echo "    -C, --min_cov"
-  echo "        type: integer"
-  echo "        example: 1"
-  echo "        Test only positions having at least this coverage. Default: 1."
-  echo "        (note: without --no-default-filter default filters (incl. coverage) kick"
-  echo "        in after predictions are done)."
-  echo ""
-  echo "    -d, --max_depth"
-  echo "        type: integer"
-  echo "        example: 1000000"
-  echo "        Cap coverage at this depth. Default: 1000000."
-  echo ""
-  echo "    --illumina_13"
-  echo "        type: boolean_true"
-  echo "        Assume the quality is Illumina-1.3-1.7/ASCII+64 encoded."
-  echo ""
-  echo "    --use_orphan"
-  echo "        type: boolean_true"
-  echo "        Count anomalous read pairs (i.e. where mate is not aligned properly)."
-  echo ""
-  echo "    --plp_summary_only"
-  echo "        type: boolean_true"
-  echo "        No variant calling. Just output pileup summary per column."
-  echo ""
-  echo "    --no_default_filter"
-  echo "        type: boolean_true"
-  echo "        Don't run default 'lofreq filter' automatically after calling variants."
-  echo ""
-  echo "    --force_overwrite"
-  echo "        type: boolean_true"
-  echo "        Overwrite any existing output."
-  echo ""
-  echo "    --verbose"
-  echo "        type: boolean_true"
-  echo "        Be verbose."
-  echo ""
-  echo "    --debug"
-  echo "        type: boolean_true"
-  echo "        Enable debugging."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -656,9 +453,9 @@ echo "lofreq: $version" > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Kai Waldrant"
 LABEL org.opencontainers.image.description="Companion container for running component lofreq lofreq_call"
-LABEL org.opencontainers.image.created="2024-12-03T10:34:05Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:43Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -773,6 +570,235 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "lofreq_call main"
+  echo ""
+  echo "Call variants from a BAM file."
+  echo ""
+  echo "LoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for"
+  echo "inferring SNVs and indels from next-generation sequencing data. It makes full"
+  echo "use of base-call qualities and other sources of errors inherent in sequencing"
+  echo "(e.g. mapping or base/indel alignment uncertainty), which are usually ignored by"
+  echo "other methods or only used for filtering."
+  echo ""
+  echo "LoFreq* can run on almost any type of aligned sequencing data (e.g. Illumina,"
+  echo "IonTorrent or Pacbio) since no machine- or sequencing-technology dependent"
+  echo "thresholds are used. It automatically adapts to changes in coverage and"
+  echo "sequencing quality and can therefore be applied to a variety of data-sets e.g."
+  echo "viral/quasispecies, bacterial, metagenomics or somatic data."
+  echo ""
+  echo "LoFreq* is very sensitive; most notably, it is able to predict variants below"
+  echo "the average base-call quality (i.e. sequencing error rate). Each variant call is"
+  echo "assigned a p-value which allows for rigorous false positive control. Even though"
+  echo "it uses no approximations or heuristics, it is very efficient due to several"
+  echo "runtime optimizations and also provides a (pseudo-)parallel implementation."
+  echo "LoFreq* is generic and fast enough to be applied to high-coverage data and large"
+  echo "genomes. On a single processor it takes a minute to analyze Dengue genome"
+  echo "sequencing data with nearly 4000X coverage, roughly one hour to call SNVs on a"
+  echo "600X coverage E.coli genome and also roughly an hour to run on a 100X coverage"
+  echo "human exome dataset."
+  echo ""
+  echo "Inputs:"
+  echo "    --input"
+  echo "        type: file, required parameter, file must exist"
+  echo "        example: normal.bam"
+  echo "        Input BAM file."
+  echo ""
+  echo "    --input_bai"
+  echo "        type: file, required parameter, file must exist"
+  echo "        example: normal.bai"
+  echo "        Index file for the input BAM file."
+  echo ""
+  echo "    -f, --ref"
+  echo "        type: file, required parameter, file must exist"
+  echo "        example: reference.fasta"
+  echo "        Indexed reference fasta file (gzip supported). Default: none."
+  echo ""
+  echo "Outputs:"
+  echo "    -o, --out"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        example: output.vcf"
+  echo "        Vcf output file. Default: stdout."
+  echo ""
+  echo "Arguments:"
+  echo "    -r, --region"
+  echo "        type: string"
+  echo "        example: chr1:1000-2000"
+  echo "        Limit calls to this region (chrom:start-end). Default: none."
+  echo ""
+  echo "    -l, --bed"
+  echo "        type: file, file must exist"
+  echo "        example: regions.bed"
+  echo "        List of positions (chr pos) or regions (BED). Default: none."
+  echo ""
+  echo "    -q, --min_bq"
+  echo "        type: integer"
+  echo "        example: 6"
+  echo "        Skip any base with baseQ smaller than INT. Default: 6."
+  echo ""
+  echo "    -Q, --min_alt_bq"
+  echo "        type: integer"
+  echo "        example: 6"
+  echo "        Skip alternate bases with baseQ smaller than INT. Default: 6."
+  echo ""
+  echo "    -R, --def_alt_bq"
+  echo "        type: integer"
+  echo "        example: 0"
+  echo "        Overwrite baseQs of alternate bases (that passed bq filter) with this"
+  echo "        value (-1: use median ref-bq; 0: keep). Default: 0."
+  echo ""
+  echo "    -j, --min_jq"
+  echo "        type: integer"
+  echo "        example: 0"
+  echo "        Skip any base with joinedQ smaller than INT. Default: 0."
+  echo ""
+  echo "    -J, --min_alt_jq"
+  echo "        type: integer"
+  echo "        example: 0"
+  echo "        Skip alternate bases with joinedQ smaller than INT. Default: 0."
+  echo ""
+  echo "    -K, --def_alt_jq"
+  echo "        type: integer"
+  echo "        example: 0"
+  echo "        Overwrite joinedQs of alternate bases (that passed jq filter) with this"
+  echo "        value (-1: use median ref-bq; 0: keep). Default: 0."
+  echo ""
+  echo "    -B, --no_baq"
+  echo "        type: boolean_true"
+  echo "        Disable use of base-alignment quality (BAQ)."
+  echo ""
+  echo "    -A, --no_idaq"
+  echo "        type: boolean_true"
+  echo "        Don't use IDAQ values (NOT recommended under ANY circumstances other"
+  echo "        than debugging)."
+  echo ""
+  echo "    -D, --del_baq"
+  echo "        type: boolean_true"
+  echo "        Delete pre-existing BAQ values, i.e. compute even if already present in"
+  echo "        BAM."
+  echo ""
+  echo "    -e, --no_ext_baq"
+  echo "        type: boolean_true"
+  echo "        Use 'normal' BAQ (samtools default) instead of extended BAQ (both"
+  echo "        computed on the fly if not already present in lb tag)."
+  echo ""
+  echo "    -m, --min_mq"
+  echo "        type: integer"
+  echo "        example: 0"
+  echo "        Skip reads with mapping quality smaller than INT. Default: 0."
+  echo ""
+  echo "    -M, --max_mq"
+  echo "        type: integer"
+  echo "        example: 255"
+  echo "        Cap mapping quality at INT. Default: 255."
+  echo ""
+  echo "    -N, --no_mq"
+  echo "        type: boolean_true"
+  echo "        Don't merge mapping quality in LoFreq's model."
+  echo ""
+  echo "    --call_indels"
+  echo "        type: boolean_true"
+  echo "        Enable indel calls (note: preprocess your file to include indel"
+  echo "        alignment qualities!)."
+  echo ""
+  echo "    --only_indels"
+  echo "        type: boolean_true"
+  echo "        Only call indels; no SNVs."
+  echo ""
+  echo "    -s, --src_qual"
+  echo "        type: boolean_true"
+  echo "        Enable computation of source quality."
+  echo ""
+  echo "    -S, --ign_vcf"
+  echo "        type: file, file must exist"
+  echo "        example: variants.vcf"
+  echo "        Ignore variants in this vcf file for source quality computation."
+  echo "        Multiple files can be given separated by commas."
+  echo ""
+  echo "    -T, --def_nm_q"
+  echo "        type: integer"
+  echo "        example: -1"
+  echo "        If >= 0, then replace non-match base qualities with this default value."
+  echo "        Default: -1."
+  echo ""
+  echo "    -a, --sig"
+  echo "        type: double"
+  echo "        example: 0.01"
+  echo "        P-Value cutoff / significance level. Default: 0.010000."
+  echo ""
+  echo "    -b, --bonf"
+  echo "        type: string"
+  echo "        example: dynamic"
+  echo "        Bonferroni factor. 'dynamic' (increase per actually performed test) or"
+  echo "        INT. Default: Dynamic."
+  echo ""
+  echo "    -C, --min_cov"
+  echo "        type: integer"
+  echo "        example: 1"
+  echo "        Test only positions having at least this coverage. Default: 1."
+  echo "        (note: without --no-default-filter default filters (incl. coverage) kick"
+  echo "        in after predictions are done)."
+  echo ""
+  echo "    -d, --max_depth"
+  echo "        type: integer"
+  echo "        example: 1000000"
+  echo "        Cap coverage at this depth. Default: 1000000."
+  echo ""
+  echo "    --illumina_13"
+  echo "        type: boolean_true"
+  echo "        Assume the quality is Illumina-1.3-1.7/ASCII+64 encoded."
+  echo ""
+  echo "    --use_orphan"
+  echo "        type: boolean_true"
+  echo "        Count anomalous read pairs (i.e. where mate is not aligned properly)."
+  echo ""
+  echo "    --plp_summary_only"
+  echo "        type: boolean_true"
+  echo "        No variant calling. Just output pileup summary per column."
+  echo ""
+  echo "    --no_default_filter"
+  echo "        type: boolean_true"
+  echo "        Don't run default 'lofreq filter' automatically after calling variants."
+  echo ""
+  echo "    --force_overwrite"
+  echo "        type: boolean_true"
+  echo "        Overwrite any existing output."
+  echo ""
+  echo "    --verbose"
+  echo "        type: boolean_true"
+  echo "        Be verbose."
+  echo ""
+  echo "    --debug"
+  echo "        type: boolean_true"
+  echo "        Enable debugging."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml b/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml
index 3501690d..216c0ea3 100644
--- a/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml
+++ b/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml
@@ -109,6 +109,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -214,16 +217,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/lofreq/lofreq_indelqual"
   executable: "target/executable/lofreq/lofreq_indelqual/lofreq_indelqual"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual b/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual
index 387537d0..b612b1d5 100755
--- a/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual
+++ b/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual
@@ -2,7 +2,7 @@
 
 # lofreq_indelqual main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,54 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "lofreq_indelqual main"
-  echo ""
-  echo "Insert indel qualities into BAM file (required for indel predictions)."
-  echo ""
-  echo "The preferred way of inserting indel qualities should be via GATK's BQSR (>=2)"
-  echo "If that's not possible, use this subcommand."
-  echo "The command has two modes: 'uniform' and 'dindel':"
-  echo "- 'uniform' will assign a given value uniformly, whereas"
-  echo "- 'dindel' will insert indel qualities based on Dindel (PMID 20980555)."
-  echo "Both will overwrite any existing values."
-  echo "Do not realign your BAM file afterwards!"
-  echo ""
-  echo "Inputs:"
-  echo "    --input"
-  echo "        type: file, required parameter, file must exist"
-  echo "        example: normal.bam"
-  echo "        Input BAM file."
-  echo ""
-  echo "    -f, --ref"
-  echo "        type: file, file must exist"
-  echo "        example: reference.fasta"
-  echo "        Reference sequence used for mapping (Only required for --dindel)."
-  echo ""
-  echo "Outputs:"
-  echo "    -o, --out"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        example: output.bam"
-  echo "        Output BAM file."
-  echo ""
-  echo "Arguments:"
-  echo "    -u, --uniform"
-  echo "        type: string"
-  echo "        example: 50,50"
-  echo "        Add this indel quality uniformly to all bases. Use two comma separated"
-  echo "        values to specify insertion and deletion quality separately. (clashes"
-  echo "        with --dindel)."
-  echo ""
-  echo "    --dindel"
-  echo "        type: boolean_true"
-  echo "        Add Dindel's indel qualities (Illumina specific) (clashes with -u; needs"
-  echo "        --ref)."
-  echo ""
-  echo "    --verbose"
-  echo "        type: boolean_true"
-  echo "        Be verbose."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -501,9 +453,9 @@ echo "lofreq: $version" > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Kai Waldrant"
 LABEL org.opencontainers.image.description="Companion container for running component lofreq lofreq_indelqual"
-LABEL org.opencontainers.image.created="2024-12-03T10:34:05Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:43Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -618,6 +570,80 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "lofreq_indelqual main"
+  echo ""
+  echo "Insert indel qualities into BAM file (required for indel predictions)."
+  echo ""
+  echo "The preferred way of inserting indel qualities should be via GATK's BQSR (>=2)"
+  echo "If that's not possible, use this subcommand."
+  echo "The command has two modes: 'uniform' and 'dindel':"
+  echo "- 'uniform' will assign a given value uniformly, whereas"
+  echo "- 'dindel' will insert indel qualities based on Dindel (PMID 20980555)."
+  echo "Both will overwrite any existing values."
+  echo "Do not realign your BAM file afterwards!"
+  echo ""
+  echo "Inputs:"
+  echo "    --input"
+  echo "        type: file, required parameter, file must exist"
+  echo "        example: normal.bam"
+  echo "        Input BAM file."
+  echo ""
+  echo "    -f, --ref"
+  echo "        type: file, file must exist"
+  echo "        example: reference.fasta"
+  echo "        Reference sequence used for mapping (Only required for --dindel)."
+  echo ""
+  echo "Outputs:"
+  echo "    -o, --out"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        example: output.bam"
+  echo "        Output BAM file."
+  echo ""
+  echo "Arguments:"
+  echo "    -u, --uniform"
+  echo "        type: string"
+  echo "        example: 50,50"
+  echo "        Add this indel quality uniformly to all bases. Use two comma separated"
+  echo "        values to specify insertion and deletion quality separately. (clashes"
+  echo "        with --dindel)."
+  echo ""
+  echo "    --dindel"
+  echo "        type: boolean_true"
+  echo "        Add Dindel's indel qualities (Illumina specific) (clashes with -u; needs"
+  echo "        --ref)."
+  echo ""
+  echo "    --verbose"
+  echo "        type: boolean_true"
+  echo "        Be verbose."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/multiqc/.config.vsh.yaml b/target/executable/multiqc/.config.vsh.yaml
index 225831b9..8826f0ae 100644
--- a/target/executable/multiqc/.config.vsh.yaml
+++ b/target/executable/multiqc/.config.vsh.yaml
@@ -357,6 +357,9 @@ info:
     doi: "10.1093/bioinformatics/btw354"
   licence: "GPL v3 or later"
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -455,16 +458,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/multiqc"
   executable: "target/executable/multiqc/multiqc"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/multiqc/multiqc b/target/executable/multiqc/multiqc
index 3b25f831..debdcfd8 100755
--- a/target/executable/multiqc/multiqc
+++ b/target/executable/multiqc/multiqc
@@ -2,7 +2,7 @@
 
 # multiqc main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,191 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "multiqc main"
-  echo ""
-  echo "MultiQC aggregates results from bioinformatics analyses across many samples into"
-  echo "a single report."
-  echo "It searches a given directory for analysis logs and compiles a HTML report. It's"
-  echo "a general use tool, perfect for summarising the output from numerous"
-  echo "bioinformatics tools."
-  echo ""
-  echo "Input:"
-  echo "    --input"
-  echo "        type: file, required parameter, multiple values allowed, file must exist"
-  echo "        example: data/results"
-  echo "        File paths to be searched for analysis results to be included in the"
-  echo "        report."
-  echo ""
-  echo "Ouput:"
-  echo "    --output_report"
-  echo "        type: file, output"
-  echo "        example: multiqc_report.html"
-  echo "        Filepath of the generated report."
-  echo ""
-  echo "    --output_data"
-  echo "        type: file, output"
-  echo "        example: multiqc_data"
-  echo "        Output directory for parsed data files. If not provided, parsed data"
-  echo "        will not be published."
-  echo ""
-  echo "    --output_plots"
-  echo "        type: file, output"
-  echo "        example: multiqc_plots"
-  echo "        Output directory for generated plots. If not provided, plots will not be"
-  echo "        published."
-  echo ""
-  echo "Modules and analyses to run:"
-  echo "    --include_modules"
-  echo "        type: string, multiple values allowed"
-  echo "        example: fastqc;cutadapt"
-  echo "        Use only these module"
-  echo ""
-  echo "    --exclude_modules"
-  echo "        type: string, multiple values allowed"
-  echo "        example: fastqc;cutadapt"
-  echo "        Do not use only these modules"
-  echo ""
-  echo "    --ignore_analysis"
-  echo "        type: string, multiple values allowed"
-  echo "        example: run_one/*;run_two/*"
-  echo ""
-  echo "    --ignore_samples"
-  echo "        type: string, multiple values allowed"
-  echo "        example: sample_1*;sample_3*"
-  echo ""
-  echo "    --ignore_symlinks"
-  echo "        type: boolean_true"
-  echo "        Ignore symlinked directories and files"
-  echo ""
-  echo "Sample name handling:"
-  echo "    --dirs"
-  echo "        type: boolean_true"
-  echo "        Prepend directory to sample names to avoid clashing filenames"
-  echo ""
-  echo "    --dirs_depth"
-  echo "        type: integer"
-  echo "        Prepend n directories to sample names. Negative number to take from"
-  echo "        start of path."
-  echo ""
-  echo "    --full_names"
-  echo "        type: boolean_true"
-  echo "        Do not clean the sample names (leave as full file name)"
-  echo ""
-  echo "    --fn_as_s_name"
-  echo "        type: boolean_true"
-  echo "        Use the log filename as the sample name"
-  echo ""
-  echo "    --replace_names"
-  echo "        type: file, file must exist"
-  echo "        example: replace_names.tsv"
-  echo "        TSV file to rename sample names during report generation"
-  echo ""
-  echo "Report Customisation:"
-  echo "    --title"
-  echo "        type: string"
-  echo "        Report title. Printed as page header, used for filename if not otherwise"
-  echo "        specified."
-  echo ""
-  echo "    --comment"
-  echo "        type: string"
-  echo "        Custom comment, will be printed at the top of the report."
-  echo ""
-  echo "    --template"
-  echo "        type: string"
-  echo "        choices: [ default, gathered, geo, highcharts, sections, simple ]"
-  echo "        Report template to use."
-  echo ""
-  echo "    --sample_names"
-  echo "        type: file, file must exist"
-  echo "        example: sample_names.tsv"
-  echo "        TSV file containing alternative sample names for renaming buttons in the"
-  echo "        report."
-  echo ""
-  echo "    --sample_filters"
-  echo "        type: file, file must exist"
-  echo "        example: sample_filters.tsv"
-  echo "        TSV file containing show/hide patterns for the report"
-  echo ""
-  echo "    --custom_css_file"
-  echo "        type: file, file must exist"
-  echo "        example: custom_style_sheet.css"
-  echo "        Custom CSS file to add to the final report"
-  echo ""
-  echo "    --profile_runtime"
-  echo "        type: boolean_true"
-  echo "        Add analysis of how long MultiQC takes to run to the report"
-  echo ""
-  echo "MultiQC behaviour:"
-  echo "    --verbose"
-  echo "        type: boolean_true"
-  echo "        Increase output verbosity."
-  echo ""
-  echo "    --quiet"
-  echo "        type: boolean_true"
-  echo "        Only show log warnings"
-  echo ""
-  echo "    --strict"
-  echo "        type: boolean_true"
-  echo "        Don't catch exceptions, run additional code checks to help development."
-  echo ""
-  echo "    --development"
-  echo "        type: boolean_true"
-  echo "        Development mode. Do not compress and minimise JS, export uncompressed"
-  echo "        plot data."
-  echo ""
-  echo "    --require_logs"
-  echo "        type: boolean_true"
-  echo "        Require all explicitly requested modules to have log files. If not,"
-  echo "        MultiQC will exit with an error."
-  echo ""
-  echo "    --no_megaqc_upload"
-  echo "        type: boolean_true"
-  echo "        Don't upload generated report to MegaQC, even if MegaQC options are"
-  echo "        found."
-  echo ""
-  echo "    --no_ansi"
-  echo "        type: boolean_true"
-  echo "        Disable coloured log output."
-  echo ""
-  echo "    --cl_config"
-  echo "        type: string"
-  echo "        example: qualimap_config: { general_stats_coverage: [20,40,200] }"
-  echo "        YAML formatted string that allows to customize MultiQC behaviour like"
-  echo "        input file detection."
-  echo ""
-  echo "Output format:"
-  echo "    --flat"
-  echo "        type: boolean_true"
-  echo "        Use only flat plots (static images)."
-  echo ""
-  echo "    --interactive"
-  echo "        type: boolean_true"
-  echo "        Use only interactive plots (in-browser Javascript)."
-  echo ""
-  echo "    --data_dir"
-  echo "        type: boolean_true"
-  echo "        Force the parsed data directory to be created."
-  echo ""
-  echo "    --no_data_dir"
-  echo "        type: boolean_true"
-  echo "        Prevent the parsed data directory from being created."
-  echo ""
-  echo "    --zip_data_dir"
-  echo "        type: boolean_true"
-  echo "        Compress the data directory."
-  echo ""
-  echo "    --data_format"
-  echo "        type: string"
-  echo "        choices: [ tsv, csv, json, yaml ]"
-  echo "        Output parsed data in a different format than the default 'txt'."
-  echo ""
-  echo "    --pdf"
-  echo "        type: boolean_true"
-  echo "        Creates PDF report with the 'simple' template. Requires Pandoc to be"
-  echo "        installed."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -637,9 +452,9 @@ RUN multiqc --version | sed 's/multiqc, version\s\(.*\)/multiqc: "\1"/' > /var/s
 
 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component multiqc"
-LABEL org.opencontainers.image.created="2024-12-03T10:33:55Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:44Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -754,6 +569,217 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "multiqc main"
+  echo ""
+  echo "MultiQC aggregates results from bioinformatics analyses across many samples into"
+  echo "a single report."
+  echo "It searches a given directory for analysis logs and compiles a HTML report. It's"
+  echo "a general use tool, perfect for summarising the output from numerous"
+  echo "bioinformatics tools."
+  echo ""
+  echo "Input:"
+  echo "    --input"
+  echo "        type: file, required parameter, multiple values allowed, file must exist"
+  echo "        example: data/results"
+  echo "        File paths to be searched for analysis results to be included in the"
+  echo "        report."
+  echo ""
+  echo "Ouput:"
+  echo "    --output_report"
+  echo "        type: file, output"
+  echo "        example: multiqc_report.html"
+  echo "        Filepath of the generated report."
+  echo ""
+  echo "    --output_data"
+  echo "        type: file, output"
+  echo "        example: multiqc_data"
+  echo "        Output directory for parsed data files. If not provided, parsed data"
+  echo "        will not be published."
+  echo ""
+  echo "    --output_plots"
+  echo "        type: file, output"
+  echo "        example: multiqc_plots"
+  echo "        Output directory for generated plots. If not provided, plots will not be"
+  echo "        published."
+  echo ""
+  echo "Modules and analyses to run:"
+  echo "    --include_modules"
+  echo "        type: string, multiple values allowed"
+  echo "        example: fastqc;cutadapt"
+  echo "        Use only these module"
+  echo ""
+  echo "    --exclude_modules"
+  echo "        type: string, multiple values allowed"
+  echo "        example: fastqc;cutadapt"
+  echo "        Do not use only these modules"
+  echo ""
+  echo "    --ignore_analysis"
+  echo "        type: string, multiple values allowed"
+  echo "        example: run_one/*;run_two/*"
+  echo ""
+  echo "    --ignore_samples"
+  echo "        type: string, multiple values allowed"
+  echo "        example: sample_1*;sample_3*"
+  echo ""
+  echo "    --ignore_symlinks"
+  echo "        type: boolean_true"
+  echo "        Ignore symlinked directories and files"
+  echo ""
+  echo "Sample name handling:"
+  echo "    --dirs"
+  echo "        type: boolean_true"
+  echo "        Prepend directory to sample names to avoid clashing filenames"
+  echo ""
+  echo "    --dirs_depth"
+  echo "        type: integer"
+  echo "        Prepend n directories to sample names. Negative number to take from"
+  echo "        start of path."
+  echo ""
+  echo "    --full_names"
+  echo "        type: boolean_true"
+  echo "        Do not clean the sample names (leave as full file name)"
+  echo ""
+  echo "    --fn_as_s_name"
+  echo "        type: boolean_true"
+  echo "        Use the log filename as the sample name"
+  echo ""
+  echo "    --replace_names"
+  echo "        type: file, file must exist"
+  echo "        example: replace_names.tsv"
+  echo "        TSV file to rename sample names during report generation"
+  echo ""
+  echo "Report Customisation:"
+  echo "    --title"
+  echo "        type: string"
+  echo "        Report title. Printed as page header, used for filename if not otherwise"
+  echo "        specified."
+  echo ""
+  echo "    --comment"
+  echo "        type: string"
+  echo "        Custom comment, will be printed at the top of the report."
+  echo ""
+  echo "    --template"
+  echo "        type: string"
+  echo "        choices: [ default, gathered, geo, highcharts, sections, simple ]"
+  echo "        Report template to use."
+  echo ""
+  echo "    --sample_names"
+  echo "        type: file, file must exist"
+  echo "        example: sample_names.tsv"
+  echo "        TSV file containing alternative sample names for renaming buttons in the"
+  echo "        report."
+  echo ""
+  echo "    --sample_filters"
+  echo "        type: file, file must exist"
+  echo "        example: sample_filters.tsv"
+  echo "        TSV file containing show/hide patterns for the report"
+  echo ""
+  echo "    --custom_css_file"
+  echo "        type: file, file must exist"
+  echo "        example: custom_style_sheet.css"
+  echo "        Custom CSS file to add to the final report"
+  echo ""
+  echo "    --profile_runtime"
+  echo "        type: boolean_true"
+  echo "        Add analysis of how long MultiQC takes to run to the report"
+  echo ""
+  echo "MultiQC behaviour:"
+  echo "    --verbose"
+  echo "        type: boolean_true"
+  echo "        Increase output verbosity."
+  echo ""
+  echo "    --quiet"
+  echo "        type: boolean_true"
+  echo "        Only show log warnings"
+  echo ""
+  echo "    --strict"
+  echo "        type: boolean_true"
+  echo "        Don't catch exceptions, run additional code checks to help development."
+  echo ""
+  echo "    --development"
+  echo "        type: boolean_true"
+  echo "        Development mode. Do not compress and minimise JS, export uncompressed"
+  echo "        plot data."
+  echo ""
+  echo "    --require_logs"
+  echo "        type: boolean_true"
+  echo "        Require all explicitly requested modules to have log files. If not,"
+  echo "        MultiQC will exit with an error."
+  echo ""
+  echo "    --no_megaqc_upload"
+  echo "        type: boolean_true"
+  echo "        Don't upload generated report to MegaQC, even if MegaQC options are"
+  echo "        found."
+  echo ""
+  echo "    --no_ansi"
+  echo "        type: boolean_true"
+  echo "        Disable coloured log output."
+  echo ""
+  echo "    --cl_config"
+  echo "        type: string"
+  echo "        example: qualimap_config: { general_stats_coverage: [20,40,200] }"
+  echo "        YAML formatted string that allows to customize MultiQC behaviour like"
+  echo "        input file detection."
+  echo ""
+  echo "Output format:"
+  echo "    --flat"
+  echo "        type: boolean_true"
+  echo "        Use only flat plots (static images)."
+  echo ""
+  echo "    --interactive"
+  echo "        type: boolean_true"
+  echo "        Use only interactive plots (in-browser Javascript)."
+  echo ""
+  echo "    --data_dir"
+  echo "        type: boolean_true"
+  echo "        Force the parsed data directory to be created."
+  echo ""
+  echo "    --no_data_dir"
+  echo "        type: boolean_true"
+  echo "        Prevent the parsed data directory from being created."
+  echo ""
+  echo "    --zip_data_dir"
+  echo "        type: boolean_true"
+  echo "        Compress the data directory."
+  echo ""
+  echo "    --data_format"
+  echo "        type: string"
+  echo "        choices: [ tsv, csv, json, yaml ]"
+  echo "        Output parsed data in a different format than the default 'txt'."
+  echo ""
+  echo "    --pdf"
+  echo "        type: boolean_true"
+  echo "        Creates PDF report with the 'simple' template. Requires Pandoc to be"
+  echo "        installed."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/nanoplot/.config.vsh.yaml b/target/executable/nanoplot/.config.vsh.yaml
index 1db24a0c..79b4f912 100644
--- a/target/executable/nanoplot/.config.vsh.yaml
+++ b/target/executable/nanoplot/.config.vsh.yaml
@@ -390,6 +390,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -491,16 +494,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/nanoplot"
   executable: "target/executable/nanoplot/nanoplot"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/nanoplot/nanoplot b/target/executable/nanoplot/nanoplot
index a5526779..69db380f 100755
--- a/target/executable/nanoplot/nanoplot
+++ b/target/executable/nanoplot/nanoplot
@@ -2,7 +2,7 @@
 
 # nanoplot main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -169,218 +169,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "nanoplot main"
-  echo ""
-  echo "Run NanoPlot on nanopore-sequenced reads."
-  echo "NanoPlot is a plotting tool for long read sequencing data and alignments."
-  echo ""
-  echo "Inputs:"
-  echo "    --fastq"
-  echo "        type: file, multiple values allowed, file must exist"
-  echo "        example: read.fq"
-  echo "        Input fastq file(s), separated by \";\"."
-  echo ""
-  echo "    --fasta"
-  echo "        type: file, multiple values allowed, file must exist"
-  echo "        example: read.fa"
-  echo "        Input fasta file(s), separated by \";\"."
-  echo ""
-  echo "    --fastq_rich"
-  echo "        type: file, multiple values allowed, file must exist"
-  echo "        example: read.fq"
-  echo "        Input fastq file(s) generated by albacore or"
-  echo "        MinKNOW with additional information concerning channel and time,"
-  echo "        separated by \";\"."
-  echo ""
-  echo "    --fastq_minimal"
-  echo "        type: file, multiple values allowed, file must exist"
-  echo "        example: read.fq"
-  echo "        Input fastq file(s) generated by albacore or MinKNOW with"
-  echo "        additional information concerning channel and time. Minimal data is"
-  echo "        extracted"
-  echo "        swiftly without elaborate checks. Separated by \";\"."
-  echo ""
-  echo "    --summary"
-  echo "        type: file, multiple values allowed, file must exist"
-  echo "        example: read.txt"
-  echo "        Input summary file(s) generated by albacore or guppy, separated by \";\"."
-  echo ""
-  echo "    --bam"
-  echo "        type: file, multiple values allowed, file must exist"
-  echo "        example: read.bam"
-  echo "        Input sorted bam file(s), separated by \";\"."
-  echo ""
-  echo "    --ubam"
-  echo "        type: file, multiple values allowed, file must exist"
-  echo "        example: read.ubam"
-  echo "        Input unmapped bam file(s), separated by \";\"."
-  echo ""
-  echo "    --cram"
-  echo "        type: file, multiple values allowed, file must exist"
-  echo "        example: read.cram"
-  echo "        Input sorted cram file(s), separated by \";\"."
-  echo ""
-  echo "    --pickle"
-  echo "        type: file, multiple values allowed, file must exist"
-  echo "        example: read.pkl"
-  echo "        Input pickle file stored earlier, separated by \";\"."
-  echo ""
-  echo "    --arrow, --feather"
-  echo "        type: file, multiple values allowed, file must exist"
-  echo "        example: read.arrow"
-  echo "        Input feather file(s), separated by \";\"."
-  echo ""
-  echo "Outputs:"
-  echo "    -o, --outdir"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        Specify directory in which output has to be created."
-  echo ""
-  echo "Options:"
-  echo "    --verbose"
-  echo "        type: boolean_true"
-  echo "        Write log messages also to terminal"
-  echo ""
-  echo "    --store"
-  echo "        type: boolean_true"
-  echo "        Store the extracted data in a pickle file for future plotting."
-  echo ""
-  echo "    --raw"
-  echo "        type: boolean_true"
-  echo "        Store the extracted data in tab separated file."
-  echo ""
-  echo "    --huge"
-  echo "        type: boolean_true"
-  echo "        Input data is one very large file."
-  echo ""
-  echo "    --no_static"
-  echo "        type: boolean_false"
-  echo "        Do not make static (png) plots."
-  echo ""
-  echo "    -p, --prefix"
-  echo "        type: string"
-  echo "        Specify an optional prefix to be used for the output files."
-  echo ""
-  echo "    --tsv_stats"
-  echo "        type: boolean_true"
-  echo "        Output the stats file as a properly formatted TSV."
-  echo ""
-  echo "    --only_report"
-  echo "        type: boolean_true"
-  echo "        Output only the report."
-  echo ""
-  echo "    --info_in_report"
-  echo "        type: boolean_true"
-  echo "        Add NanoPlot run info in the report."
-  echo ""
-  echo "Filtering or transforming input:"
-  echo "    --maxlength"
-  echo "        type: integer"
-  echo "        Drop reads longer than length specified."
-  echo ""
-  echo "    --minlength"
-  echo "        type: integer"
-  echo "        Drop reads shorter than length specified."
-  echo ""
-  echo "    --drop_outliers"
-  echo "        type: boolean_false"
-  echo "        Drop outlier reads with extreme long length."
-  echo ""
-  echo "    --downsample"
-  echo "        type: integer"
-  echo "        Reduce dataset to N reads by random sampling."
-  echo ""
-  echo "    --loglength"
-  echo "        type: boolean_true"
-  echo "        Logarithmic scaling of lengths in plots."
-  echo ""
-  echo "    --percentqual"
-  echo "        type: boolean_true"
-  echo "        Use qualities as theoretical percent identities."
-  echo ""
-  echo "    --alength"
-  echo "        type: boolean_true"
-  echo "        Use aligned read lengths rather than sequenced length (bam mode)."
-  echo ""
-  echo "    --minqual"
-  echo "        type: integer"
-  echo "        Drop reads with an average quality lower than specified."
-  echo ""
-  echo "    --runtime_until"
-  echo "        type: integer"
-  echo "        Only take the N first hours of a run."
-  echo ""
-  echo "    --readtype"
-  echo "        type: string"
-  echo "        Which read type to extract information about from summary."
-  echo "        Options are 1D, 2D, 1D2"
-  echo ""
-  echo "    --barcoded"
-  echo "        type: boolean_true"
-  echo "        Use if you want to split the summary file by barcode."
-  echo ""
-  echo "    --no_supplementary"
-  echo "        type: boolean_false"
-  echo "        Use if you want to remove supplementary alignments."
-  echo ""
-  echo "Customizing plots:"
-  echo "    -c, --color"
-  echo "        type: string"
-  echo "        Specify a color for the plots, must be a valid matplotlib color."
-  echo ""
-  echo "    -cm, --colormap"
-  echo "        type: string"
-  echo "        Specify a valid matplotlib colormap for the heatmap."
-  echo ""
-  echo "    -f, --format"
-  echo "        type: string"
-  echo "        default: png"
-  echo "        Specify the output format of the plots."
-  echo "        {eps,jpeg,jpg,pdf,pgf,png,ps,raw,rgba,svg,svgz,tif,tiff}"
-  echo ""
-  echo "    --plots"
-  echo "        type: string"
-  echo "        Specify which bivariate plots have to be made."
-  echo "        [{kde,hex,dot} ...]"
-  echo ""
-  echo "    --legacy"
-  echo "        type: string"
-  echo "        Specify which bivariate plots have to be made (legacy mode)."
-  echo "        [{kde,dot,hex} ...]"
-  echo ""
-  echo "    --listcolors"
-  echo "        type: boolean_true"
-  echo "        List the colors which are available for plotting and exit."
-  echo ""
-  echo "    --listcolormaps"
-  echo "        type: boolean_true"
-  echo "        List the colormaps which are available for plotting and exit."
-  echo ""
-  echo "    --no_N50"
-  echo "        type: boolean_false"
-  echo "        Hide the N50 mark in the read length histogram."
-  echo ""
-  echo "    --N50"
-  echo "        type: boolean_true"
-  echo "        Show the N50 mark in the read length histogram."
-  echo ""
-  echo "    --title"
-  echo "        type: string"
-  echo "        Add a title to all plots, requires quoting if using spaces."
-  echo ""
-  echo "    --font_scale"
-  echo "        type: double"
-  echo "        Scale the font of the plots by a factor."
-  echo ""
-  echo "    --dpi"
-  echo "        type: integer"
-  echo "        Set the dpi for saving images."
-  echo ""
-  echo "    --hide_stats"
-  echo "        type: boolean_false"
-  echo "        Not adding Pearson R stats in some bivariate plots."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -661,9 +449,9 @@ RUN version=$(NanoPlot --version) && \
 echo "$version" > /var/software_versions.txt
 
 LABEL org.opencontainers.image.description="Companion container for running component nanoplot"
-LABEL org.opencontainers.image.created="2024-12-03T10:33:56Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:37Z"
 LABEL org.opencontainers.image.source="https://github.com/wdecoster/NanoPlot"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -778,6 +566,244 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "nanoplot main"
+  echo ""
+  echo "Run NanoPlot on nanopore-sequenced reads."
+  echo "NanoPlot is a plotting tool for long read sequencing data and alignments."
+  echo ""
+  echo "Inputs:"
+  echo "    --fastq"
+  echo "        type: file, multiple values allowed, file must exist"
+  echo "        example: read.fq"
+  echo "        Input fastq file(s), separated by \";\"."
+  echo ""
+  echo "    --fasta"
+  echo "        type: file, multiple values allowed, file must exist"
+  echo "        example: read.fa"
+  echo "        Input fasta file(s), separated by \";\"."
+  echo ""
+  echo "    --fastq_rich"
+  echo "        type: file, multiple values allowed, file must exist"
+  echo "        example: read.fq"
+  echo "        Input fastq file(s) generated by albacore or"
+  echo "        MinKNOW with additional information concerning channel and time,"
+  echo "        separated by \";\"."
+  echo ""
+  echo "    --fastq_minimal"
+  echo "        type: file, multiple values allowed, file must exist"
+  echo "        example: read.fq"
+  echo "        Input fastq file(s) generated by albacore or MinKNOW with"
+  echo "        additional information concerning channel and time. Minimal data is"
+  echo "        extracted"
+  echo "        swiftly without elaborate checks. Separated by \";\"."
+  echo ""
+  echo "    --summary"
+  echo "        type: file, multiple values allowed, file must exist"
+  echo "        example: read.txt"
+  echo "        Input summary file(s) generated by albacore or guppy, separated by \";\"."
+  echo ""
+  echo "    --bam"
+  echo "        type: file, multiple values allowed, file must exist"
+  echo "        example: read.bam"
+  echo "        Input sorted bam file(s), separated by \";\"."
+  echo ""
+  echo "    --ubam"
+  echo "        type: file, multiple values allowed, file must exist"
+  echo "        example: read.ubam"
+  echo "        Input unmapped bam file(s), separated by \";\"."
+  echo ""
+  echo "    --cram"
+  echo "        type: file, multiple values allowed, file must exist"
+  echo "        example: read.cram"
+  echo "        Input sorted cram file(s), separated by \";\"."
+  echo ""
+  echo "    --pickle"
+  echo "        type: file, multiple values allowed, file must exist"
+  echo "        example: read.pkl"
+  echo "        Input pickle file stored earlier, separated by \";\"."
+  echo ""
+  echo "    --arrow, --feather"
+  echo "        type: file, multiple values allowed, file must exist"
+  echo "        example: read.arrow"
+  echo "        Input feather file(s), separated by \";\"."
+  echo ""
+  echo "Outputs:"
+  echo "    -o, --outdir"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        Specify directory in which output has to be created."
+  echo ""
+  echo "Options:"
+  echo "    --verbose"
+  echo "        type: boolean_true"
+  echo "        Write log messages also to terminal"
+  echo ""
+  echo "    --store"
+  echo "        type: boolean_true"
+  echo "        Store the extracted data in a pickle file for future plotting."
+  echo ""
+  echo "    --raw"
+  echo "        type: boolean_true"
+  echo "        Store the extracted data in tab separated file."
+  echo ""
+  echo "    --huge"
+  echo "        type: boolean_true"
+  echo "        Input data is one very large file."
+  echo ""
+  echo "    --no_static"
+  echo "        type: boolean_false"
+  echo "        Do not make static (png) plots."
+  echo ""
+  echo "    -p, --prefix"
+  echo "        type: string"
+  echo "        Specify an optional prefix to be used for the output files."
+  echo ""
+  echo "    --tsv_stats"
+  echo "        type: boolean_true"
+  echo "        Output the stats file as a properly formatted TSV."
+  echo ""
+  echo "    --only_report"
+  echo "        type: boolean_true"
+  echo "        Output only the report."
+  echo ""
+  echo "    --info_in_report"
+  echo "        type: boolean_true"
+  echo "        Add NanoPlot run info in the report."
+  echo ""
+  echo "Filtering or transforming input:"
+  echo "    --maxlength"
+  echo "        type: integer"
+  echo "        Drop reads longer than length specified."
+  echo ""
+  echo "    --minlength"
+  echo "        type: integer"
+  echo "        Drop reads shorter than length specified."
+  echo ""
+  echo "    --drop_outliers"
+  echo "        type: boolean_false"
+  echo "        Drop outlier reads with extreme long length."
+  echo ""
+  echo "    --downsample"
+  echo "        type: integer"
+  echo "        Reduce dataset to N reads by random sampling."
+  echo ""
+  echo "    --loglength"
+  echo "        type: boolean_true"
+  echo "        Logarithmic scaling of lengths in plots."
+  echo ""
+  echo "    --percentqual"
+  echo "        type: boolean_true"
+  echo "        Use qualities as theoretical percent identities."
+  echo ""
+  echo "    --alength"
+  echo "        type: boolean_true"
+  echo "        Use aligned read lengths rather than sequenced length (bam mode)."
+  echo ""
+  echo "    --minqual"
+  echo "        type: integer"
+  echo "        Drop reads with an average quality lower than specified."
+  echo ""
+  echo "    --runtime_until"
+  echo "        type: integer"
+  echo "        Only take the N first hours of a run."
+  echo ""
+  echo "    --readtype"
+  echo "        type: string"
+  echo "        Which read type to extract information about from summary."
+  echo "        Options are 1D, 2D, 1D2"
+  echo ""
+  echo "    --barcoded"
+  echo "        type: boolean_true"
+  echo "        Use if you want to split the summary file by barcode."
+  echo ""
+  echo "    --no_supplementary"
+  echo "        type: boolean_false"
+  echo "        Use if you want to remove supplementary alignments."
+  echo ""
+  echo "Customizing plots:"
+  echo "    -c, --color"
+  echo "        type: string"
+  echo "        Specify a color for the plots, must be a valid matplotlib color."
+  echo ""
+  echo "    -cm, --colormap"
+  echo "        type: string"
+  echo "        Specify a valid matplotlib colormap for the heatmap."
+  echo ""
+  echo "    -f, --format"
+  echo "        type: string"
+  echo "        default: png"
+  echo "        Specify the output format of the plots."
+  echo "        {eps,jpeg,jpg,pdf,pgf,png,ps,raw,rgba,svg,svgz,tif,tiff}"
+  echo ""
+  echo "    --plots"
+  echo "        type: string"
+  echo "        Specify which bivariate plots have to be made."
+  echo "        [{kde,hex,dot} ...]"
+  echo ""
+  echo "    --legacy"
+  echo "        type: string"
+  echo "        Specify which bivariate plots have to be made (legacy mode)."
+  echo "        [{kde,dot,hex} ...]"
+  echo ""
+  echo "    --listcolors"
+  echo "        type: boolean_true"
+  echo "        List the colors which are available for plotting and exit."
+  echo ""
+  echo "    --listcolormaps"
+  echo "        type: boolean_true"
+  echo "        List the colormaps which are available for plotting and exit."
+  echo ""
+  echo "    --no_N50"
+  echo "        type: boolean_false"
+  echo "        Hide the N50 mark in the read length histogram."
+  echo ""
+  echo "    --N50"
+  echo "        type: boolean_true"
+  echo "        Show the N50 mark in the read length histogram."
+  echo ""
+  echo "    --title"
+  echo "        type: string"
+  echo "        Add a title to all plots, requires quoting if using spaces."
+  echo ""
+  echo "    --font_scale"
+  echo "        type: double"
+  echo "        Scale the font of the plots by a factor."
+  echo ""
+  echo "    --dpi"
+  echo "        type: integer"
+  echo "        Set the dpi for saving images."
+  echo ""
+  echo "    --hide_stats"
+  echo "        type: boolean_false"
+  echo "        Not adding Pearson R stats in some bivariate plots."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/pear/.config.vsh.yaml b/target/executable/pear/.config.vsh.yaml
index ddfa2de3..8194853a 100644
--- a/target/executable/pear/.config.vsh.yaml
+++ b/target/executable/pear/.config.vsh.yaml
@@ -295,6 +295,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -397,16 +400,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/pear"
   executable: "target/executable/pear/pear"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/pear/pear b/target/executable/pear/pear
index 15ec8b34..0efc9bed 100755
--- a/target/executable/pear/pear
+++ b/target/executable/pear/pear
@@ -2,7 +2,7 @@
 
 # pear main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,150 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "pear main"
-  echo ""
-  echo "PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger."
-  echo "It is fully parallelized and can run with as low as just a few kilobytes of"
-  echo "memory."
-  echo ""
-  echo "PEAR evaluates all possible paired-end read overlaps and without requiring the"
-  echo "target fragment size as input. In addition, it implements a statistical test for"
-  echo "minimizing false-positive results. Together with a highly optimized"
-  echo "implementation, it can merge millions of paired end reads within a couple of"
-  echo "minutes on a standard desktop computer."
-  echo ""
-  echo "Inputs:"
-  echo "    -f, --forward_fastq"
-  echo "        type: file, required parameter, file must exist"
-  echo "        example: forward.fastq"
-  echo "        Forward paired-end FASTQ file"
-  echo ""
-  echo "    -r, --reverse_fastq"
-  echo "        type: file, required parameter, file must exist"
-  echo "        example: reverse.fastq"
-  echo "        Reverse paired-end FASTQ file"
-  echo ""
-  echo "Outputs:"
-  echo "    --assembled"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        The output file containing assembled reads. Can be compressed with gzip."
-  echo ""
-  echo "    --unassembled_forward"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        The output file containing forward reads that could not be assembled."
-  echo "        Can be compressed with gzip."
-  echo ""
-  echo "    --unassembled_reverse"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        The output file containing reverse reads that could not be assembled."
-  echo "        Can be compressed with gzip."
-  echo ""
-  echo "    --discarded"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        The output file containing reads that were discarded due to too low"
-  echo "        quality or too many uncalled bases. Can be compressed with gzip."
-  echo ""
-  echo "Arguments:"
-  echo "    -p, --p_value"
-  echo "        type: double"
-  echo "        example: 0.01"
-  echo "        Specify a p-value for the statistical test. If the computed p-value of a"
-  echo "        possible assembly exceeds the specified p-value then paired-end read"
-  echo "        will not be assembled. Valid options are: 0.0001, 0.001, 0.01, 0.05 and"
-  echo "        1.0. Setting 1.0 disables the test."
-  echo ""
-  echo "    -v, --min_overlap"
-  echo "        type: integer"
-  echo "        example: 10"
-  echo "        Specify the minimum overlap size. The minimum overlap may be set to 1"
-  echo "        when the statistical test is used. However, further restricting the"
-  echo "        minimum overlap size to a proper value may reduce false-positive"
-  echo "        assembles."
-  echo ""
-  echo "    -m, --max_assembly_length"
-  echo "        type: integer"
-  echo "        example: 0"
-  echo "        Specify the maximum possible length of the assembled sequences. Setting"
-  echo "        this value to 0 disables the restriction and assembled sequences may be"
-  echo "        arbitrary long."
-  echo ""
-  echo "    -n, --min_assembly_length"
-  echo "        type: integer"
-  echo "        example: 0"
-  echo "        Specify the minimum possible length of the assembled sequences. Setting"
-  echo "        this value to 0 disables the restriction and assembled sequences may be"
-  echo "        arbitrary short."
-  echo ""
-  echo "    -t, --min_trim_length"
-  echo "        type: integer"
-  echo "        example: 1"
-  echo "        Specify  the  minimum length of reads after trimming the low quality"
-  echo "        part (see option -q)"
-  echo ""
-  echo "    -q, --quality_threshold"
-  echo "        type: integer"
-  echo "        example: 0"
-  echo "        Specify the quality threshold for trimming the low quality part of a"
-  echo "        read. If the quality scores of two consecutive bases are strictly less"
-  echo "        than the specified threshold, the rest of the read will be trimmed."
-  echo ""
-  echo "    -u, --max_uncalled_base"
-  echo "        type: double"
-  echo "        example: 1.0"
-  echo "        Specify the maximal proportion of uncalled bases in a read. Setting this"
-  echo "        value to 0 will cause PEAR to discard all reads containing uncalled"
-  echo "        bases. The other extreme setting is 1 which causes PEAR to process all"
-  echo "        reads independent on the number of uncalled bases."
-  echo ""
-  echo "    -g, --test_method"
-  echo "        type: integer"
-  echo "        example: 1"
-  echo "        Specify the type of statistical test. Two options are available. 1:"
-  echo "        Given the minimum allowed overlap, test using the highest OES. Note that"
-  echo "        due to its discrete nature, this test usually yields a lower p-value for"
-  echo "        the assembled read than the cut- off (specified by -p). For example,"
-  echo "        setting the cut-off to 0.05 using this test, the assembled reads might"
-  echo "        have an actual p-value of 0.02."
-  echo "        2. Use the acceptance probability (m.a.p). This test methods computes"
-  echo "        the same probability as test method 1. However, it assumes that the"
-  echo "        minimal overlap is the observed overlap with the highest OES, instead of"
-  echo "        the one specified by -v. Therefore, this is not a valid statistical test"
-  echo "        and the 'p-value' is in fact the maximal probability for accepting the"
-  echo "        assembly. Nevertheless, we observed in practice that for the case the"
-  echo "        actual overlap sizes are relatively small, test 2 can correctly assemble"
-  echo "        more reads with only slightly higher false-positive rate."
-  echo ""
-  echo "    -e, --emperical_freqs"
-  echo "        type: boolean_true"
-  echo "        Disable empirical base frequencies."
-  echo ""
-  echo "    -s, --score_method"
-  echo "        type: integer"
-  echo "        example: 2"
-  echo "        Specify the scoring method. 1. OES with +1 for match and -1 for"
-  echo "        mismatch. 2: Assembly score (AS). Use +1 for match and -1 for mismatch"
-  echo "        multiplied by base quality scores. 3: Ignore quality scores and use +1"
-  echo "        for a match and -1 for a mismatch."
-  echo ""
-  echo "    -b, --phred_base"
-  echo "        type: integer"
-  echo "        example: 33"
-  echo "        Base PHRED quality score."
-  echo ""
-  echo "    -c, --cap"
-  echo "        type: integer"
-  echo "        example: 40"
-  echo "        Specify  the upper bound for the resulting quality score. If set to"
-  echo "        zero, capping is disabled."
-  echo ""
-  echo "    -z, --nbase"
-  echo "        type: boolean_true"
-  echo "        When merging a base-pair that consists of two non-equal bases out of"
-  echo "        which none is degenerate, set the merged base to N and use the highest"
-  echo "        quality score of the two bases"
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -597,9 +453,9 @@ echo "pear: $version" > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Kai Waldrant"
 LABEL org.opencontainers.image.description="Companion container for running component pear"
-LABEL org.opencontainers.image.created="2024-12-03T10:33:59Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:36Z"
 LABEL org.opencontainers.image.source="https://github.com/tseemann/PEAR"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -714,6 +570,176 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "pear main"
+  echo ""
+  echo "PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger."
+  echo "It is fully parallelized and can run with as low as just a few kilobytes of"
+  echo "memory."
+  echo ""
+  echo "PEAR evaluates all possible paired-end read overlaps and without requiring the"
+  echo "target fragment size as input. In addition, it implements a statistical test for"
+  echo "minimizing false-positive results. Together with a highly optimized"
+  echo "implementation, it can merge millions of paired end reads within a couple of"
+  echo "minutes on a standard desktop computer."
+  echo ""
+  echo "Inputs:"
+  echo "    -f, --forward_fastq"
+  echo "        type: file, required parameter, file must exist"
+  echo "        example: forward.fastq"
+  echo "        Forward paired-end FASTQ file"
+  echo ""
+  echo "    -r, --reverse_fastq"
+  echo "        type: file, required parameter, file must exist"
+  echo "        example: reverse.fastq"
+  echo "        Reverse paired-end FASTQ file"
+  echo ""
+  echo "Outputs:"
+  echo "    --assembled"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        The output file containing assembled reads. Can be compressed with gzip."
+  echo ""
+  echo "    --unassembled_forward"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        The output file containing forward reads that could not be assembled."
+  echo "        Can be compressed with gzip."
+  echo ""
+  echo "    --unassembled_reverse"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        The output file containing reverse reads that could not be assembled."
+  echo "        Can be compressed with gzip."
+  echo ""
+  echo "    --discarded"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        The output file containing reads that were discarded due to too low"
+  echo "        quality or too many uncalled bases. Can be compressed with gzip."
+  echo ""
+  echo "Arguments:"
+  echo "    -p, --p_value"
+  echo "        type: double"
+  echo "        example: 0.01"
+  echo "        Specify a p-value for the statistical test. If the computed p-value of a"
+  echo "        possible assembly exceeds the specified p-value then paired-end read"
+  echo "        will not be assembled. Valid options are: 0.0001, 0.001, 0.01, 0.05 and"
+  echo "        1.0. Setting 1.0 disables the test."
+  echo ""
+  echo "    -v, --min_overlap"
+  echo "        type: integer"
+  echo "        example: 10"
+  echo "        Specify the minimum overlap size. The minimum overlap may be set to 1"
+  echo "        when the statistical test is used. However, further restricting the"
+  echo "        minimum overlap size to a proper value may reduce false-positive"
+  echo "        assembles."
+  echo ""
+  echo "    -m, --max_assembly_length"
+  echo "        type: integer"
+  echo "        example: 0"
+  echo "        Specify the maximum possible length of the assembled sequences. Setting"
+  echo "        this value to 0 disables the restriction and assembled sequences may be"
+  echo "        arbitrary long."
+  echo ""
+  echo "    -n, --min_assembly_length"
+  echo "        type: integer"
+  echo "        example: 0"
+  echo "        Specify the minimum possible length of the assembled sequences. Setting"
+  echo "        this value to 0 disables the restriction and assembled sequences may be"
+  echo "        arbitrary short."
+  echo ""
+  echo "    -t, --min_trim_length"
+  echo "        type: integer"
+  echo "        example: 1"
+  echo "        Specify  the  minimum length of reads after trimming the low quality"
+  echo "        part (see option -q)"
+  echo ""
+  echo "    -q, --quality_threshold"
+  echo "        type: integer"
+  echo "        example: 0"
+  echo "        Specify the quality threshold for trimming the low quality part of a"
+  echo "        read. If the quality scores of two consecutive bases are strictly less"
+  echo "        than the specified threshold, the rest of the read will be trimmed."
+  echo ""
+  echo "    -u, --max_uncalled_base"
+  echo "        type: double"
+  echo "        example: 1.0"
+  echo "        Specify the maximal proportion of uncalled bases in a read. Setting this"
+  echo "        value to 0 will cause PEAR to discard all reads containing uncalled"
+  echo "        bases. The other extreme setting is 1 which causes PEAR to process all"
+  echo "        reads independent on the number of uncalled bases."
+  echo ""
+  echo "    -g, --test_method"
+  echo "        type: integer"
+  echo "        example: 1"
+  echo "        Specify the type of statistical test. Two options are available. 1:"
+  echo "        Given the minimum allowed overlap, test using the highest OES. Note that"
+  echo "        due to its discrete nature, this test usually yields a lower p-value for"
+  echo "        the assembled read than the cut- off (specified by -p). For example,"
+  echo "        setting the cut-off to 0.05 using this test, the assembled reads might"
+  echo "        have an actual p-value of 0.02."
+  echo "        2. Use the acceptance probability (m.a.p). This test methods computes"
+  echo "        the same probability as test method 1. However, it assumes that the"
+  echo "        minimal overlap is the observed overlap with the highest OES, instead of"
+  echo "        the one specified by -v. Therefore, this is not a valid statistical test"
+  echo "        and the 'p-value' is in fact the maximal probability for accepting the"
+  echo "        assembly. Nevertheless, we observed in practice that for the case the"
+  echo "        actual overlap sizes are relatively small, test 2 can correctly assemble"
+  echo "        more reads with only slightly higher false-positive rate."
+  echo ""
+  echo "    -e, --emperical_freqs"
+  echo "        type: boolean_true"
+  echo "        Disable empirical base frequencies."
+  echo ""
+  echo "    -s, --score_method"
+  echo "        type: integer"
+  echo "        example: 2"
+  echo "        Specify the scoring method. 1. OES with +1 for match and -1 for"
+  echo "        mismatch. 2: Assembly score (AS). Use +1 for match and -1 for mismatch"
+  echo "        multiplied by base quality scores. 3: Ignore quality scores and use +1"
+  echo "        for a match and -1 for a mismatch."
+  echo ""
+  echo "    -b, --phred_base"
+  echo "        type: integer"
+  echo "        example: 33"
+  echo "        Base PHRED quality score."
+  echo ""
+  echo "    -c, --cap"
+  echo "        type: integer"
+  echo "        example: 40"
+  echo "        Specify  the upper bound for the resulting quality score. If set to"
+  echo "        zero, capping is disabled."
+  echo ""
+  echo "    -z, --nbase"
+  echo "        type: boolean_true"
+  echo "        When merging a base-pair that consists of two non-equal bases out of"
+  echo "        which none is degenerate, set the merged base to N and use the highest"
+  echo "        quality score of the two bases"
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml b/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml
index 5e9ed110..d97d6cae 100644
--- a/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml
+++ b/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml
@@ -161,6 +161,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -263,16 +266,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/qualimap/qualimap_rnaseq"
   executable: "target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq b/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq
index fbe92281..ac1eca89 100755
--- a/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq
+++ b/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq
@@ -2,7 +2,7 @@
 
 # qualimap_rnaseq main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,81 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "qualimap_rnaseq main"
-  echo ""
-  echo "Qualimap RNA-seq QC reports quality control metrics and bias estimations"
-  echo "which are specific for whole transcriptome sequencing, including reads genomic"
-  echo "origin, junction analysis, transcript coverage and 5’-3’ bias computation."
-  echo ""
-  echo "Input:"
-  echo "    --bam"
-  echo "        type: file, required parameter, file must exist"
-  echo "        example: alignment.bam"
-  echo "        Path to the sequence alignment file in BAM format, produced by a"
-  echo "        splicing-aware aligner."
-  echo ""
-  echo "    --gtf"
-  echo "        type: file, required parameter, file must exist"
-  echo "        example: annotations.gtf"
-  echo "        Path to genomic annotations in Ensembl GTF format."
-  echo ""
-  echo "Output:"
-  echo "    --qc_results"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        example: rnaseq_qc_results.txt"
-  echo "        Text file containing the RNAseq QC results."
-  echo ""
-  echo "    --counts"
-  echo "        type: file, output, file must exist"
-  echo "        Output file for computed counts."
-  echo ""
-  echo "    --report"
-  echo "        type: file, output, file must exist"
-  echo "        example: report.html"
-  echo "        Report output file. Supported formats are PDF or HTML."
-  echo ""
-  echo "Optional:"
-  echo "    --num_pr_bases"
-  echo "        type: integer"
-  echo "        min: 1"
-  echo "        Number of upstream/downstream nucleotide bases to compute 5'-3' bias"
-  echo "        (default = 100)."
-  echo ""
-  echo "    --num_tr_bias"
-  echo "        type: integer"
-  echo "        min: 1"
-  echo "        Number of top highly expressed transcripts to compute 5'-3' bias"
-  echo "        (default = 1000)."
-  echo ""
-  echo "    --algorithm"
-  echo "        type: string"
-  echo "        choices: [ uniquely-mapped-reads, proportional ]"
-  echo "        Counting algorithm (uniquely-mapped-reads (default) or proportional)."
-  echo ""
-  echo "    --sequencing_protocol"
-  echo "        type: string"
-  echo "        choices: [ non-strand-specific, strand-specific-reverse,"
-  echo "strand-specific-forward ]"
-  echo "        Sequencing library protocol (strand-specific-forward,"
-  echo "        strand-specific-reverse or non-strand-specific (default))."
-  echo ""
-  echo "    --paired"
-  echo "        type: boolean_true"
-  echo "        Setting this flag for paired-end experiments will result in counting"
-  echo "        fragments instead of reads."
-  echo ""
-  echo "    --sorted"
-  echo "        type: boolean_true"
-  echo "        Setting this flag indicates that the input file is already sorted by"
-  echo "        name. If flag is not set, additional sorting by name will be performed."
-  echo "        Only requiredfor paired-end analysis."
-  echo ""
-  echo "    --java_memory_size"
-  echo "        type: string"
-  echo "        maximum Java heap memory size, default = 4G."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -527,9 +452,9 @@ RUN echo QualiMap: $(qualimap 2>&1 | grep QualiMap | sed 's/^.*QualiMap//') > /v
 
 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component qualimap qualimap_rnaseq"
-LABEL org.opencontainers.image.created="2024-12-03T10:33:53Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:45Z"
 LABEL org.opencontainers.image.source="https://bitbucket.org/kokonech/qualimap/commits/branch/master"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -644,6 +569,107 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "qualimap_rnaseq main"
+  echo ""
+  echo "Qualimap RNA-seq QC reports quality control metrics and bias estimations"
+  echo "which are specific for whole transcriptome sequencing, including reads genomic"
+  echo "origin, junction analysis, transcript coverage and 5’-3’ bias computation."
+  echo ""
+  echo "Input:"
+  echo "    --bam"
+  echo "        type: file, required parameter, file must exist"
+  echo "        example: alignment.bam"
+  echo "        Path to the sequence alignment file in BAM format, produced by a"
+  echo "        splicing-aware aligner."
+  echo ""
+  echo "    --gtf"
+  echo "        type: file, required parameter, file must exist"
+  echo "        example: annotations.gtf"
+  echo "        Path to genomic annotations in Ensembl GTF format."
+  echo ""
+  echo "Output:"
+  echo "    --qc_results"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        example: rnaseq_qc_results.txt"
+  echo "        Text file containing the RNAseq QC results."
+  echo ""
+  echo "    --counts"
+  echo "        type: file, output, file must exist"
+  echo "        Output file for computed counts."
+  echo ""
+  echo "    --report"
+  echo "        type: file, output, file must exist"
+  echo "        example: report.html"
+  echo "        Report output file. Supported formats are PDF or HTML."
+  echo ""
+  echo "Optional:"
+  echo "    --num_pr_bases"
+  echo "        type: integer"
+  echo "        min: 1"
+  echo "        Number of upstream/downstream nucleotide bases to compute 5'-3' bias"
+  echo "        (default = 100)."
+  echo ""
+  echo "    --num_tr_bias"
+  echo "        type: integer"
+  echo "        min: 1"
+  echo "        Number of top highly expressed transcripts to compute 5'-3' bias"
+  echo "        (default = 1000)."
+  echo ""
+  echo "    --algorithm"
+  echo "        type: string"
+  echo "        choices: [ uniquely-mapped-reads, proportional ]"
+  echo "        Counting algorithm (uniquely-mapped-reads (default) or proportional)."
+  echo ""
+  echo "    --sequencing_protocol"
+  echo "        type: string"
+  echo "        choices: [ non-strand-specific, strand-specific-reverse,"
+  echo "strand-specific-forward ]"
+  echo "        Sequencing library protocol (strand-specific-forward,"
+  echo "        strand-specific-reverse or non-strand-specific (default))."
+  echo ""
+  echo "    --paired"
+  echo "        type: boolean_true"
+  echo "        Setting this flag for paired-end experiments will result in counting"
+  echo "        fragments instead of reads."
+  echo ""
+  echo "    --sorted"
+  echo "        type: boolean_true"
+  echo "        Setting this flag indicates that the input file is already sorted by"
+  echo "        name. If flag is not set, additional sorting by name will be performed."
+  echo "        Only requiredfor paired-end analysis."
+  echo ""
+  echo "    --java_memory_size"
+  echo "        type: string"
+  echo "        maximum Java heap memory size, default = 4G."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml b/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml
index 6151faca..c1edd507 100644
--- a/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml
+++ b/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml
@@ -724,6 +724,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -851,16 +854,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/rsem/rsem_calculate_expression"
   executable: "target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression b/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression
index e60508ae..4ad46d89 100755
--- a/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression
+++ b/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression
@@ -2,7 +2,7 @@
 
 # rsem_calculate_expression main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -169,6 +169,425 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
+
+# initialise variables
+VIASH_MODE='run'
+VIASH_ENGINE_ID='docker'
+
+######## Helper functions for setting up Docker images for viash ########
+# expects: ViashDockerBuild
+
+# ViashDockerInstallationCheck: check whether Docker is installed correctly
+#
+# examples:
+#   ViashDockerInstallationCheck
+function ViashDockerInstallationCheck {
+  ViashDebug "Checking whether Docker is installed"
+  if [ ! command -v docker &> /dev/null ]; then
+    ViashCritical "Docker doesn't seem to be installed. See 'https://docs.docker.com/get-docker/' for instructions."
+    exit 1
+  fi
+
+  ViashDebug "Checking whether the Docker daemon is running"
+  local save=$-; set +e
+  local docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
+  local out=$?
+  [[ $save =~ e ]] && set -e
+  if [ $out -ne 0 ]; then
+    ViashCritical "Docker daemon does not seem to be running. Try one of the following:"
+    ViashCritical "- Try running 'dockerd' in the command line"
+    ViashCritical "- See https://docs.docker.com/config/daemon/"
+    exit 1
+  fi
+}
+
+# ViashDockerRemoteTagCheck: check whether a Docker image is available 
+# on a remote. Assumes `docker login` has been performed, if relevant.
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   ViashDockerRemoteTagCheck python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerRemoteTagCheck sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerRemoteTagCheck {
+  docker manifest inspect $1 > /dev/null 2> /dev/null
+}
+
+# ViashDockerLocalTagCheck: check whether a Docker image is available locally
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   docker pull python:latest
+#   ViashDockerLocalTagCheck python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerLocalTagCheck sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerLocalTagCheck {
+  [ -n "$(docker images -q $1)" ]
+}
+
+# ViashDockerPull: pull a Docker image
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   ViashDockerPull python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerPull sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerPull {
+  ViashNotice "Checking if Docker image is available at '$1'"
+  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
+    docker pull $1 && return 0 || return 1
+  else
+    local save=$-; set +e
+    docker pull $1 2> /dev/null > /dev/null
+    local out=$?
+    [[ $save =~ e ]] && set -e
+    if [ $out -ne 0 ]; then
+      ViashWarning "Could not pull from '$1'. Docker image doesn't exist or is not accessible."
+    fi
+    return $out
+  fi
+}
+
+# ViashDockerPush: push a Docker image
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   ViashDockerPush python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerPush sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerPush {
+  ViashNotice "Pushing image to '$1'"
+  local save=$-; set +e
+  local out
+  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
+    docker push $1
+    out=$?
+  else
+    docker push $1 2> /dev/null > /dev/null
+    out=$?
+  fi
+  [[ $save =~ e ]] && set -e
+  if [ $out -eq 0 ]; then
+    ViashNotice "Container '$1' push succeeded."
+  else
+    ViashError "Container '$1' push errored. You might not be logged in or have the necessary permissions."
+  fi
+  return $out
+}
+
+# ViashDockerPullElseBuild: pull a Docker image, else build it
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# ViashDockerBuild    : a Bash function which builds a docker image, takes image identifier as argument.
+# examples:
+#   ViashDockerPullElseBuild mynewcomponent
+function ViashDockerPullElseBuild {
+  local save=$-; set +e
+  ViashDockerPull $1
+  local out=$?
+  [[ $save =~ e ]] && set -e
+  if [ $out -ne 0 ]; then
+    ViashDockerBuild $@
+  fi
+}
+
+# ViashDockerSetup: create a Docker image, according to specified docker setup strategy
+#
+# $1          : image identifier with format `[registry/]image[:tag]`
+# $2          : docker setup strategy, see DockerSetupStrategy.scala
+# examples:
+#   ViashDockerSetup mynewcomponent alwaysbuild
+function ViashDockerSetup {
+  local image_id="$1"
+  local setup_strategy="$2"
+  if [ "$setup_strategy" == "alwaysbuild" -o "$setup_strategy" == "build" -o "$setup_strategy" == "b" ]; then
+    ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+  elif [ "$setup_strategy" == "alwayspull" -o "$setup_strategy" == "pull" -o "$setup_strategy" == "p" ]; then
+    ViashDockerPull $image_id
+  elif [ "$setup_strategy" == "alwayspullelsebuild" -o "$setup_strategy" == "pullelsebuild" ]; then
+    ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+  elif [ "$setup_strategy" == "alwayspullelsecachedbuild" -o "$setup_strategy" == "pullelsecachedbuild" ]; then
+    ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+  elif [ "$setup_strategy" == "alwayscachedbuild" -o "$setup_strategy" == "cachedbuild" -o "$setup_strategy" == "cb" ]; then
+    ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+  elif [[ "$setup_strategy" =~ ^ifneedbe ]]; then
+    local save=$-; set +e
+    ViashDockerLocalTagCheck $image_id
+    local outCheck=$?
+    [[ $save =~ e ]] && set -e
+    if [ $outCheck -eq 0 ]; then
+      ViashInfo "Image $image_id already exists"
+    elif [ "$setup_strategy" == "ifneedbebuild" ]; then
+      ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+    elif [ "$setup_strategy" == "ifneedbecachedbuild" ]; then
+      ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+    elif [ "$setup_strategy" == "ifneedbepull" ]; then
+      ViashDockerPull $image_id
+    elif [ "$setup_strategy" == "ifneedbepullelsebuild" ]; then
+      ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+    elif [ "$setup_strategy" == "ifneedbepullelsecachedbuild" ]; then
+      ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+    else
+      ViashError "Unrecognised Docker strategy: $setup_strategy"
+      exit 1
+    fi
+  elif [ "$setup_strategy" == "push" -o "$setup_strategy" == "forcepush" -o "$setup_strategy" == "alwayspush" ]; then
+    ViashDockerPush "$image_id"
+  elif [ "$setup_strategy" == "pushifnotpresent" -o "$setup_strategy" == "gentlepush" -o "$setup_strategy" == "maybepush" ]; then
+    local save=$-; set +e
+    ViashDockerRemoteTagCheck $image_id
+    local outCheck=$?
+    [[ $save =~ e ]] && set -e
+    if [ $outCheck -eq 0 ]; then
+      ViashNotice "Container '$image_id' exists, doing nothing."
+    else
+      ViashNotice "Container '$image_id' does not yet exist."
+      ViashDockerPush "$image_id"
+    fi
+  elif [ "$setup_strategy" == "donothing" -o "$setup_strategy" == "meh" ]; then
+    ViashNotice "Skipping setup."
+  else
+    ViashError "Unrecognised Docker strategy: $setup_strategy"
+    exit 1
+  fi
+}
+
+# ViashDockerCheckCommands: Check whether a docker container has the required commands
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# $@                  : commands to verify being present
+# examples:
+#   ViashDockerCheckCommands bash:4.0 bash ps foo
+function ViashDockerCheckCommands {
+  local image_id="$1"
+  shift 1
+  local commands="$@"
+  local save=$-; set +e
+  local missing # mark 'missing' as local in advance, otherwise the exit code of the command will be missing and always be '0'
+  missing=$(docker run --rm --entrypoint=sh "$image_id" -c "for command in $commands; do command -v \$command >/dev/null 2>&1; if [ \$? -ne 0 ]; then echo \$command; exit 1; fi; done")
+  local outCheck=$?
+  [[ $save =~ e ]] && set -e
+  if [ $outCheck -ne 0 ]; then
+  	ViashError "Docker container '$image_id' does not contain command '$missing'."
+  	exit 1
+  fi
+}
+
+# ViashDockerBuild: build a docker image
+# $1                               : image identifier with format `[registry/]image[:tag]`
+# $...                             : additional arguments to pass to docker build
+# $VIASH_META_TEMP_DIR             : temporary directory to store dockerfile & optional resources in
+# $VIASH_META_NAME                 : name of the component
+# $VIASH_META_RESOURCES_DIR        : directory containing the resources
+# $VIASH_VERBOSITY                 : verbosity level
+# exit code $?                     : whether or not the image was built successfully
+function ViashDockerBuild {
+  local image_id="$1"
+  shift 1
+
+  # create temporary directory to store dockerfile & optional resources in
+  local tmpdir=$(mktemp -d "$VIASH_META_TEMP_DIR/dockerbuild-$VIASH_META_NAME-XXXXXX")
+  local dockerfile="$tmpdir/Dockerfile"
+  function clean_up {
+    rm -rf "$tmpdir"
+  }
+  trap clean_up EXIT
+
+  # store dockerfile and resources
+  ViashDockerfile "$VIASH_ENGINE_ID" > "$dockerfile"
+
+  # generate the build command
+  local docker_build_cmd="docker build -t '$image_id' $@ '$VIASH_META_RESOURCES_DIR' -f '$dockerfile'"
+
+  # build the container
+  ViashNotice "Building container '$image_id' with Dockerfile"
+  ViashInfo "$docker_build_cmd"
+  local save=$-; set +e
+  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
+    eval $docker_build_cmd
+  else
+    eval $docker_build_cmd &> "$tmpdir/docker_build.log"
+  fi
+
+  # check exit code
+  local out=$?
+  [[ $save =~ e ]] && set -e
+  if [ $out -ne 0 ]; then
+    ViashError "Error occurred while building container '$image_id'"
+    if [ $VIASH_VERBOSITY -lt $VIASH_LOGCODE_INFO ]; then
+      ViashError "Transcript: --------------------------------"
+      cat "$tmpdir/docker_build.log"
+      ViashError "End of transcript --------------------------"
+    fi
+    exit 1
+  fi
+}
+
+######## End of helper functions for setting up Docker images for viash ########
+
+# ViashDockerFile: print the dockerfile to stdout
+# $1    : engine identifier
+# return : dockerfile required to run this component
+# examples:
+#   ViashDockerFile
+function ViashDockerfile {
+  local engine_id="$1"
+
+  if [[ "$engine_id" == "docker" ]]; then
+    cat << 'VIASHDOCKER'
+FROM ubuntu:22.04
+ENTRYPOINT []
+RUN apt-get update && \
+  DEBIAN_FRONTEND=noninteractive apt-get install -y build-essential gcc g++ make wget zlib1g-dev unzip && \
+  rm -rf /var/lib/apt/lists/*
+
+ENV STAR_VERSION=2.7.11b
+ENV RSEM_VERSION=1.3.3
+RUN apt-get update && \
+apt-get clean && \
+wget --no-check-certificate https://github.com/alexdobin/STAR/archive/refs/tags/2.7.11a.zip && \
+unzip 2.7.11a.zip && \
+cp STAR-2.7.11a/bin/Linux_x86_64_static/STAR /usr/local/bin  && \
+cd && \
+wget --no-check-certificate https://github.com/deweylab/RSEM/archive/refs/tags/v1.3.3.zip && \
+unzip v1.3.3.zip && \
+cd RSEM-1.3.3 && \
+make && \
+make install
+
+RUN echo "RSEM: `rsem-calculate-expression --version | sed -e 's/Current version: RSEM v//g'`" > /var/software_versions.txt && \
+echo "STAR: `STAR --version`" >> /var/software_versions.txt && \
+echo "bowtie2: `bowtie2 --version | grep -oP '\d+\.\d+\.\d+'`" >> /var/software_versions.txt && \
+echo "bowtie: `bowtie --version | grep -oP 'bowtie-align-s version \K\d+\.\d+\.\d+'`" >> /var/software_versions.txt && \
+echo "HISAT2: `hisat2 --version | grep -oP 'hisat2-align-s version \K\d+\.\d+\.\d+'`" >> /var/software_versions.txt
+
+LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_calculate_expression"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:41Z"
+LABEL org.opencontainers.image.source="https://github.com/deweylab/RSEM"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+LABEL org.opencontainers.image.version="main"
+
+VIASHDOCKER
+  fi
+}
+
+# ViashDockerBuildArgs: return the arguments to pass to docker build
+# $1    : engine identifier
+# return : arguments to pass to docker build
+function ViashDockerBuildArgs {
+  local engine_id="$1"
+
+  if [[ "$engine_id" == "docker" ]]; then
+    echo ""
+  fi
+}
+
+# ViashAbsolutePath: generate absolute path from relative path
+# borrowed from https://stackoverflow.com/a/21951256
+# $1     : relative filename
+# return : absolute path
+# examples:
+#   ViashAbsolutePath some_file.txt   # returns /path/to/some_file.txt
+#   ViashAbsolutePath /foo/bar/..     # returns /foo
+function ViashAbsolutePath {
+  local thePath
+  local parr
+  local outp
+  local len
+  if [[ ! "$1" =~ ^/ ]]; then
+    thePath="$PWD/$1"
+  else
+    thePath="$1"
+  fi
+  echo "$thePath" | (
+    IFS=/
+    read -a parr
+    declare -a outp
+    for i in "${parr[@]}"; do
+      case "$i" in
+      ''|.) continue ;;
+      ..)
+        len=${#outp[@]}
+        if ((len==0)); then
+          continue
+        else
+          unset outp[$((len-1))]
+        fi
+        ;;
+      *)
+        len=${#outp[@]}
+        outp[$len]="$i"
+      ;;
+      esac
+    done
+    echo /"${outp[*]}"
+  )
+}
+# ViashDockerAutodetectMount: auto configuring docker mounts from parameters
+# $1                             : The parameter value
+# returns                        : New parameter
+# $VIASH_DIRECTORY_MOUNTS        : Added another parameter to be passed to docker
+# $VIASH_DOCKER_AUTOMOUNT_PREFIX : The prefix to be used for the automounts
+# examples:
+#   ViashDockerAutodetectMount /path/to/bar      # returns '/viash_automount/path/to/bar'
+#   ViashDockerAutodetectMountArg /path/to/bar   # returns '--volume="/path/to:/viash_automount/path/to"'
+function ViashDockerAutodetectMount {
+  local abs_path=$(ViashAbsolutePath "$1")
+  local mount_source
+  local base_name
+  if [ -d "$abs_path" ]; then
+    mount_source="$abs_path"
+    base_name=""
+  else
+    mount_source=`dirname "$abs_path"`
+    base_name=`basename "$abs_path"`
+  fi
+  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
+  if [ -z "$base_name" ]; then
+    echo "$mount_target"
+  else
+    echo "$mount_target/$base_name"
+  fi
+}
+function ViashDockerAutodetectMountArg {
+  local abs_path=$(ViashAbsolutePath "$1")
+  local mount_source
+  local base_name
+  if [ -d "$abs_path" ]; then
+    mount_source="$abs_path"
+    base_name=""
+  else
+    mount_source=`dirname "$abs_path"`
+    base_name=`basename "$abs_path"`
+  fi
+  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
+  ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target"
+  echo "--volume=\"$mount_source:$mount_target\""
+}
+function ViashDockerStripAutomount {
+  local abs_path=$(ViashAbsolutePath "$1")
+  echo "${abs_path#$VIASH_DOCKER_AUTOMOUNT_PREFIX}"
+}
+# initialise variables
+VIASH_DIRECTORY_MOUNTS=()
+
+# configure default docker automount prefix if it is unset
+if [ -z "${VIASH_DOCKER_AUTOMOUNT_PREFIX+x}" ]; then
+  VIASH_DOCKER_AUTOMOUNT_PREFIX="/viash_automount"
+fi
+
+# initialise docker variables
+VIASH_DOCKER_RUN_ARGS=(-i --rm)
+
+
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
   echo "rsem_calculate_expression main"
@@ -689,425 +1108,32 @@ function ViashHelp {
   echo "        Parameters for all the above models are learned from a training set. For"
   echo "        detailed explanations, please"
   echo "        see prior-enhanced RSEM's paper. (Default: 'pk')"
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
 }
 
-# initialise variables
-VIASH_MODE='run'
-VIASH_ENGINE_ID='docker'
-
-######## Helper functions for setting up Docker images for viash ########
-# expects: ViashDockerBuild
-
-# ViashDockerInstallationCheck: check whether Docker is installed correctly
-#
-# examples:
-#   ViashDockerInstallationCheck
-function ViashDockerInstallationCheck {
-  ViashDebug "Checking whether Docker is installed"
-  if [ ! command -v docker &> /dev/null ]; then
-    ViashCritical "Docker doesn't seem to be installed. See 'https://docs.docker.com/get-docker/' for instructions."
-    exit 1
-  fi
-
-  ViashDebug "Checking whether the Docker daemon is running"
-  local save=$-; set +e
-  local docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
-  local out=$?
-  [[ $save =~ e ]] && set -e
-  if [ $out -ne 0 ]; then
-    ViashCritical "Docker daemon does not seem to be running. Try one of the following:"
-    ViashCritical "- Try running 'dockerd' in the command line"
-    ViashCritical "- See https://docs.docker.com/config/daemon/"
-    exit 1
-  fi
-}
-
-# ViashDockerRemoteTagCheck: check whether a Docker image is available 
-# on a remote. Assumes `docker login` has been performed, if relevant.
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   ViashDockerRemoteTagCheck python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerRemoteTagCheck sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerRemoteTagCheck {
-  docker manifest inspect $1 > /dev/null 2> /dev/null
-}
-
-# ViashDockerLocalTagCheck: check whether a Docker image is available locally
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   docker pull python:latest
-#   ViashDockerLocalTagCheck python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerLocalTagCheck sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerLocalTagCheck {
-  [ -n "$(docker images -q $1)" ]
-}
-
-# ViashDockerPull: pull a Docker image
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   ViashDockerPull python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerPull sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerPull {
-  ViashNotice "Checking if Docker image is available at '$1'"
-  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
-    docker pull $1 && return 0 || return 1
-  else
-    local save=$-; set +e
-    docker pull $1 2> /dev/null > /dev/null
-    local out=$?
-    [[ $save =~ e ]] && set -e
-    if [ $out -ne 0 ]; then
-      ViashWarning "Could not pull from '$1'. Docker image doesn't exist or is not accessible."
-    fi
-    return $out
-  fi
-}
-
-# ViashDockerPush: push a Docker image
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   ViashDockerPush python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerPush sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerPush {
-  ViashNotice "Pushing image to '$1'"
-  local save=$-; set +e
-  local out
-  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
-    docker push $1
-    out=$?
-  else
-    docker push $1 2> /dev/null > /dev/null
-    out=$?
-  fi
-  [[ $save =~ e ]] && set -e
-  if [ $out -eq 0 ]; then
-    ViashNotice "Container '$1' push succeeded."
-  else
-    ViashError "Container '$1' push errored. You might not be logged in or have the necessary permissions."
-  fi
-  return $out
-}
-
-# ViashDockerPullElseBuild: pull a Docker image, else build it
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# ViashDockerBuild    : a Bash function which builds a docker image, takes image identifier as argument.
-# examples:
-#   ViashDockerPullElseBuild mynewcomponent
-function ViashDockerPullElseBuild {
-  local save=$-; set +e
-  ViashDockerPull $1
-  local out=$?
-  [[ $save =~ e ]] && set -e
-  if [ $out -ne 0 ]; then
-    ViashDockerBuild $@
-  fi
-}
-
-# ViashDockerSetup: create a Docker image, according to specified docker setup strategy
-#
-# $1          : image identifier with format `[registry/]image[:tag]`
-# $2          : docker setup strategy, see DockerSetupStrategy.scala
-# examples:
-#   ViashDockerSetup mynewcomponent alwaysbuild
-function ViashDockerSetup {
-  local image_id="$1"
-  local setup_strategy="$2"
-  if [ "$setup_strategy" == "alwaysbuild" -o "$setup_strategy" == "build" -o "$setup_strategy" == "b" ]; then
-    ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-  elif [ "$setup_strategy" == "alwayspull" -o "$setup_strategy" == "pull" -o "$setup_strategy" == "p" ]; then
-    ViashDockerPull $image_id
-  elif [ "$setup_strategy" == "alwayspullelsebuild" -o "$setup_strategy" == "pullelsebuild" ]; then
-    ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-  elif [ "$setup_strategy" == "alwayspullelsecachedbuild" -o "$setup_strategy" == "pullelsecachedbuild" ]; then
-    ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-  elif [ "$setup_strategy" == "alwayscachedbuild" -o "$setup_strategy" == "cachedbuild" -o "$setup_strategy" == "cb" ]; then
-    ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-  elif [[ "$setup_strategy" =~ ^ifneedbe ]]; then
-    local save=$-; set +e
-    ViashDockerLocalTagCheck $image_id
-    local outCheck=$?
-    [[ $save =~ e ]] && set -e
-    if [ $outCheck -eq 0 ]; then
-      ViashInfo "Image $image_id already exists"
-    elif [ "$setup_strategy" == "ifneedbebuild" ]; then
-      ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-    elif [ "$setup_strategy" == "ifneedbecachedbuild" ]; then
-      ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-    elif [ "$setup_strategy" == "ifneedbepull" ]; then
-      ViashDockerPull $image_id
-    elif [ "$setup_strategy" == "ifneedbepullelsebuild" ]; then
-      ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-    elif [ "$setup_strategy" == "ifneedbepullelsecachedbuild" ]; then
-      ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-    else
-      ViashError "Unrecognised Docker strategy: $setup_strategy"
-      exit 1
-    fi
-  elif [ "$setup_strategy" == "push" -o "$setup_strategy" == "forcepush" -o "$setup_strategy" == "alwayspush" ]; then
-    ViashDockerPush "$image_id"
-  elif [ "$setup_strategy" == "pushifnotpresent" -o "$setup_strategy" == "gentlepush" -o "$setup_strategy" == "maybepush" ]; then
-    local save=$-; set +e
-    ViashDockerRemoteTagCheck $image_id
-    local outCheck=$?
-    [[ $save =~ e ]] && set -e
-    if [ $outCheck -eq 0 ]; then
-      ViashNotice "Container '$image_id' exists, doing nothing."
-    else
-      ViashNotice "Container '$image_id' does not yet exist."
-      ViashDockerPush "$image_id"
-    fi
-  elif [ "$setup_strategy" == "donothing" -o "$setup_strategy" == "meh" ]; then
-    ViashNotice "Skipping setup."
-  else
-    ViashError "Unrecognised Docker strategy: $setup_strategy"
-    exit 1
-  fi
-}
-
-# ViashDockerCheckCommands: Check whether a docker container has the required commands
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# $@                  : commands to verify being present
-# examples:
-#   ViashDockerCheckCommands bash:4.0 bash ps foo
-function ViashDockerCheckCommands {
-  local image_id="$1"
-  shift 1
-  local commands="$@"
-  local save=$-; set +e
-  local missing # mark 'missing' as local in advance, otherwise the exit code of the command will be missing and always be '0'
-  missing=$(docker run --rm --entrypoint=sh "$image_id" -c "for command in $commands; do command -v \$command >/dev/null 2>&1; if [ \$? -ne 0 ]; then echo \$command; exit 1; fi; done")
-  local outCheck=$?
-  [[ $save =~ e ]] && set -e
-  if [ $outCheck -ne 0 ]; then
-  	ViashError "Docker container '$image_id' does not contain command '$missing'."
-  	exit 1
-  fi
-}
-
-# ViashDockerBuild: build a docker image
-# $1                               : image identifier with format `[registry/]image[:tag]`
-# $...                             : additional arguments to pass to docker build
-# $VIASH_META_TEMP_DIR             : temporary directory to store dockerfile & optional resources in
-# $VIASH_META_NAME                 : name of the component
-# $VIASH_META_RESOURCES_DIR        : directory containing the resources
-# $VIASH_VERBOSITY                 : verbosity level
-# exit code $?                     : whether or not the image was built successfully
-function ViashDockerBuild {
-  local image_id="$1"
-  shift 1
-
-  # create temporary directory to store dockerfile & optional resources in
-  local tmpdir=$(mktemp -d "$VIASH_META_TEMP_DIR/dockerbuild-$VIASH_META_NAME-XXXXXX")
-  local dockerfile="$tmpdir/Dockerfile"
-  function clean_up {
-    rm -rf "$tmpdir"
-  }
-  trap clean_up EXIT
-
-  # store dockerfile and resources
-  ViashDockerfile "$VIASH_ENGINE_ID" > "$dockerfile"
-
-  # generate the build command
-  local docker_build_cmd="docker build -t '$image_id' $@ '$VIASH_META_RESOURCES_DIR' -f '$dockerfile'"
-
-  # build the container
-  ViashNotice "Building container '$image_id' with Dockerfile"
-  ViashInfo "$docker_build_cmd"
-  local save=$-; set +e
-  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
-    eval $docker_build_cmd
-  else
-    eval $docker_build_cmd &> "$tmpdir/docker_build.log"
-  fi
-
-  # check exit code
-  local out=$?
-  [[ $save =~ e ]] && set -e
-  if [ $out -ne 0 ]; then
-    ViashError "Error occurred while building container '$image_id'"
-    if [ $VIASH_VERBOSITY -lt $VIASH_LOGCODE_INFO ]; then
-      ViashError "Transcript: --------------------------------"
-      cat "$tmpdir/docker_build.log"
-      ViashError "End of transcript --------------------------"
-    fi
-    exit 1
-  fi
-}
-
-######## End of helper functions for setting up Docker images for viash ########
-
-# ViashDockerFile: print the dockerfile to stdout
-# $1    : engine identifier
-# return : dockerfile required to run this component
-# examples:
-#   ViashDockerFile
-function ViashDockerfile {
-  local engine_id="$1"
-
-  if [[ "$engine_id" == "docker" ]]; then
-    cat << 'VIASHDOCKER'
-FROM ubuntu:22.04
-ENTRYPOINT []
-RUN apt-get update && \
-  DEBIAN_FRONTEND=noninteractive apt-get install -y build-essential gcc g++ make wget zlib1g-dev unzip && \
-  rm -rf /var/lib/apt/lists/*
-
-ENV STAR_VERSION=2.7.11b
-ENV RSEM_VERSION=1.3.3
-RUN apt-get update && \
-apt-get clean && \
-wget --no-check-certificate https://github.com/alexdobin/STAR/archive/refs/tags/2.7.11a.zip && \
-unzip 2.7.11a.zip && \
-cp STAR-2.7.11a/bin/Linux_x86_64_static/STAR /usr/local/bin  && \
-cd && \
-wget --no-check-certificate https://github.com/deweylab/RSEM/archive/refs/tags/v1.3.3.zip && \
-unzip v1.3.3.zip && \
-cd RSEM-1.3.3 && \
-make && \
-make install
-
-RUN echo "RSEM: `rsem-calculate-expression --version | sed -e 's/Current version: RSEM v//g'`" > /var/software_versions.txt && \
-echo "STAR: `STAR --version`" >> /var/software_versions.txt && \
-echo "bowtie2: `bowtie2 --version | grep -oP '\d+\.\d+\.\d+'`" >> /var/software_versions.txt && \
-echo "bowtie: `bowtie --version | grep -oP 'bowtie-align-s version \K\d+\.\d+\.\d+'`" >> /var/software_versions.txt && \
-echo "HISAT2: `hisat2 --version | grep -oP 'hisat2-align-s version \K\d+\.\d+\.\d+'`" >> /var/software_versions.txt
-
-LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_calculate_expression"
-LABEL org.opencontainers.image.created="2024-12-03T10:33:52Z"
-LABEL org.opencontainers.image.source="https://github.com/deweylab/RSEM"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-LABEL org.opencontainers.image.version="main"
-
-VIASHDOCKER
-  fi
-}
-
-# ViashDockerBuildArgs: return the arguments to pass to docker build
-# $1    : engine identifier
-# return : arguments to pass to docker build
-function ViashDockerBuildArgs {
-  local engine_id="$1"
-
-  if [[ "$engine_id" == "docker" ]]; then
-    echo ""
-  fi
-}
-
-# ViashAbsolutePath: generate absolute path from relative path
-# borrowed from https://stackoverflow.com/a/21951256
-# $1     : relative filename
-# return : absolute path
-# examples:
-#   ViashAbsolutePath some_file.txt   # returns /path/to/some_file.txt
-#   ViashAbsolutePath /foo/bar/..     # returns /foo
-function ViashAbsolutePath {
-  local thePath
-  local parr
-  local outp
-  local len
-  if [[ ! "$1" =~ ^/ ]]; then
-    thePath="$PWD/$1"
-  else
-    thePath="$1"
-  fi
-  echo "$thePath" | (
-    IFS=/
-    read -a parr
-    declare -a outp
-    for i in "${parr[@]}"; do
-      case "$i" in
-      ''|.) continue ;;
-      ..)
-        len=${#outp[@]}
-        if ((len==0)); then
-          continue
-        else
-          unset outp[$((len-1))]
-        fi
-        ;;
-      *)
-        len=${#outp[@]}
-        outp[$len]="$i"
-      ;;
-      esac
-    done
-    echo /"${outp[*]}"
-  )
-}
-# ViashDockerAutodetectMount: auto configuring docker mounts from parameters
-# $1                             : The parameter value
-# returns                        : New parameter
-# $VIASH_DIRECTORY_MOUNTS        : Added another parameter to be passed to docker
-# $VIASH_DOCKER_AUTOMOUNT_PREFIX : The prefix to be used for the automounts
-# examples:
-#   ViashDockerAutodetectMount /path/to/bar      # returns '/viash_automount/path/to/bar'
-#   ViashDockerAutodetectMountArg /path/to/bar   # returns '--volume="/path/to:/viash_automount/path/to"'
-function ViashDockerAutodetectMount {
-  local abs_path=$(ViashAbsolutePath "$1")
-  local mount_source
-  local base_name
-  if [ -d "$abs_path" ]; then
-    mount_source="$abs_path"
-    base_name=""
-  else
-    mount_source=`dirname "$abs_path"`
-    base_name=`basename "$abs_path"`
-  fi
-  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
-  if [ -z "$base_name" ]; then
-    echo "$mount_target"
-  else
-    echo "$mount_target/$base_name"
-  fi
-}
-function ViashDockerAutodetectMountArg {
-  local abs_path=$(ViashAbsolutePath "$1")
-  local mount_source
-  local base_name
-  if [ -d "$abs_path" ]; then
-    mount_source="$abs_path"
-    base_name=""
-  else
-    mount_source=`dirname "$abs_path"`
-    base_name=`basename "$abs_path"`
-  fi
-  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
-  ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target"
-  echo "--volume=\"$mount_source:$mount_target\""
-}
-function ViashDockerStripAutomount {
-  local abs_path=$(ViashAbsolutePath "$1")
-  echo "${abs_path#$VIASH_DOCKER_AUTOMOUNT_PREFIX}"
-}
-# initialise variables
-VIASH_DIRECTORY_MOUNTS=()
-
-# configure default docker automount prefix if it is unset
-if [ -z "${VIASH_DOCKER_AUTOMOUNT_PREFIX+x}" ]; then
-  VIASH_DOCKER_AUTOMOUNT_PREFIX="/viash_automount"
-fi
-
-# initialise docker variables
-VIASH_DOCKER_RUN_ARGS=(-i --rm)
-
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/rsem/rsem_prepare_reference/.config.vsh.yaml b/target/executable/rsem/rsem_prepare_reference/.config.vsh.yaml
index 6a4e3891..a96f3460 100644
--- a/target/executable/rsem/rsem_prepare_reference/.config.vsh.yaml
+++ b/target/executable/rsem/rsem_prepare_reference/.config.vsh.yaml
@@ -268,6 +268,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -415,16 +418,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/rsem/rsem_prepare_reference"
   executable: "target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference b/target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference
index d54f8faa..44a05792 100755
--- a/target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference
+++ b/target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference
@@ -2,7 +2,7 @@
 
 # rsem_prepare_reference main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,168 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "rsem_prepare_reference main"
-  echo ""
-  echo "RSEM is a software package for estimating gene and isoform expression levels"
-  echo "from RNA-Seq data. This component prepares transcript references for RSEM."
-  echo ""
-  echo "Inputs:"
-  echo "    --reference_fasta_files"
-  echo "        type: file, required parameter, multiple values allowed, file must exist"
-  echo "        example: read1.fasta"
-  echo "        Semi-colon separated list of Multi-FASTA formatted files OR a directory"
-  echo "        name. If a directory name is specified, RSEM will read all files with"
-  echo "        suffix \".fa\" or \".fasta\" in this directory. The files should contain"
-  echo "        either the sequences of transcripts or an entire genome, depending on"
-  echo "        whether the '--gtf' option is used."
-  echo ""
-  echo "    --reference_name"
-  echo "        type: string, required parameter"
-  echo "        example: /ref/mm9"
-  echo "        The name of the reference used. RSEM will generate several"
-  echo "        reference-related files that are prefixed by this name. This name can"
-  echo "        contain path information (e.g. '/ref/mm9')."
-  echo ""
-  echo "Outputs:"
-  echo "    --output"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        Directory containing reference files generated by RSEM."
-  echo ""
-  echo "Other options:"
-  echo "    --gtf"
-  echo "        type: file, file must exist"
-  echo "        example: annotations.gtf"
-  echo "        Assume that 'reference_fasta_files' contains the sequence of a genome,"
-  echo "        and extract transcript reference sequences using the gene annotations"
-  echo "        specified in the GTF file. If this and '--gff3' options are not"
-  echo "        provided, RSEM will assume 'reference_fasta_files' contains the"
-  echo "        reference transcripts. In this case, RSEM assumes that name of each"
-  echo "        sequence in the Multi-FASTA files is its transcript_id."
-  echo ""
-  echo "    --gff3"
-  echo "        type: file, file must exist"
-  echo "        example: annotations.gff"
-  echo "        GFF3 annotation file. Converted to GTF format with the file name"
-  echo "        'reference_name.gtf'. Please make sure that 'reference_name.gtf' does"
-  echo "        not exist."
-  echo ""
-  echo "    --gff3_rna_patterns"
-  echo "        type: string, multiple values allowed"
-  echo "        example: mRNA;rRNA"
-  echo "        List of transcript categories (separated by semi-colon). Only"
-  echo "        transcripts that match the string will be extracted."
-  echo ""
-  echo "    --gff3_genes_as_transcripts"
-  echo "        type: boolean_true"
-  echo "        This option is designed for untypical organisms, such as viruses, whose"
-  echo "        GFF3 files only contain genes. RSEM will assume each gene as a unique"
-  echo "        transcript when it converts the GFF3 file into GTF format."
-  echo ""
-  echo "    --trusted_sources"
-  echo "        type: string, multiple values allowed"
-  echo "        example: ENSEMBL;HAVANA"
-  echo "        List of trusted sources (separated by semi-colon). Only transcripts"
-  echo "        coming from these sources will be extracted. If this option is off, all"
-  echo "        sources are accepted."
-  echo ""
-  echo "    --transcript_to_gene_map"
-  echo "        type: file, file must exist"
-  echo "        example: isoforms.txt"
-  echo "        Use information from this file to map from transcript (isoform) ids to"
-  echo "        gene ids. Each line of this file should be of the form:"
-  echo "          gene_id transcript_id"
-  echo "        with the two fields separated by a tab character."
-  echo "        If you are using a GTF file for the \"UCSC Genes\" gene set from the UCSC"
-  echo "        Genome Browser, then the \"knownIsoforms.txt\" file (obtained from the"
-  echo "        \"Downloads\" section of the UCSC Genome Browser site) is of this format."
-  echo "        If this option is off, then the mapping of isoforms to genes depends on"
-  echo "        whether the '--gtf' option is specified. If '--gtf' is specified, then"
-  echo "        RSEM uses the \"gene_id\" and \"transcript_id\" attributes in the GTF file."
-  echo "        Otherwise, RSEM assumes that each sequence in the reference sequence"
-  echo "        files is a separate gene."
-  echo ""
-  echo "    --allele_to_gene_map"
-  echo "        type: file, file must exist"
-  echo "        Use information from <file> to provide gene_id and transcript_id"
-  echo "        information for each allele-specific transcript. Each line of <file>"
-  echo "        should be of the form:"
-  echo "          gene_id transcript_id allele_id"
-  echo "        with the fields separated by a tab character."
-  echo "        This option is designed for quantifying allele-specific expression. It"
-  echo "        is only valid if '--gtf' option is not specified. allele_id should be"
-  echo "        the sequence names presented in the Multi-FASTA-formatted files."
-  echo ""
-  echo "    --polyA"
-  echo "        type: boolean_true"
-  echo "        Add poly(A) tails to the end of all reference isoforms. The length of"
-  echo "        poly(A) tail added is specified by '--polyA-length' option. STAR aligner"
-  echo "        users may not want to use this option."
-  echo ""
-  echo "    --polyA_length"
-  echo "        type: integer"
-  echo "        example: 125"
-  echo "        The length of the poly(A) tails to be added."
-  echo ""
-  echo "    --no_polyA_subset"
-  echo "        type: file, file must exist"
-  echo "        example: transcript_ids.txt"
-  echo "        Only meaningful if '--polyA' is specified. Do not add poly(A) tails to"
-  echo "        those transcripts listed in this file containing a list of"
-  echo "        transcript_ids."
-  echo ""
-  echo "    --bowtie"
-  echo "        type: boolean_true"
-  echo "        Build Bowtie indices."
-  echo ""
-  echo "    --bowtie2"
-  echo "        type: boolean_true"
-  echo "        Build Bowtie 2 indices."
-  echo ""
-  echo "    --star"
-  echo "        type: boolean_true"
-  echo "        Build STAR indices."
-  echo ""
-  echo "    --star_sjdboverhang"
-  echo "        type: integer"
-  echo "        example: 100"
-  echo "        Length of the genomic sequence around annotated junction. It is only"
-  echo "        used for STAR to build splice junctions database and not needed for"
-  echo "        Bowtie or Bowtie2. It will be passed as the --sjdbOverhang option to"
-  echo "        STAR. According to STAR's manual, its ideal value is max(ReadLength)-1,"
-  echo "        e.g. for 2x101 paired-end reads, the ideal value is 101-1=100. In most"
-  echo "        cases, the default value of 100 will work as well as the ideal value."
-  echo "        (Default is 100)"
-  echo ""
-  echo "    --hisat2_hca"
-  echo "        type: boolean_true"
-  echo "        Build HISAT2 indices on the transcriptome according to Human Cell Atlas"
-  echo "        (HCA) SMART-Seq2 pipeline."
-  echo ""
-  echo "    -q, --quiet"
-  echo "        type: boolean_true"
-  echo "        Suppress the output of logging information."
-  echo ""
-  echo "Prior-enhanced RSEM options:"
-  echo "    --prep_pRSEM"
-  echo "        type: boolean_true"
-  echo "        A Boolean indicating whether to prepare reference files for pRSEM,"
-  echo "        including building Bowtie indices for a genome and selecting training"
-  echo "        set isoforms. The index files will be used for aligning ChIP-seq reads"
-  echo "        in prior-enhanced RSEM and the training set isoforms will be used for"
-  echo "        learning prior. A path to Bowtie executables and a mappability file in"
-  echo "        bigWig format are required when this option is on. Currently, Bowtie2 is"
-  echo "        not supported for prior-enhanced RSEM."
-  echo ""
-  echo "    --mappability_bigwig_file"
-  echo "        type: file, file must exist"
-  echo "        Full path to a whole-genome mappability file in bigWig format. This file"
-  echo "        is required for running prior-enhanced RSEM. It is used for selecting a"
-  echo "        training set of isoforms for prior-learning. This file can be either"
-  echo "        downloaded from UCSC Genome Browser or generated by GEM (Derrien et al.,"
-  echo "        2012, PLoS One)."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -656,9 +494,9 @@ echo "HISAT2: `hisat2 --version | grep -oP 'hisat2-align-s version \K\d+\.\d+\.\
 
 LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
 LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_prepare_reference"
-LABEL org.opencontainers.image.created="2024-12-03T10:33:52Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:41Z"
 LABEL org.opencontainers.image.source="https://github.com/deweylab/RSEM"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -773,6 +611,194 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "rsem_prepare_reference main"
+  echo ""
+  echo "RSEM is a software package for estimating gene and isoform expression levels"
+  echo "from RNA-Seq data. This component prepares transcript references for RSEM."
+  echo ""
+  echo "Inputs:"
+  echo "    --reference_fasta_files"
+  echo "        type: file, required parameter, multiple values allowed, file must exist"
+  echo "        example: read1.fasta"
+  echo "        Semi-colon separated list of Multi-FASTA formatted files OR a directory"
+  echo "        name. If a directory name is specified, RSEM will read all files with"
+  echo "        suffix \".fa\" or \".fasta\" in this directory. The files should contain"
+  echo "        either the sequences of transcripts or an entire genome, depending on"
+  echo "        whether the '--gtf' option is used."
+  echo ""
+  echo "    --reference_name"
+  echo "        type: string, required parameter"
+  echo "        example: /ref/mm9"
+  echo "        The name of the reference used. RSEM will generate several"
+  echo "        reference-related files that are prefixed by this name. This name can"
+  echo "        contain path information (e.g. '/ref/mm9')."
+  echo ""
+  echo "Outputs:"
+  echo "    --output"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        Directory containing reference files generated by RSEM."
+  echo ""
+  echo "Other options:"
+  echo "    --gtf"
+  echo "        type: file, file must exist"
+  echo "        example: annotations.gtf"
+  echo "        Assume that 'reference_fasta_files' contains the sequence of a genome,"
+  echo "        and extract transcript reference sequences using the gene annotations"
+  echo "        specified in the GTF file. If this and '--gff3' options are not"
+  echo "        provided, RSEM will assume 'reference_fasta_files' contains the"
+  echo "        reference transcripts. In this case, RSEM assumes that name of each"
+  echo "        sequence in the Multi-FASTA files is its transcript_id."
+  echo ""
+  echo "    --gff3"
+  echo "        type: file, file must exist"
+  echo "        example: annotations.gff"
+  echo "        GFF3 annotation file. Converted to GTF format with the file name"
+  echo "        'reference_name.gtf'. Please make sure that 'reference_name.gtf' does"
+  echo "        not exist."
+  echo ""
+  echo "    --gff3_rna_patterns"
+  echo "        type: string, multiple values allowed"
+  echo "        example: mRNA;rRNA"
+  echo "        List of transcript categories (separated by semi-colon). Only"
+  echo "        transcripts that match the string will be extracted."
+  echo ""
+  echo "    --gff3_genes_as_transcripts"
+  echo "        type: boolean_true"
+  echo "        This option is designed for untypical organisms, such as viruses, whose"
+  echo "        GFF3 files only contain genes. RSEM will assume each gene as a unique"
+  echo "        transcript when it converts the GFF3 file into GTF format."
+  echo ""
+  echo "    --trusted_sources"
+  echo "        type: string, multiple values allowed"
+  echo "        example: ENSEMBL;HAVANA"
+  echo "        List of trusted sources (separated by semi-colon). Only transcripts"
+  echo "        coming from these sources will be extracted. If this option is off, all"
+  echo "        sources are accepted."
+  echo ""
+  echo "    --transcript_to_gene_map"
+  echo "        type: file, file must exist"
+  echo "        example: isoforms.txt"
+  echo "        Use information from this file to map from transcript (isoform) ids to"
+  echo "        gene ids. Each line of this file should be of the form:"
+  echo "          gene_id transcript_id"
+  echo "        with the two fields separated by a tab character."
+  echo "        If you are using a GTF file for the \"UCSC Genes\" gene set from the UCSC"
+  echo "        Genome Browser, then the \"knownIsoforms.txt\" file (obtained from the"
+  echo "        \"Downloads\" section of the UCSC Genome Browser site) is of this format."
+  echo "        If this option is off, then the mapping of isoforms to genes depends on"
+  echo "        whether the '--gtf' option is specified. If '--gtf' is specified, then"
+  echo "        RSEM uses the \"gene_id\" and \"transcript_id\" attributes in the GTF file."
+  echo "        Otherwise, RSEM assumes that each sequence in the reference sequence"
+  echo "        files is a separate gene."
+  echo ""
+  echo "    --allele_to_gene_map"
+  echo "        type: file, file must exist"
+  echo "        Use information from <file> to provide gene_id and transcript_id"
+  echo "        information for each allele-specific transcript. Each line of <file>"
+  echo "        should be of the form:"
+  echo "          gene_id transcript_id allele_id"
+  echo "        with the fields separated by a tab character."
+  echo "        This option is designed for quantifying allele-specific expression. It"
+  echo "        is only valid if '--gtf' option is not specified. allele_id should be"
+  echo "        the sequence names presented in the Multi-FASTA-formatted files."
+  echo ""
+  echo "    --polyA"
+  echo "        type: boolean_true"
+  echo "        Add poly(A) tails to the end of all reference isoforms. The length of"
+  echo "        poly(A) tail added is specified by '--polyA-length' option. STAR aligner"
+  echo "        users may not want to use this option."
+  echo ""
+  echo "    --polyA_length"
+  echo "        type: integer"
+  echo "        example: 125"
+  echo "        The length of the poly(A) tails to be added."
+  echo ""
+  echo "    --no_polyA_subset"
+  echo "        type: file, file must exist"
+  echo "        example: transcript_ids.txt"
+  echo "        Only meaningful if '--polyA' is specified. Do not add poly(A) tails to"
+  echo "        those transcripts listed in this file containing a list of"
+  echo "        transcript_ids."
+  echo ""
+  echo "    --bowtie"
+  echo "        type: boolean_true"
+  echo "        Build Bowtie indices."
+  echo ""
+  echo "    --bowtie2"
+  echo "        type: boolean_true"
+  echo "        Build Bowtie 2 indices."
+  echo ""
+  echo "    --star"
+  echo "        type: boolean_true"
+  echo "        Build STAR indices."
+  echo ""
+  echo "    --star_sjdboverhang"
+  echo "        type: integer"
+  echo "        example: 100"
+  echo "        Length of the genomic sequence around annotated junction. It is only"
+  echo "        used for STAR to build splice junctions database and not needed for"
+  echo "        Bowtie or Bowtie2. It will be passed as the --sjdbOverhang option to"
+  echo "        STAR. According to STAR's manual, its ideal value is max(ReadLength)-1,"
+  echo "        e.g. for 2x101 paired-end reads, the ideal value is 101-1=100. In most"
+  echo "        cases, the default value of 100 will work as well as the ideal value."
+  echo "        (Default is 100)"
+  echo ""
+  echo "    --hisat2_hca"
+  echo "        type: boolean_true"
+  echo "        Build HISAT2 indices on the transcriptome according to Human Cell Atlas"
+  echo "        (HCA) SMART-Seq2 pipeline."
+  echo ""
+  echo "    -q, --quiet"
+  echo "        type: boolean_true"
+  echo "        Suppress the output of logging information."
+  echo ""
+  echo "Prior-enhanced RSEM options:"
+  echo "    --prep_pRSEM"
+  echo "        type: boolean_true"
+  echo "        A Boolean indicating whether to prepare reference files for pRSEM,"
+  echo "        including building Bowtie indices for a genome and selecting training"
+  echo "        set isoforms. The index files will be used for aligning ChIP-seq reads"
+  echo "        in prior-enhanced RSEM and the training set isoforms will be used for"
+  echo "        learning prior. A path to Bowtie executables and a mappability file in"
+  echo "        bigWig format are required when this option is on. Currently, Bowtie2 is"
+  echo "        not supported for prior-enhanced RSEM."
+  echo ""
+  echo "    --mappability_bigwig_file"
+  echo "        type: file, file must exist"
+  echo "        Full path to a whole-genome mappability file in bigWig format. This file"
+  echo "        is required for running prior-enhanced RSEM. It is used for selecting a"
+  echo "        training set of isoforms for prior-learning. This file can be either"
+  echo "        downloaded from UCSC Genome Browser or generated by GEM (Derrien et al.,"
+  echo "        2012, PLoS One)."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml b/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml
index 280b60bf..6d73df43 100644
--- a/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml
+++ b/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml
@@ -68,6 +68,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -174,16 +177,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/rseqc/rseqc_bamstat"
   executable: "target/executable/rseqc/rseqc_bamstat/rseqc_bamstat"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat b/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat
index 12df111e..c44379e3 100755
--- a/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat
+++ b/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat
@@ -2,7 +2,7 @@
 
 # rseqc_bamstat main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,28 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "rseqc_bamstat main"
-  echo ""
-  echo "Generate statistics from a bam file."
-  echo ""
-  echo "Input:"
-  echo "    -i, --input_file"
-  echo "        type: file, required parameter, file must exist"
-  echo "        Input alignment file in BAM or SAM format."
-  echo ""
-  echo "    -q, --mapq"
-  echo "        type: integer"
-  echo "        example: 30"
-  echo "        Minimum mapping quality (phred scaled) to determine uniquely mapped"
-  echo "        reads. Default: '30'."
-  echo ""
-  echo "Output:"
-  echo "    --output"
-  echo "        type: file, output, file must exist"
-  echo "        Output file (txt) with mapping quality statistics."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -477,9 +455,9 @@ RUN echo "RSeQC bam_stat.py: $(bam_stat.py --version | cut -d' ' -f2-)" > /var/s
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_bamstat"
-LABEL org.opencontainers.image.created="2024-12-03T10:33:58Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:37Z"
 LABEL org.opencontainers.image.source="https://github.com/MonashBioinformaticsPlatform/RSeQC"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -594,6 +572,54 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "rseqc_bamstat main"
+  echo ""
+  echo "Generate statistics from a bam file."
+  echo ""
+  echo "Input:"
+  echo "    -i, --input_file"
+  echo "        type: file, required parameter, file must exist"
+  echo "        Input alignment file in BAM or SAM format."
+  echo ""
+  echo "    -q, --mapq"
+  echo "        type: integer"
+  echo "        example: 30"
+  echo "        Minimum mapping quality (phred scaled) to determine uniquely mapped"
+  echo "        reads. Default: '30'."
+  echo ""
+  echo "Output:"
+  echo "    --output"
+  echo "        type: file, output, file must exist"
+  echo "        Output file (txt) with mapping quality statistics."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml b/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml
index 16703dc0..b5d69d14 100644
--- a/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml
+++ b/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml
@@ -96,6 +96,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -200,16 +203,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/rseqc/rseqc_inferexperiment"
   executable: "target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment b/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment
index ca87c154..21255b62 100755
--- a/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment
+++ b/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment
@@ -2,7 +2,7 @@
 
 # rseqc_inferexperiment main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,39 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "rseqc_inferexperiment main"
-  echo ""
-  echo "Infer strandedness from sequencing reads"
-  echo ""
-  echo "Input:"
-  echo "    -i, --input_file"
-  echo "        type: file, required parameter, file must exist"
-  echo "        input alignment file in BAM or SAM format"
-  echo ""
-  echo "    -r, --refgene"
-  echo "        type: file, required parameter, file must exist"
-  echo "        Reference gene model in bed format"
-  echo ""
-  echo "Output:"
-  echo "    --output"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        example: \$id.strandedness.txt"
-  echo "        Output file (txt) of strandness report."
-  echo ""
-  echo "Options:"
-  echo "    -s, --sample_size"
-  echo "        type: integer"
-  echo "        example: 200000"
-  echo "        Number of reads sampled from SAM/BAM file. Default: 200000"
-  echo ""
-  echo "    -q, --mapq"
-  echo "        type: integer"
-  echo "        example: 30"
-  echo "        Minimum mapping quality (phred scaled) to determine uniquely mapped"
-  echo "        reads. Default: 30"
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -488,9 +455,9 @@ RUN echo "RSeQC - infer_experiment.py: $(infer_experiment.py --version | cut -d'
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_inferexperiment"
-LABEL org.opencontainers.image.created="2024-12-03T10:33:59Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:36Z"
 LABEL org.opencontainers.image.source="https://github.com/MonashBioinformaticsPlatform/RSeQC"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -605,6 +572,65 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "rseqc_inferexperiment main"
+  echo ""
+  echo "Infer strandedness from sequencing reads"
+  echo ""
+  echo "Input:"
+  echo "    -i, --input_file"
+  echo "        type: file, required parameter, file must exist"
+  echo "        input alignment file in BAM or SAM format"
+  echo ""
+  echo "    -r, --refgene"
+  echo "        type: file, required parameter, file must exist"
+  echo "        Reference gene model in bed format"
+  echo ""
+  echo "Output:"
+  echo "    --output"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        example: \$id.strandedness.txt"
+  echo "        Output file (txt) of strandness report."
+  echo ""
+  echo "Options:"
+  echo "    -s, --sample_size"
+  echo "        type: integer"
+  echo "        example: 200000"
+  echo "        Number of reads sampled from SAM/BAM file. Default: 200000"
+  echo ""
+  echo "    -q, --mapq"
+  echo "        type: integer"
+  echo "        example: 30"
+  echo "        Minimum mapping quality (phred scaled) to determine uniquely mapped"
+  echo "        reads. Default: 30"
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/rseqc/rseqc_inner_distance/.config.vsh.yaml b/target/executable/rseqc/rseqc_inner_distance/.config.vsh.yaml
index e2c5ed2a..7e003aad 100644
--- a/target/executable/rseqc/rseqc_inner_distance/.config.vsh.yaml
+++ b/target/executable/rseqc/rseqc_inner_distance/.config.vsh.yaml
@@ -185,6 +185,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -293,16 +296,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/rseqc/rseqc_inner_distance"
   executable: "target/executable/rseqc/rseqc_inner_distance/rseqc_inner_distance"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/rseqc/rseqc_inner_distance/rseqc_inner_distance b/target/executable/rseqc/rseqc_inner_distance/rseqc_inner_distance
index 386ad6f3..79cb0882 100755
--- a/target/executable/rseqc/rseqc_inner_distance/rseqc_inner_distance
+++ b/target/executable/rseqc/rseqc_inner_distance/rseqc_inner_distance
@@ -2,7 +2,7 @@
 
 # rseqc_inner_distance main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,79 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "rseqc_inner_distance main"
-  echo ""
-  echo "Calculate inner distance between read pairs."
-  echo ""
-  echo "Input:"
-  echo "    -i, --input_file"
-  echo "        type: file, required parameter, file must exist"
-  echo "        input alignment file in BAM or SAM format"
-  echo ""
-  echo "    -r, --refgene"
-  echo "        type: file, required parameter, file must exist"
-  echo "        Reference gene model in bed format"
-  echo ""
-  echo "    -k, --sample_size"
-  echo "        type: integer"
-  echo "        example: 1000000"
-  echo "        Numer of reads sampled from SAM/BAM file, default = 1000000."
-  echo ""
-  echo "    -q, --mapq"
-  echo "        type: integer"
-  echo "        example: 30"
-  echo "        Minimum mapping quality (phred scaled) to determine uniquely mapped"
-  echo "        reads, default=30."
-  echo ""
-  echo "    -l, --lower_bound"
-  echo "        type: integer"
-  echo "        example: -250"
-  echo "        Lower bound of inner distance (bp). This option is used for ploting"
-  echo "        histograme, default=-250."
-  echo ""
-  echo "    -u, --upper_bound"
-  echo "        type: integer"
-  echo "        example: 250"
-  echo "        Upper bound of inner distance (bp). This option is used for ploting"
-  echo "        histograme, default=250."
-  echo ""
-  echo "    -s, --step"
-  echo "        type: integer"
-  echo "        example: 5"
-  echo "        Step size (bp) of histograme. This option is used for plotting"
-  echo "        histogram, default=5."
-  echo ""
-  echo "Output:"
-  echo "    -o, --output_prefix"
-  echo "        type: string, required parameter"
-  echo "        Rrefix of output files."
-  echo ""
-  echo "    --output_stats"
-  echo "        type: file, output, file must exist"
-  echo "        output file (txt) with summary statistics of inner distances of paired"
-  echo "        reads"
-  echo ""
-  echo "    --output_dist"
-  echo "        type: file, output, file must exist"
-  echo "        output file (txt) with inner distances of all paired reads"
-  echo ""
-  echo "    --output_freq"
-  echo "        type: file, output, file must exist"
-  echo "        output file (txt) with frequencies of inner distances of all paired"
-  echo "        reads"
-  echo ""
-  echo "    --output_plot"
-  echo "        type: file, output, file must exist"
-  echo "        output file (pdf) with histogram plot of of inner distances of all"
-  echo "        paired reads"
-  echo ""
-  echo "    --output_plot_r"
-  echo "        type: file, output, file must exist"
-  echo "        output file (R) with script of histogram plot of of inner distances of"
-  echo "        all paired reads"
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -532,9 +459,9 @@ RUN echo "RSeQC - inner_distance.py: $(inner_distance.py --version | cut -d' ' -
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_inner_distance"
-LABEL org.opencontainers.image.created="2024-12-03T10:33:58Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:36Z"
 LABEL org.opencontainers.image.source="https://github.com/MonashBioinformaticsPlatform/RSeQC"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -649,6 +576,105 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "rseqc_inner_distance main"
+  echo ""
+  echo "Calculate inner distance between read pairs."
+  echo ""
+  echo "Input:"
+  echo "    -i, --input_file"
+  echo "        type: file, required parameter, file must exist"
+  echo "        input alignment file in BAM or SAM format"
+  echo ""
+  echo "    -r, --refgene"
+  echo "        type: file, required parameter, file must exist"
+  echo "        Reference gene model in bed format"
+  echo ""
+  echo "    -k, --sample_size"
+  echo "        type: integer"
+  echo "        example: 1000000"
+  echo "        Numer of reads sampled from SAM/BAM file, default = 1000000."
+  echo ""
+  echo "    -q, --mapq"
+  echo "        type: integer"
+  echo "        example: 30"
+  echo "        Minimum mapping quality (phred scaled) to determine uniquely mapped"
+  echo "        reads, default=30."
+  echo ""
+  echo "    -l, --lower_bound"
+  echo "        type: integer"
+  echo "        example: -250"
+  echo "        Lower bound of inner distance (bp). This option is used for ploting"
+  echo "        histograme, default=-250."
+  echo ""
+  echo "    -u, --upper_bound"
+  echo "        type: integer"
+  echo "        example: 250"
+  echo "        Upper bound of inner distance (bp). This option is used for ploting"
+  echo "        histograme, default=250."
+  echo ""
+  echo "    -s, --step"
+  echo "        type: integer"
+  echo "        example: 5"
+  echo "        Step size (bp) of histograme. This option is used for plotting"
+  echo "        histogram, default=5."
+  echo ""
+  echo "Output:"
+  echo "    -o, --output_prefix"
+  echo "        type: string, required parameter"
+  echo "        Rrefix of output files."
+  echo ""
+  echo "    --output_stats"
+  echo "        type: file, output, file must exist"
+  echo "        output file (txt) with summary statistics of inner distances of paired"
+  echo "        reads"
+  echo ""
+  echo "    --output_dist"
+  echo "        type: file, output, file must exist"
+  echo "        output file (txt) with inner distances of all paired reads"
+  echo ""
+  echo "    --output_freq"
+  echo "        type: file, output, file must exist"
+  echo "        output file (txt) with frequencies of inner distances of all paired"
+  echo "        reads"
+  echo ""
+  echo "    --output_plot"
+  echo "        type: file, output, file must exist"
+  echo "        output file (pdf) with histogram plot of of inner distances of all"
+  echo "        paired reads"
+  echo ""
+  echo "    --output_plot_r"
+  echo "        type: file, output, file must exist"
+  echo "        output file (R) with script of histogram plot of of inner distances of"
+  echo "        all paired reads"
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/salmon/salmon_index/.config.vsh.yaml b/target/executable/salmon/salmon_index/.config.vsh.yaml
index 9a9aa6db..6c0cf5ea 100644
--- a/target/executable/salmon/salmon_index/.config.vsh.yaml
+++ b/target/executable/salmon/salmon_index/.config.vsh.yaml
@@ -176,6 +176,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -276,16 +279,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/salmon/salmon_index"
   executable: "target/executable/salmon/salmon_index/salmon_index"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/salmon/salmon_index/salmon_index b/target/executable/salmon/salmon_index/salmon_index
index 5bb7aeb9..9eb84369 100755
--- a/target/executable/salmon/salmon_index/salmon_index
+++ b/target/executable/salmon/salmon_index/salmon_index
@@ -2,7 +2,7 @@
 
 # salmon_index main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,100 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "salmon_index main"
-  echo ""
-  echo "Salmon is a tool for wicked-fast transcript quantification from RNA-seq data. It"
-  echo "can either make use of pre-computed alignments (in the form of a SAM/BAM file)"
-  echo "to the transcripts rather than the raw reads, or can be run in the mapping-based"
-  echo "mode. This component creates a salmon index for the transcriptome to use Salmon"
-  echo "in the mapping-based mode. It is generally recommend that you build a"
-  echo "decoy-aware transcriptome file. This is done using the entire genome of the"
-  echo "organism as the decoy sequence by concatenating the genome to the end of the"
-  echo "transcriptome to be indexed and populating the decoys.txt file with the"
-  echo "chromosome names."
-  echo ""
-  echo "Inputs:"
-  echo "    --genome"
-  echo "        type: file, file must exist"
-  echo "        example: genome.fasta"
-  echo "        Genome of the organism to prepare the set of decoy sequences. Required"
-  echo "        to build decoy-aware transcriptome."
-  echo ""
-  echo "    -t, --transcripts"
-  echo "        type: file, required parameter, file must exist"
-  echo "        example: transcriptome.fasta"
-  echo "        Transcript fasta file."
-  echo ""
-  echo "    -k, --kmer_len"
-  echo "        type: integer"
-  echo "        example: 31"
-  echo "        The size of k-mers that should be used for the quasi index."
-  echo ""
-  echo "    --gencode"
-  echo "        type: boolean_true"
-  echo "        This flag will expect the input transcript fasta to be in GENCODE"
-  echo "        format, and will split the transcript name at the first '|' character."
-  echo "        These reduced names will be used in the output and when looking for"
-  echo "        these transcripts in a gene to transcript GTF."
-  echo ""
-  echo "    --features"
-  echo "        type: boolean_true"
-  echo "        This flag will expect the input reference to be in the tsv file format,"
-  echo "        and will split the feature name at the first 'tab' character. These"
-  echo "        reduced names will be used in the output and when looking for the"
-  echo "        sequence of the features.GTF."
-  echo ""
-  echo "    --keep_duplicates"
-  echo "        type: boolean_true"
-  echo "        This flag will disable the default indexing behavior of discarding"
-  echo "        sequence-identical duplicate transcripts. If this flag is passed, then"
-  echo "        duplicate transcripts that appear in the input will be retained and"
-  echo "        quantified separately."
-  echo ""
-  echo "    --keep_fixed_fasta"
-  echo "        type: boolean_true"
-  echo "        Retain the fixed fasta file (without short transcripts and duplicates,"
-  echo "        clipped, etc.) generated during indexing."
-  echo ""
-  echo "    -f, --filter_size"
-  echo "        type: integer"
-  echo "        example: -1"
-  echo "        The size of the Bloom filter that will be used by TwoPaCo during"
-  echo "        indexing. The filter will be of size 2^{filter_size}. The default value"
-  echo "        of -1 means that the filter size will be automatically set based on the"
-  echo "        number of distinct k-mers in the input, as estimated by nthll."
-  echo ""
-  echo "    --sparse"
-  echo "        type: boolean_true"
-  echo "        Build the index using a sparse sampling of k-mer positions This will"
-  echo "        require less memory (especially during quantification), but will take"
-  echo "        longer to construct and can slow down mapping / alignment."
-  echo ""
-  echo "    -d, --decoys"
-  echo "        type: file, file must exist"
-  echo "        example: decoys.txt"
-  echo "        Treat these sequences ids from the reference as the decoys that may have"
-  echo "        sequence homologous to some known transcript. For example in case of the"
-  echo "        genome, provide a list of chromosome names (one per line)."
-  echo ""
-  echo "    --no_clip"
-  echo "        type: boolean_true"
-  echo "        Don't clip poly-A tails from the ends of target sequences."
-  echo ""
-  echo "    -n, --type"
-  echo "        type: string"
-  echo "        example: puff"
-  echo "        The type of index to build; the only option is \"puff\" in this version of"
-  echo "        salmon."
-  echo ""
-  echo "Output:"
-  echo "    -i, --index"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        example: Salmon_index"
-  echo "        Salmon index"
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -546,9 +452,9 @@ RUN salmon index -v 2>&1 | sed 's/salmon \([0-9.]*\)/salmon: \1/' > /var/softwar
 
 LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
 LABEL org.opencontainers.image.description="Companion container for running component salmon salmon_index"
-LABEL org.opencontainers.image.created="2024-12-03T10:34:02Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:41Z"
 LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -663,6 +569,126 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "salmon_index main"
+  echo ""
+  echo "Salmon is a tool for wicked-fast transcript quantification from RNA-seq data. It"
+  echo "can either make use of pre-computed alignments (in the form of a SAM/BAM file)"
+  echo "to the transcripts rather than the raw reads, or can be run in the mapping-based"
+  echo "mode. This component creates a salmon index for the transcriptome to use Salmon"
+  echo "in the mapping-based mode. It is generally recommend that you build a"
+  echo "decoy-aware transcriptome file. This is done using the entire genome of the"
+  echo "organism as the decoy sequence by concatenating the genome to the end of the"
+  echo "transcriptome to be indexed and populating the decoys.txt file with the"
+  echo "chromosome names."
+  echo ""
+  echo "Inputs:"
+  echo "    --genome"
+  echo "        type: file, file must exist"
+  echo "        example: genome.fasta"
+  echo "        Genome of the organism to prepare the set of decoy sequences. Required"
+  echo "        to build decoy-aware transcriptome."
+  echo ""
+  echo "    -t, --transcripts"
+  echo "        type: file, required parameter, file must exist"
+  echo "        example: transcriptome.fasta"
+  echo "        Transcript fasta file."
+  echo ""
+  echo "    -k, --kmer_len"
+  echo "        type: integer"
+  echo "        example: 31"
+  echo "        The size of k-mers that should be used for the quasi index."
+  echo ""
+  echo "    --gencode"
+  echo "        type: boolean_true"
+  echo "        This flag will expect the input transcript fasta to be in GENCODE"
+  echo "        format, and will split the transcript name at the first '|' character."
+  echo "        These reduced names will be used in the output and when looking for"
+  echo "        these transcripts in a gene to transcript GTF."
+  echo ""
+  echo "    --features"
+  echo "        type: boolean_true"
+  echo "        This flag will expect the input reference to be in the tsv file format,"
+  echo "        and will split the feature name at the first 'tab' character. These"
+  echo "        reduced names will be used in the output and when looking for the"
+  echo "        sequence of the features.GTF."
+  echo ""
+  echo "    --keep_duplicates"
+  echo "        type: boolean_true"
+  echo "        This flag will disable the default indexing behavior of discarding"
+  echo "        sequence-identical duplicate transcripts. If this flag is passed, then"
+  echo "        duplicate transcripts that appear in the input will be retained and"
+  echo "        quantified separately."
+  echo ""
+  echo "    --keep_fixed_fasta"
+  echo "        type: boolean_true"
+  echo "        Retain the fixed fasta file (without short transcripts and duplicates,"
+  echo "        clipped, etc.) generated during indexing."
+  echo ""
+  echo "    -f, --filter_size"
+  echo "        type: integer"
+  echo "        example: -1"
+  echo "        The size of the Bloom filter that will be used by TwoPaCo during"
+  echo "        indexing. The filter will be of size 2^{filter_size}. The default value"
+  echo "        of -1 means that the filter size will be automatically set based on the"
+  echo "        number of distinct k-mers in the input, as estimated by nthll."
+  echo ""
+  echo "    --sparse"
+  echo "        type: boolean_true"
+  echo "        Build the index using a sparse sampling of k-mer positions This will"
+  echo "        require less memory (especially during quantification), but will take"
+  echo "        longer to construct and can slow down mapping / alignment."
+  echo ""
+  echo "    -d, --decoys"
+  echo "        type: file, file must exist"
+  echo "        example: decoys.txt"
+  echo "        Treat these sequences ids from the reference as the decoys that may have"
+  echo "        sequence homologous to some known transcript. For example in case of the"
+  echo "        genome, provide a list of chromosome names (one per line)."
+  echo ""
+  echo "    --no_clip"
+  echo "        type: boolean_true"
+  echo "        Don't clip poly-A tails from the ends of target sequences."
+  echo ""
+  echo "    -n, --type"
+  echo "        type: string"
+  echo "        example: puff"
+  echo "        The type of index to build; the only option is \"puff\" in this version of"
+  echo "        salmon."
+  echo ""
+  echo "Output:"
+  echo "    -i, --index"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        example: Salmon_index"
+  echo "        Salmon index"
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/salmon/salmon_quant/.config.vsh.yaml b/target/executable/salmon/salmon_quant/.config.vsh.yaml
index aa5c90c5..859a4d82 100644
--- a/target/executable/salmon/salmon_quant/.config.vsh.yaml
+++ b/target/executable/salmon/salmon_quant/.config.vsh.yaml
@@ -1072,6 +1072,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -1172,16 +1175,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/salmon/salmon_quant"
   executable: "target/executable/salmon/salmon_quant/salmon_quant"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/salmon/salmon_quant/salmon_quant b/target/executable/salmon/salmon_quant/salmon_quant
index 8339019b..b999158d 100755
--- a/target/executable/salmon/salmon_quant/salmon_quant
+++ b/target/executable/salmon/salmon_quant/salmon_quant
@@ -2,7 +2,7 @@
 
 # salmon_quant main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,6 +172,404 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
+
+# initialise variables
+VIASH_MODE='run'
+VIASH_ENGINE_ID='docker'
+
+######## Helper functions for setting up Docker images for viash ########
+# expects: ViashDockerBuild
+
+# ViashDockerInstallationCheck: check whether Docker is installed correctly
+#
+# examples:
+#   ViashDockerInstallationCheck
+function ViashDockerInstallationCheck {
+  ViashDebug "Checking whether Docker is installed"
+  if [ ! command -v docker &> /dev/null ]; then
+    ViashCritical "Docker doesn't seem to be installed. See 'https://docs.docker.com/get-docker/' for instructions."
+    exit 1
+  fi
+
+  ViashDebug "Checking whether the Docker daemon is running"
+  local save=$-; set +e
+  local docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
+  local out=$?
+  [[ $save =~ e ]] && set -e
+  if [ $out -ne 0 ]; then
+    ViashCritical "Docker daemon does not seem to be running. Try one of the following:"
+    ViashCritical "- Try running 'dockerd' in the command line"
+    ViashCritical "- See https://docs.docker.com/config/daemon/"
+    exit 1
+  fi
+}
+
+# ViashDockerRemoteTagCheck: check whether a Docker image is available 
+# on a remote. Assumes `docker login` has been performed, if relevant.
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   ViashDockerRemoteTagCheck python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerRemoteTagCheck sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerRemoteTagCheck {
+  docker manifest inspect $1 > /dev/null 2> /dev/null
+}
+
+# ViashDockerLocalTagCheck: check whether a Docker image is available locally
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   docker pull python:latest
+#   ViashDockerLocalTagCheck python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerLocalTagCheck sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerLocalTagCheck {
+  [ -n "$(docker images -q $1)" ]
+}
+
+# ViashDockerPull: pull a Docker image
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   ViashDockerPull python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerPull sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerPull {
+  ViashNotice "Checking if Docker image is available at '$1'"
+  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
+    docker pull $1 && return 0 || return 1
+  else
+    local save=$-; set +e
+    docker pull $1 2> /dev/null > /dev/null
+    local out=$?
+    [[ $save =~ e ]] && set -e
+    if [ $out -ne 0 ]; then
+      ViashWarning "Could not pull from '$1'. Docker image doesn't exist or is not accessible."
+    fi
+    return $out
+  fi
+}
+
+# ViashDockerPush: push a Docker image
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   ViashDockerPush python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerPush sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerPush {
+  ViashNotice "Pushing image to '$1'"
+  local save=$-; set +e
+  local out
+  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
+    docker push $1
+    out=$?
+  else
+    docker push $1 2> /dev/null > /dev/null
+    out=$?
+  fi
+  [[ $save =~ e ]] && set -e
+  if [ $out -eq 0 ]; then
+    ViashNotice "Container '$1' push succeeded."
+  else
+    ViashError "Container '$1' push errored. You might not be logged in or have the necessary permissions."
+  fi
+  return $out
+}
+
+# ViashDockerPullElseBuild: pull a Docker image, else build it
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# ViashDockerBuild    : a Bash function which builds a docker image, takes image identifier as argument.
+# examples:
+#   ViashDockerPullElseBuild mynewcomponent
+function ViashDockerPullElseBuild {
+  local save=$-; set +e
+  ViashDockerPull $1
+  local out=$?
+  [[ $save =~ e ]] && set -e
+  if [ $out -ne 0 ]; then
+    ViashDockerBuild $@
+  fi
+}
+
+# ViashDockerSetup: create a Docker image, according to specified docker setup strategy
+#
+# $1          : image identifier with format `[registry/]image[:tag]`
+# $2          : docker setup strategy, see DockerSetupStrategy.scala
+# examples:
+#   ViashDockerSetup mynewcomponent alwaysbuild
+function ViashDockerSetup {
+  local image_id="$1"
+  local setup_strategy="$2"
+  if [ "$setup_strategy" == "alwaysbuild" -o "$setup_strategy" == "build" -o "$setup_strategy" == "b" ]; then
+    ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+  elif [ "$setup_strategy" == "alwayspull" -o "$setup_strategy" == "pull" -o "$setup_strategy" == "p" ]; then
+    ViashDockerPull $image_id
+  elif [ "$setup_strategy" == "alwayspullelsebuild" -o "$setup_strategy" == "pullelsebuild" ]; then
+    ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+  elif [ "$setup_strategy" == "alwayspullelsecachedbuild" -o "$setup_strategy" == "pullelsecachedbuild" ]; then
+    ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+  elif [ "$setup_strategy" == "alwayscachedbuild" -o "$setup_strategy" == "cachedbuild" -o "$setup_strategy" == "cb" ]; then
+    ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+  elif [[ "$setup_strategy" =~ ^ifneedbe ]]; then
+    local save=$-; set +e
+    ViashDockerLocalTagCheck $image_id
+    local outCheck=$?
+    [[ $save =~ e ]] && set -e
+    if [ $outCheck -eq 0 ]; then
+      ViashInfo "Image $image_id already exists"
+    elif [ "$setup_strategy" == "ifneedbebuild" ]; then
+      ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+    elif [ "$setup_strategy" == "ifneedbecachedbuild" ]; then
+      ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+    elif [ "$setup_strategy" == "ifneedbepull" ]; then
+      ViashDockerPull $image_id
+    elif [ "$setup_strategy" == "ifneedbepullelsebuild" ]; then
+      ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+    elif [ "$setup_strategy" == "ifneedbepullelsecachedbuild" ]; then
+      ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+    else
+      ViashError "Unrecognised Docker strategy: $setup_strategy"
+      exit 1
+    fi
+  elif [ "$setup_strategy" == "push" -o "$setup_strategy" == "forcepush" -o "$setup_strategy" == "alwayspush" ]; then
+    ViashDockerPush "$image_id"
+  elif [ "$setup_strategy" == "pushifnotpresent" -o "$setup_strategy" == "gentlepush" -o "$setup_strategy" == "maybepush" ]; then
+    local save=$-; set +e
+    ViashDockerRemoteTagCheck $image_id
+    local outCheck=$?
+    [[ $save =~ e ]] && set -e
+    if [ $outCheck -eq 0 ]; then
+      ViashNotice "Container '$image_id' exists, doing nothing."
+    else
+      ViashNotice "Container '$image_id' does not yet exist."
+      ViashDockerPush "$image_id"
+    fi
+  elif [ "$setup_strategy" == "donothing" -o "$setup_strategy" == "meh" ]; then
+    ViashNotice "Skipping setup."
+  else
+    ViashError "Unrecognised Docker strategy: $setup_strategy"
+    exit 1
+  fi
+}
+
+# ViashDockerCheckCommands: Check whether a docker container has the required commands
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# $@                  : commands to verify being present
+# examples:
+#   ViashDockerCheckCommands bash:4.0 bash ps foo
+function ViashDockerCheckCommands {
+  local image_id="$1"
+  shift 1
+  local commands="$@"
+  local save=$-; set +e
+  local missing # mark 'missing' as local in advance, otherwise the exit code of the command will be missing and always be '0'
+  missing=$(docker run --rm --entrypoint=sh "$image_id" -c "for command in $commands; do command -v \$command >/dev/null 2>&1; if [ \$? -ne 0 ]; then echo \$command; exit 1; fi; done")
+  local outCheck=$?
+  [[ $save =~ e ]] && set -e
+  if [ $outCheck -ne 0 ]; then
+  	ViashError "Docker container '$image_id' does not contain command '$missing'."
+  	exit 1
+  fi
+}
+
+# ViashDockerBuild: build a docker image
+# $1                               : image identifier with format `[registry/]image[:tag]`
+# $...                             : additional arguments to pass to docker build
+# $VIASH_META_TEMP_DIR             : temporary directory to store dockerfile & optional resources in
+# $VIASH_META_NAME                 : name of the component
+# $VIASH_META_RESOURCES_DIR        : directory containing the resources
+# $VIASH_VERBOSITY                 : verbosity level
+# exit code $?                     : whether or not the image was built successfully
+function ViashDockerBuild {
+  local image_id="$1"
+  shift 1
+
+  # create temporary directory to store dockerfile & optional resources in
+  local tmpdir=$(mktemp -d "$VIASH_META_TEMP_DIR/dockerbuild-$VIASH_META_NAME-XXXXXX")
+  local dockerfile="$tmpdir/Dockerfile"
+  function clean_up {
+    rm -rf "$tmpdir"
+  }
+  trap clean_up EXIT
+
+  # store dockerfile and resources
+  ViashDockerfile "$VIASH_ENGINE_ID" > "$dockerfile"
+
+  # generate the build command
+  local docker_build_cmd="docker build -t '$image_id' $@ '$VIASH_META_RESOURCES_DIR' -f '$dockerfile'"
+
+  # build the container
+  ViashNotice "Building container '$image_id' with Dockerfile"
+  ViashInfo "$docker_build_cmd"
+  local save=$-; set +e
+  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
+    eval $docker_build_cmd
+  else
+    eval $docker_build_cmd &> "$tmpdir/docker_build.log"
+  fi
+
+  # check exit code
+  local out=$?
+  [[ $save =~ e ]] && set -e
+  if [ $out -ne 0 ]; then
+    ViashError "Error occurred while building container '$image_id'"
+    if [ $VIASH_VERBOSITY -lt $VIASH_LOGCODE_INFO ]; then
+      ViashError "Transcript: --------------------------------"
+      cat "$tmpdir/docker_build.log"
+      ViashError "End of transcript --------------------------"
+    fi
+    exit 1
+  fi
+}
+
+######## End of helper functions for setting up Docker images for viash ########
+
+# ViashDockerFile: print the dockerfile to stdout
+# $1    : engine identifier
+# return : dockerfile required to run this component
+# examples:
+#   ViashDockerFile
+function ViashDockerfile {
+  local engine_id="$1"
+
+  if [[ "$engine_id" == "docker" ]]; then
+    cat << 'VIASHDOCKER'
+FROM quay.io/biocontainers/salmon:1.10.2--hecfa306_0
+ENTRYPOINT []
+RUN salmon index -v 2>&1 | sed 's/salmon \([0-9.]*\)/salmon: \1/' > /var/software_versions.txt
+
+LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
+LABEL org.opencontainers.image.description="Companion container for running component salmon salmon_quant"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:41Z"
+LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+LABEL org.opencontainers.image.version="main"
+
+VIASHDOCKER
+  fi
+}
+
+# ViashDockerBuildArgs: return the arguments to pass to docker build
+# $1    : engine identifier
+# return : arguments to pass to docker build
+function ViashDockerBuildArgs {
+  local engine_id="$1"
+
+  if [[ "$engine_id" == "docker" ]]; then
+    echo ""
+  fi
+}
+
+# ViashAbsolutePath: generate absolute path from relative path
+# borrowed from https://stackoverflow.com/a/21951256
+# $1     : relative filename
+# return : absolute path
+# examples:
+#   ViashAbsolutePath some_file.txt   # returns /path/to/some_file.txt
+#   ViashAbsolutePath /foo/bar/..     # returns /foo
+function ViashAbsolutePath {
+  local thePath
+  local parr
+  local outp
+  local len
+  if [[ ! "$1" =~ ^/ ]]; then
+    thePath="$PWD/$1"
+  else
+    thePath="$1"
+  fi
+  echo "$thePath" | (
+    IFS=/
+    read -a parr
+    declare -a outp
+    for i in "${parr[@]}"; do
+      case "$i" in
+      ''|.) continue ;;
+      ..)
+        len=${#outp[@]}
+        if ((len==0)); then
+          continue
+        else
+          unset outp[$((len-1))]
+        fi
+        ;;
+      *)
+        len=${#outp[@]}
+        outp[$len]="$i"
+      ;;
+      esac
+    done
+    echo /"${outp[*]}"
+  )
+}
+# ViashDockerAutodetectMount: auto configuring docker mounts from parameters
+# $1                             : The parameter value
+# returns                        : New parameter
+# $VIASH_DIRECTORY_MOUNTS        : Added another parameter to be passed to docker
+# $VIASH_DOCKER_AUTOMOUNT_PREFIX : The prefix to be used for the automounts
+# examples:
+#   ViashDockerAutodetectMount /path/to/bar      # returns '/viash_automount/path/to/bar'
+#   ViashDockerAutodetectMountArg /path/to/bar   # returns '--volume="/path/to:/viash_automount/path/to"'
+function ViashDockerAutodetectMount {
+  local abs_path=$(ViashAbsolutePath "$1")
+  local mount_source
+  local base_name
+  if [ -d "$abs_path" ]; then
+    mount_source="$abs_path"
+    base_name=""
+  else
+    mount_source=`dirname "$abs_path"`
+    base_name=`basename "$abs_path"`
+  fi
+  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
+  if [ -z "$base_name" ]; then
+    echo "$mount_target"
+  else
+    echo "$mount_target/$base_name"
+  fi
+}
+function ViashDockerAutodetectMountArg {
+  local abs_path=$(ViashAbsolutePath "$1")
+  local mount_source
+  local base_name
+  if [ -d "$abs_path" ]; then
+    mount_source="$abs_path"
+    base_name=""
+  else
+    mount_source=`dirname "$abs_path"`
+    base_name=`basename "$abs_path"`
+  fi
+  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
+  ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target"
+  echo "--volume=\"$mount_source:$mount_target\""
+}
+function ViashDockerStripAutomount {
+  local abs_path=$(ViashAbsolutePath "$1")
+  echo "${abs_path#$VIASH_DOCKER_AUTOMOUNT_PREFIX}"
+}
+# initialise variables
+VIASH_DIRECTORY_MOUNTS=()
+
+# configure default docker automount prefix if it is unset
+if [ -z "${VIASH_DOCKER_AUTOMOUNT_PREFIX+x}" ]; then
+  VIASH_DOCKER_AUTOMOUNT_PREFIX="/viash_automount"
+fi
+
+# initialise docker variables
+VIASH_DOCKER_RUN_ARGS=(-i --rm)
+
+
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
   echo "salmon_quant main"
@@ -887,404 +1285,32 @@ function ViashHelp {
   echo "        but setting it large enough to accommodate all of the mapped read can"
   echo "        substantially speed up inference on \"small\" files that contain only a"
   echo "        few million reads."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
 }
 
-# initialise variables
-VIASH_MODE='run'
-VIASH_ENGINE_ID='docker'
-
-######## Helper functions for setting up Docker images for viash ########
-# expects: ViashDockerBuild
-
-# ViashDockerInstallationCheck: check whether Docker is installed correctly
-#
-# examples:
-#   ViashDockerInstallationCheck
-function ViashDockerInstallationCheck {
-  ViashDebug "Checking whether Docker is installed"
-  if [ ! command -v docker &> /dev/null ]; then
-    ViashCritical "Docker doesn't seem to be installed. See 'https://docs.docker.com/get-docker/' for instructions."
-    exit 1
-  fi
-
-  ViashDebug "Checking whether the Docker daemon is running"
-  local save=$-; set +e
-  local docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
-  local out=$?
-  [[ $save =~ e ]] && set -e
-  if [ $out -ne 0 ]; then
-    ViashCritical "Docker daemon does not seem to be running. Try one of the following:"
-    ViashCritical "- Try running 'dockerd' in the command line"
-    ViashCritical "- See https://docs.docker.com/config/daemon/"
-    exit 1
-  fi
-}
-
-# ViashDockerRemoteTagCheck: check whether a Docker image is available 
-# on a remote. Assumes `docker login` has been performed, if relevant.
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   ViashDockerRemoteTagCheck python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerRemoteTagCheck sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerRemoteTagCheck {
-  docker manifest inspect $1 > /dev/null 2> /dev/null
-}
-
-# ViashDockerLocalTagCheck: check whether a Docker image is available locally
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   docker pull python:latest
-#   ViashDockerLocalTagCheck python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerLocalTagCheck sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerLocalTagCheck {
-  [ -n "$(docker images -q $1)" ]
-}
-
-# ViashDockerPull: pull a Docker image
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   ViashDockerPull python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerPull sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerPull {
-  ViashNotice "Checking if Docker image is available at '$1'"
-  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
-    docker pull $1 && return 0 || return 1
-  else
-    local save=$-; set +e
-    docker pull $1 2> /dev/null > /dev/null
-    local out=$?
-    [[ $save =~ e ]] && set -e
-    if [ $out -ne 0 ]; then
-      ViashWarning "Could not pull from '$1'. Docker image doesn't exist or is not accessible."
-    fi
-    return $out
-  fi
-}
-
-# ViashDockerPush: push a Docker image
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   ViashDockerPush python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerPush sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerPush {
-  ViashNotice "Pushing image to '$1'"
-  local save=$-; set +e
-  local out
-  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
-    docker push $1
-    out=$?
-  else
-    docker push $1 2> /dev/null > /dev/null
-    out=$?
-  fi
-  [[ $save =~ e ]] && set -e
-  if [ $out -eq 0 ]; then
-    ViashNotice "Container '$1' push succeeded."
-  else
-    ViashError "Container '$1' push errored. You might not be logged in or have the necessary permissions."
-  fi
-  return $out
-}
-
-# ViashDockerPullElseBuild: pull a Docker image, else build it
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# ViashDockerBuild    : a Bash function which builds a docker image, takes image identifier as argument.
-# examples:
-#   ViashDockerPullElseBuild mynewcomponent
-function ViashDockerPullElseBuild {
-  local save=$-; set +e
-  ViashDockerPull $1
-  local out=$?
-  [[ $save =~ e ]] && set -e
-  if [ $out -ne 0 ]; then
-    ViashDockerBuild $@
-  fi
-}
-
-# ViashDockerSetup: create a Docker image, according to specified docker setup strategy
-#
-# $1          : image identifier with format `[registry/]image[:tag]`
-# $2          : docker setup strategy, see DockerSetupStrategy.scala
-# examples:
-#   ViashDockerSetup mynewcomponent alwaysbuild
-function ViashDockerSetup {
-  local image_id="$1"
-  local setup_strategy="$2"
-  if [ "$setup_strategy" == "alwaysbuild" -o "$setup_strategy" == "build" -o "$setup_strategy" == "b" ]; then
-    ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-  elif [ "$setup_strategy" == "alwayspull" -o "$setup_strategy" == "pull" -o "$setup_strategy" == "p" ]; then
-    ViashDockerPull $image_id
-  elif [ "$setup_strategy" == "alwayspullelsebuild" -o "$setup_strategy" == "pullelsebuild" ]; then
-    ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-  elif [ "$setup_strategy" == "alwayspullelsecachedbuild" -o "$setup_strategy" == "pullelsecachedbuild" ]; then
-    ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-  elif [ "$setup_strategy" == "alwayscachedbuild" -o "$setup_strategy" == "cachedbuild" -o "$setup_strategy" == "cb" ]; then
-    ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-  elif [[ "$setup_strategy" =~ ^ifneedbe ]]; then
-    local save=$-; set +e
-    ViashDockerLocalTagCheck $image_id
-    local outCheck=$?
-    [[ $save =~ e ]] && set -e
-    if [ $outCheck -eq 0 ]; then
-      ViashInfo "Image $image_id already exists"
-    elif [ "$setup_strategy" == "ifneedbebuild" ]; then
-      ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-    elif [ "$setup_strategy" == "ifneedbecachedbuild" ]; then
-      ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-    elif [ "$setup_strategy" == "ifneedbepull" ]; then
-      ViashDockerPull $image_id
-    elif [ "$setup_strategy" == "ifneedbepullelsebuild" ]; then
-      ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-    elif [ "$setup_strategy" == "ifneedbepullelsecachedbuild" ]; then
-      ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-    else
-      ViashError "Unrecognised Docker strategy: $setup_strategy"
-      exit 1
-    fi
-  elif [ "$setup_strategy" == "push" -o "$setup_strategy" == "forcepush" -o "$setup_strategy" == "alwayspush" ]; then
-    ViashDockerPush "$image_id"
-  elif [ "$setup_strategy" == "pushifnotpresent" -o "$setup_strategy" == "gentlepush" -o "$setup_strategy" == "maybepush" ]; then
-    local save=$-; set +e
-    ViashDockerRemoteTagCheck $image_id
-    local outCheck=$?
-    [[ $save =~ e ]] && set -e
-    if [ $outCheck -eq 0 ]; then
-      ViashNotice "Container '$image_id' exists, doing nothing."
-    else
-      ViashNotice "Container '$image_id' does not yet exist."
-      ViashDockerPush "$image_id"
-    fi
-  elif [ "$setup_strategy" == "donothing" -o "$setup_strategy" == "meh" ]; then
-    ViashNotice "Skipping setup."
-  else
-    ViashError "Unrecognised Docker strategy: $setup_strategy"
-    exit 1
-  fi
-}
-
-# ViashDockerCheckCommands: Check whether a docker container has the required commands
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# $@                  : commands to verify being present
-# examples:
-#   ViashDockerCheckCommands bash:4.0 bash ps foo
-function ViashDockerCheckCommands {
-  local image_id="$1"
-  shift 1
-  local commands="$@"
-  local save=$-; set +e
-  local missing # mark 'missing' as local in advance, otherwise the exit code of the command will be missing and always be '0'
-  missing=$(docker run --rm --entrypoint=sh "$image_id" -c "for command in $commands; do command -v \$command >/dev/null 2>&1; if [ \$? -ne 0 ]; then echo \$command; exit 1; fi; done")
-  local outCheck=$?
-  [[ $save =~ e ]] && set -e
-  if [ $outCheck -ne 0 ]; then
-  	ViashError "Docker container '$image_id' does not contain command '$missing'."
-  	exit 1
-  fi
-}
-
-# ViashDockerBuild: build a docker image
-# $1                               : image identifier with format `[registry/]image[:tag]`
-# $...                             : additional arguments to pass to docker build
-# $VIASH_META_TEMP_DIR             : temporary directory to store dockerfile & optional resources in
-# $VIASH_META_NAME                 : name of the component
-# $VIASH_META_RESOURCES_DIR        : directory containing the resources
-# $VIASH_VERBOSITY                 : verbosity level
-# exit code $?                     : whether or not the image was built successfully
-function ViashDockerBuild {
-  local image_id="$1"
-  shift 1
-
-  # create temporary directory to store dockerfile & optional resources in
-  local tmpdir=$(mktemp -d "$VIASH_META_TEMP_DIR/dockerbuild-$VIASH_META_NAME-XXXXXX")
-  local dockerfile="$tmpdir/Dockerfile"
-  function clean_up {
-    rm -rf "$tmpdir"
-  }
-  trap clean_up EXIT
-
-  # store dockerfile and resources
-  ViashDockerfile "$VIASH_ENGINE_ID" > "$dockerfile"
-
-  # generate the build command
-  local docker_build_cmd="docker build -t '$image_id' $@ '$VIASH_META_RESOURCES_DIR' -f '$dockerfile'"
-
-  # build the container
-  ViashNotice "Building container '$image_id' with Dockerfile"
-  ViashInfo "$docker_build_cmd"
-  local save=$-; set +e
-  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
-    eval $docker_build_cmd
-  else
-    eval $docker_build_cmd &> "$tmpdir/docker_build.log"
-  fi
-
-  # check exit code
-  local out=$?
-  [[ $save =~ e ]] && set -e
-  if [ $out -ne 0 ]; then
-    ViashError "Error occurred while building container '$image_id'"
-    if [ $VIASH_VERBOSITY -lt $VIASH_LOGCODE_INFO ]; then
-      ViashError "Transcript: --------------------------------"
-      cat "$tmpdir/docker_build.log"
-      ViashError "End of transcript --------------------------"
-    fi
-    exit 1
-  fi
-}
-
-######## End of helper functions for setting up Docker images for viash ########
-
-# ViashDockerFile: print the dockerfile to stdout
-# $1    : engine identifier
-# return : dockerfile required to run this component
-# examples:
-#   ViashDockerFile
-function ViashDockerfile {
-  local engine_id="$1"
-
-  if [[ "$engine_id" == "docker" ]]; then
-    cat << 'VIASHDOCKER'
-FROM quay.io/biocontainers/salmon:1.10.2--hecfa306_0
-ENTRYPOINT []
-RUN salmon index -v 2>&1 | sed 's/salmon \([0-9.]*\)/salmon: \1/' > /var/software_versions.txt
-
-LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
-LABEL org.opencontainers.image.description="Companion container for running component salmon salmon_quant"
-LABEL org.opencontainers.image.created="2024-12-03T10:34:01Z"
-LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-LABEL org.opencontainers.image.version="main"
-
-VIASHDOCKER
-  fi
-}
-
-# ViashDockerBuildArgs: return the arguments to pass to docker build
-# $1    : engine identifier
-# return : arguments to pass to docker build
-function ViashDockerBuildArgs {
-  local engine_id="$1"
-
-  if [[ "$engine_id" == "docker" ]]; then
-    echo ""
-  fi
-}
-
-# ViashAbsolutePath: generate absolute path from relative path
-# borrowed from https://stackoverflow.com/a/21951256
-# $1     : relative filename
-# return : absolute path
-# examples:
-#   ViashAbsolutePath some_file.txt   # returns /path/to/some_file.txt
-#   ViashAbsolutePath /foo/bar/..     # returns /foo
-function ViashAbsolutePath {
-  local thePath
-  local parr
-  local outp
-  local len
-  if [[ ! "$1" =~ ^/ ]]; then
-    thePath="$PWD/$1"
-  else
-    thePath="$1"
-  fi
-  echo "$thePath" | (
-    IFS=/
-    read -a parr
-    declare -a outp
-    for i in "${parr[@]}"; do
-      case "$i" in
-      ''|.) continue ;;
-      ..)
-        len=${#outp[@]}
-        if ((len==0)); then
-          continue
-        else
-          unset outp[$((len-1))]
-        fi
-        ;;
-      *)
-        len=${#outp[@]}
-        outp[$len]="$i"
-      ;;
-      esac
-    done
-    echo /"${outp[*]}"
-  )
-}
-# ViashDockerAutodetectMount: auto configuring docker mounts from parameters
-# $1                             : The parameter value
-# returns                        : New parameter
-# $VIASH_DIRECTORY_MOUNTS        : Added another parameter to be passed to docker
-# $VIASH_DOCKER_AUTOMOUNT_PREFIX : The prefix to be used for the automounts
-# examples:
-#   ViashDockerAutodetectMount /path/to/bar      # returns '/viash_automount/path/to/bar'
-#   ViashDockerAutodetectMountArg /path/to/bar   # returns '--volume="/path/to:/viash_automount/path/to"'
-function ViashDockerAutodetectMount {
-  local abs_path=$(ViashAbsolutePath "$1")
-  local mount_source
-  local base_name
-  if [ -d "$abs_path" ]; then
-    mount_source="$abs_path"
-    base_name=""
-  else
-    mount_source=`dirname "$abs_path"`
-    base_name=`basename "$abs_path"`
-  fi
-  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
-  if [ -z "$base_name" ]; then
-    echo "$mount_target"
-  else
-    echo "$mount_target/$base_name"
-  fi
-}
-function ViashDockerAutodetectMountArg {
-  local abs_path=$(ViashAbsolutePath "$1")
-  local mount_source
-  local base_name
-  if [ -d "$abs_path" ]; then
-    mount_source="$abs_path"
-    base_name=""
-  else
-    mount_source=`dirname "$abs_path"`
-    base_name=`basename "$abs_path"`
-  fi
-  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
-  ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target"
-  echo "--volume=\"$mount_source:$mount_target\""
-}
-function ViashDockerStripAutomount {
-  local abs_path=$(ViashAbsolutePath "$1")
-  echo "${abs_path#$VIASH_DOCKER_AUTOMOUNT_PREFIX}"
-}
-# initialise variables
-VIASH_DIRECTORY_MOUNTS=()
-
-# configure default docker automount prefix if it is unset
-if [ -z "${VIASH_DOCKER_AUTOMOUNT_PREFIX+x}" ]; then
-  VIASH_DOCKER_AUTOMOUNT_PREFIX="/viash_automount"
-fi
-
-# initialise docker variables
-VIASH_DOCKER_RUN_ARGS=(-i --rm)
-
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/samtools/samtools_collate/.config.vsh.yaml b/target/executable/samtools/samtools_collate/.config.vsh.yaml
index 8a00ae2f..86e95721 100644
--- a/target/executable/samtools/samtools_collate/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_collate/.config.vsh.yaml
@@ -158,6 +158,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -263,16 +266,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/samtools/samtools_collate"
   executable: "target/executable/samtools/samtools_collate/samtools_collate"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/samtools/samtools_collate/samtools_collate b/target/executable/samtools/samtools_collate/samtools_collate
index fd96d64e..4ab294f1 100755
--- a/target/executable/samtools/samtools_collate/samtools_collate
+++ b/target/executable/samtools/samtools_collate/samtools_collate
@@ -2,7 +2,7 @@
 
 # samtools_collate main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,72 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "samtools_collate main"
-  echo ""
-  echo "Shuffles and groups reads in SAM/BAM/CRAM files together by their names."
-  echo ""
-  echo "Inputs:"
-  echo "    --input"
-  echo "        type: file, required parameter, file must exist"
-  echo "        The input BAM file."
-  echo ""
-  echo "    --reference"
-  echo "        type: file, file must exist"
-  echo "        Reference sequence FASTA FILE."
-  echo ""
-  echo "Outputs:"
-  echo "    -o, --output"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        The output filename."
-  echo ""
-  echo "Options:"
-  echo "    -u, --uncompressed"
-  echo "        type: boolean_true"
-  echo "        Output uncompressed BAM."
-  echo ""
-  echo "    -f, --fast"
-  echo "        type: boolean_true"
-  echo "        Fast mode, only primary alignments."
-  echo ""
-  echo "    -r, --working_reads"
-  echo "        type: integer"
-  echo "        default: 10000"
-  echo "        Working reads stored (for use with -f)."
-  echo ""
-  echo "    -l, --compression"
-  echo "        type: integer"
-  echo "        default: 1"
-  echo "        Compression level."
-  echo ""
-  echo "    -n, --nb_tmp_files"
-  echo "        type: integer"
-  echo "        default: 64"
-  echo "        Number of temporary files."
-  echo ""
-  echo "    -T, --tmp_prefix"
-  echo "        type: string"
-  echo "        Write temporary files to PREFIX.nnnn.bam."
-  echo ""
-  echo "    --no_pg"
-  echo "        type: boolean_true"
-  echo "        Do not add a PG line."
-  echo ""
-  echo "    --input_fmt_option"
-  echo "        type: string"
-  echo "        Specify a single input file format option in the form of OPTION or"
-  echo "        OPTION=VALUE."
-  echo ""
-  echo "    --output_fmt"
-  echo "        type: string"
-  echo "        Specify output format (SAM, BAM, CRAM)."
-  echo ""
-  echo "    --output_fmt_option"
-  echo "        type: string"
-  echo "        Specify a single output file format option in the form of OPTION or"
-  echo "        OPTION=VALUE."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -519,9 +453,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_collate"
-LABEL org.opencontainers.image.created="2024-12-03T10:33:58Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:39Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -636,6 +570,98 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "samtools_collate main"
+  echo ""
+  echo "Shuffles and groups reads in SAM/BAM/CRAM files together by their names."
+  echo ""
+  echo "Inputs:"
+  echo "    --input"
+  echo "        type: file, required parameter, file must exist"
+  echo "        The input BAM file."
+  echo ""
+  echo "    --reference"
+  echo "        type: file, file must exist"
+  echo "        Reference sequence FASTA FILE."
+  echo ""
+  echo "Outputs:"
+  echo "    -o, --output"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        The output filename."
+  echo ""
+  echo "Options:"
+  echo "    -u, --uncompressed"
+  echo "        type: boolean_true"
+  echo "        Output uncompressed BAM."
+  echo ""
+  echo "    -f, --fast"
+  echo "        type: boolean_true"
+  echo "        Fast mode, only primary alignments."
+  echo ""
+  echo "    -r, --working_reads"
+  echo "        type: integer"
+  echo "        default: 10000"
+  echo "        Working reads stored (for use with -f)."
+  echo ""
+  echo "    -l, --compression"
+  echo "        type: integer"
+  echo "        default: 1"
+  echo "        Compression level."
+  echo ""
+  echo "    -n, --nb_tmp_files"
+  echo "        type: integer"
+  echo "        default: 64"
+  echo "        Number of temporary files."
+  echo ""
+  echo "    -T, --tmp_prefix"
+  echo "        type: string"
+  echo "        Write temporary files to PREFIX.nnnn.bam."
+  echo ""
+  echo "    --no_pg"
+  echo "        type: boolean_true"
+  echo "        Do not add a PG line."
+  echo ""
+  echo "    --input_fmt_option"
+  echo "        type: string"
+  echo "        Specify a single input file format option in the form of OPTION or"
+  echo "        OPTION=VALUE."
+  echo ""
+  echo "    --output_fmt"
+  echo "        type: string"
+  echo "        Specify output format (SAM, BAM, CRAM)."
+  echo ""
+  echo "    --output_fmt_option"
+  echo "        type: string"
+  echo "        Specify a single output file format option in the form of OPTION or"
+  echo "        OPTION=VALUE."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/samtools/samtools_faidx/.config.vsh.yaml b/target/executable/samtools/samtools_faidx/.config.vsh.yaml
index f0645096..8b83baae 100644
--- a/target/executable/samtools/samtools_faidx/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_faidx/.config.vsh.yaml
@@ -139,6 +139,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -242,16 +245,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/samtools/samtools_faidx"
   executable: "target/executable/samtools/samtools_faidx/samtools_faidx"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/samtools/samtools_faidx/samtools_faidx b/target/executable/samtools/samtools_faidx/samtools_faidx
index e3782810..c5fdc0b1 100755
--- a/target/executable/samtools/samtools_faidx/samtools_faidx
+++ b/target/executable/samtools/samtools_faidx/samtools_faidx
@@ -2,7 +2,7 @@
 
 # samtools_faidx main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,65 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "samtools_faidx main"
-  echo ""
-  echo "Indexes FASTA files to enable random access to fasta and fastq files."
-  echo ""
-  echo "Inputs:"
-  echo "    --input"
-  echo "        type: file, file must exist"
-  echo "        FASTA input file."
-  echo ""
-  echo "    -n, --length"
-  echo "        type: integer"
-  echo "        default: 60"
-  echo "        Length for FASTA sequence line wrapping. If zero, this means do not"
-  echo "        line wrap. Defaults to the line length in the input file."
-  echo ""
-  echo "    -r, --region_file"
-  echo "        type: file, file must exist"
-  echo "        File of regions. Format is chr:from-to. One per line."
-  echo "        Must be used with --output to avoid sending output to stdout."
-  echo ""
-  echo "Options:"
-  echo "    --continue"
-  echo "        type: boolean_true"
-  echo "        Continue working if a non-existent region is requested."
-  echo ""
-  echo "    -i, --reverse_complement"
-  echo "        type: boolean_true"
-  echo "        Reverse complement sequences."
-  echo ""
-  echo "Outputs:"
-  echo "    -o, --output"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        example: output.fasta"
-  echo "        Write output to file."
-  echo ""
-  echo "    --mark_strand"
-  echo "        type: string"
-  echo "        default: rc"
-  echo "        Add strand indicator to sequence name. Options are:"
-  echo "        [ rc, no, sign, custom,<pos>,<neg> ]"
-  echo ""
-  echo "    --fai_idx"
-  echo "        type: file, output, file must exist"
-  echo "        example: file.fa.fai"
-  echo "        Read/Write to specified index file (default file.fa.fai)."
-  echo ""
-  echo "    --gzi_idx"
-  echo "        type: file, output, file must exist"
-  echo "        example: file.fa.gz.gzi"
-  echo "        Read/Write to specified compressed file index (used with .gz files,"
-  echo "        default file.fa.gz.gzi)."
-  echo ""
-  echo "    --fastq"
-  echo "        type: boolean_true"
-  echo "        Read FASTQ files and output extracted sequences in FASTQ format. Same as"
-  echo "        using samtools fqidx."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -512,9 +453,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_faidx"
-LABEL org.opencontainers.image.created="2024-12-03T10:34:00Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:37Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -629,6 +570,91 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "samtools_faidx main"
+  echo ""
+  echo "Indexes FASTA files to enable random access to fasta and fastq files."
+  echo ""
+  echo "Inputs:"
+  echo "    --input"
+  echo "        type: file, file must exist"
+  echo "        FASTA input file."
+  echo ""
+  echo "    -n, --length"
+  echo "        type: integer"
+  echo "        default: 60"
+  echo "        Length for FASTA sequence line wrapping. If zero, this means do not"
+  echo "        line wrap. Defaults to the line length in the input file."
+  echo ""
+  echo "    -r, --region_file"
+  echo "        type: file, file must exist"
+  echo "        File of regions. Format is chr:from-to. One per line."
+  echo "        Must be used with --output to avoid sending output to stdout."
+  echo ""
+  echo "Options:"
+  echo "    --continue"
+  echo "        type: boolean_true"
+  echo "        Continue working if a non-existent region is requested."
+  echo ""
+  echo "    -i, --reverse_complement"
+  echo "        type: boolean_true"
+  echo "        Reverse complement sequences."
+  echo ""
+  echo "Outputs:"
+  echo "    -o, --output"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        example: output.fasta"
+  echo "        Write output to file."
+  echo ""
+  echo "    --mark_strand"
+  echo "        type: string"
+  echo "        default: rc"
+  echo "        Add strand indicator to sequence name. Options are:"
+  echo "        [ rc, no, sign, custom,<pos>,<neg> ]"
+  echo ""
+  echo "    --fai_idx"
+  echo "        type: file, output, file must exist"
+  echo "        example: file.fa.fai"
+  echo "        Read/Write to specified index file (default file.fa.fai)."
+  echo ""
+  echo "    --gzi_idx"
+  echo "        type: file, output, file must exist"
+  echo "        example: file.fa.gz.gzi"
+  echo "        Read/Write to specified compressed file index (used with .gz files,"
+  echo "        default file.fa.gz.gzi)."
+  echo ""
+  echo "    --fastq"
+  echo "        type: boolean_true"
+  echo "        Read FASTQ files and output extracted sequences in FASTQ format. Same as"
+  echo "        using samtools fqidx."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/samtools/samtools_fasta/.config.vsh.yaml b/target/executable/samtools/samtools_fasta/.config.vsh.yaml
index 4cdf517e..337aa2e8 100644
--- a/target/executable/samtools/samtools_fasta/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_fasta/.config.vsh.yaml
@@ -328,6 +328,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -432,16 +435,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/samtools/samtools_fasta"
   executable: "target/executable/samtools/samtools_fasta/samtools_fasta"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/samtools/samtools_fasta/samtools_fasta b/target/executable/samtools/samtools_fasta/samtools_fasta
index 22c425f0..cc12c0fe 100755
--- a/target/executable/samtools/samtools_fasta/samtools_fasta
+++ b/target/executable/samtools/samtools_fasta/samtools_fasta
@@ -2,7 +2,7 @@
 
 # samtools_fasta main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,178 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "samtools_fasta main"
-  echo ""
-  echo "Converts a SAM, BAM or CRAM to FASTA format."
-  echo ""
-  echo "Inputs:"
-  echo "    --input"
-  echo "        type: file, required parameter, file must exist"
-  echo "        input SAM/BAM/CRAM file"
-  echo ""
-  echo "Outputs:"
-  echo "    --output"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        output FASTA file"
-  echo ""
-  echo "Options:"
-  echo "    -n, --no_suffix"
-  echo "        type: boolean_true"
-  echo "        By default, either '/1' or '/2' is added to the end of read names where"
-  echo "        the corresponding"
-  echo "        READ1 or READ2 FLAG bit is set. Using -n causes read names to be left as"
-  echo "        they are."
-  echo ""
-  echo "    -N, --suffix"
-  echo "        type: boolean_true"
-  echo "        Always add either '/1' or '/2' to the end of read names even when put"
-  echo "        into different files."
-  echo ""
-  echo "    -O, --use_oq"
-  echo "        type: boolean_true"
-  echo "        Use quality values from OQ tags in preference to standard quality string"
-  echo "        if available."
-  echo ""
-  echo "    -s, --singleton"
-  echo "        type: file, file must exist"
-  echo "        write singleton reads to FILE."
-  echo ""
-  echo "    -t, --copy_tags"
-  echo "        type: boolean_true"
-  echo "        Copy RG, BC and QT tags to the FASTA header line, if they exist."
-  echo ""
-  echo "    -T, --copy_tags_list"
-  echo "        type: string"
-  echo "        Specify a comma-separated list of tags to copy to the FASTA header line,"
-  echo "        if they exist."
-  echo "        TAGLIST can be blank or \`*\` to indicate all tags should be copied to the"
-  echo "        output. If using \`*\`,"
-  echo "        be careful to quote it to avoid unwanted shell expansion."
-  echo ""
-  echo "    -1, --read1"
-  echo "        type: file, output, file must exist"
-  echo "        Write reads with the READ1 FLAG set (and READ2 not set) to FILE instead"
-  echo "        of outputting them."
-  echo "        If the -s option is used, only paired reads will be written to this"
-  echo "        file."
-  echo ""
-  echo "    -2, --read2"
-  echo "        type: file, output, file must exist"
-  echo "        Write reads with the READ2 FLAG set (and READ1 not set) to FILE instead"
-  echo "        of outputting them."
-  echo "        If the -s option is used, only paired reads will be written to this"
-  echo "        file."
-  echo ""
-  echo "    -o, --output_reads"
-  echo "        type: file, output, file must exist"
-  echo "        Write reads with either READ1 FLAG or READ2 flag set to FILE instead of"
-  echo "        outputting them to stdout."
-  echo "        This is equivalent to -1 FILE -2 FILE."
-  echo ""
-  echo "    0, --output_reads_both"
-  echo "        type: file, output, file must exist"
-  echo "        Write reads where the READ1 and READ2 FLAG bits set are either both set"
-  echo "        or both unset to FILE"
-  echo "        instead of outputting them."
-  echo ""
-  echo "    -f, --filter_flags"
-  echo "        type: integer"
-  echo "        example: 0"
-  echo "        Only output alignments with all bits set in INT present in the FLAG"
-  echo "        field. INT can be specified"
-  echo "        in hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/) or in octal by"
-  echo "        beginning with '0'"
-  echo "        (i.e. /^0[0-7]+/). Default: \`0\`."
-  echo ""
-  echo "    -F, --excl_flags"
-  echo "        type: string"
-  echo "        example: 0x900"
-  echo "        Do not output alignments with any bits set in INT present in the FLAG"
-  echo "        field. INT can be specified"
-  echo "        in hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/) or in octal by"
-  echo "        beginning with '0'"
-  echo "        (i.e. /^0[0-7]+/). This defaults to 0x900 representing filtering of"
-  echo "        secondary and"
-  echo "        supplementary alignments. Default: \`0x900\`."
-  echo ""
-  echo "    --rf, --incl_flags"
-  echo "        type: string"
-  echo "        example: 0"
-  echo "        Only output alignments with any bits set in INT present in the FLAG"
-  echo "        field. INT can be specified"
-  echo "        in hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/), in octal by"
-  echo "        beginning with '0'"
-  echo "        (i.e. /^0[0-7]+/), as a decimal number not beginning with '0' or as a"
-  echo "        comma-separated list of"
-  echo "        flag names. Default: \`0\`."
-  echo ""
-  echo "    -G, --excl_flags_all"
-  echo "        type: integer"
-  echo "        example: 0"
-  echo "        Only EXCLUDE reads with all of the bits set in INT present in the FLAG"
-  echo "        field. INT can be specified"
-  echo "        in hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/) or in octal by"
-  echo "        beginning with '0' (i.e. /^0[0-7]+/)."
-  echo "        Default: \`0\`."
-  echo ""
-  echo "    -d, --aux_tag"
-  echo "        type: string"
-  echo "        Only output alignments containing an auxiliary tag matching both TAG and"
-  echo "        VAL. If VAL is omitted"
-  echo "        then any value is accepted. The tag types supported are i, f, Z, A and"
-  echo "        H. \"B\" arrays are not"
-  echo "        supported. This is comparable to the method used in samtools view --tag."
-  echo "        The option may be specified"
-  echo "        multiple times and is equivalent to using the --aux_tag_file option."
-  echo ""
-  echo "    -D, --aux_tag_file"
-  echo "        type: string"
-  echo "        Only output alignments containing an auxiliary tag matching TAG and"
-  echo "        having a value listed in FILE."
-  echo "        The format of the file is one line per value. This is equivalent to"
-  echo "        specifying --aux_tag multiple times."
-  echo ""
-  echo "    -i, --casava"
-  echo "        type: boolean_true"
-  echo "        add Illumina Casava 1.8 format entry to header (eg 1:N:0:ATCACG)"
-  echo ""
-  echo "    -c, --compression"
-  echo "        type: integer"
-  echo "        example: 0"
-  echo "        set compression level when writing gz or bgzf fasta files."
-  echo ""
-  echo "    --i1, --index1"
-  echo "        type: file, file must exist"
-  echo "        write first index reads to FILE."
-  echo ""
-  echo "    --i2, --index2"
-  echo "        type: file, file must exist"
-  echo "        write second index reads to FILE."
-  echo ""
-  echo "    --barcode_tag"
-  echo "        type: string"
-  echo "        example: BC"
-  echo "        Auxiliary tag to find index reads in. Default: \`BC\`."
-  echo ""
-  echo "    --quality_tag"
-  echo "        type: string"
-  echo "        example: QT"
-  echo "        Auxiliary tag to find index quality in. Default: \`QT\`."
-  echo ""
-  echo "    --index_format"
-  echo "        type: string"
-  echo "        string to describe how to parse the barcode and quality tags. For"
-  echo "        example:"
-  echo "        * \`i14i8\`: the first 14 characters are index 1, the next 8 characters"
-  echo "        are index 2."
-  echo "        * \`n8i14\`: ignore the first 8 characters, and use the next 14 characters"
-  echo "        for index 1."
-  echo "        If the tag contains a separator, then the numeric part can be replaced"
-  echo "        with\`*\` to mean"
-  echo "        'read until the separator or end of tag', for example: \`n*i*\`."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -625,9 +453,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_fasta"
-LABEL org.opencontainers.image.created="2024-12-03T10:34:00Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:39Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -742,6 +570,204 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "samtools_fasta main"
+  echo ""
+  echo "Converts a SAM, BAM or CRAM to FASTA format."
+  echo ""
+  echo "Inputs:"
+  echo "    --input"
+  echo "        type: file, required parameter, file must exist"
+  echo "        input SAM/BAM/CRAM file"
+  echo ""
+  echo "Outputs:"
+  echo "    --output"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        output FASTA file"
+  echo ""
+  echo "Options:"
+  echo "    -n, --no_suffix"
+  echo "        type: boolean_true"
+  echo "        By default, either '/1' or '/2' is added to the end of read names where"
+  echo "        the corresponding"
+  echo "        READ1 or READ2 FLAG bit is set. Using -n causes read names to be left as"
+  echo "        they are."
+  echo ""
+  echo "    -N, --suffix"
+  echo "        type: boolean_true"
+  echo "        Always add either '/1' or '/2' to the end of read names even when put"
+  echo "        into different files."
+  echo ""
+  echo "    -O, --use_oq"
+  echo "        type: boolean_true"
+  echo "        Use quality values from OQ tags in preference to standard quality string"
+  echo "        if available."
+  echo ""
+  echo "    -s, --singleton"
+  echo "        type: file, file must exist"
+  echo "        write singleton reads to FILE."
+  echo ""
+  echo "    -t, --copy_tags"
+  echo "        type: boolean_true"
+  echo "        Copy RG, BC and QT tags to the FASTA header line, if they exist."
+  echo ""
+  echo "    -T, --copy_tags_list"
+  echo "        type: string"
+  echo "        Specify a comma-separated list of tags to copy to the FASTA header line,"
+  echo "        if they exist."
+  echo "        TAGLIST can be blank or \`*\` to indicate all tags should be copied to the"
+  echo "        output. If using \`*\`,"
+  echo "        be careful to quote it to avoid unwanted shell expansion."
+  echo ""
+  echo "    -1, --read1"
+  echo "        type: file, output, file must exist"
+  echo "        Write reads with the READ1 FLAG set (and READ2 not set) to FILE instead"
+  echo "        of outputting them."
+  echo "        If the -s option is used, only paired reads will be written to this"
+  echo "        file."
+  echo ""
+  echo "    -2, --read2"
+  echo "        type: file, output, file must exist"
+  echo "        Write reads with the READ2 FLAG set (and READ1 not set) to FILE instead"
+  echo "        of outputting them."
+  echo "        If the -s option is used, only paired reads will be written to this"
+  echo "        file."
+  echo ""
+  echo "    -o, --output_reads"
+  echo "        type: file, output, file must exist"
+  echo "        Write reads with either READ1 FLAG or READ2 flag set to FILE instead of"
+  echo "        outputting them to stdout."
+  echo "        This is equivalent to -1 FILE -2 FILE."
+  echo ""
+  echo "    0, --output_reads_both"
+  echo "        type: file, output, file must exist"
+  echo "        Write reads where the READ1 and READ2 FLAG bits set are either both set"
+  echo "        or both unset to FILE"
+  echo "        instead of outputting them."
+  echo ""
+  echo "    -f, --filter_flags"
+  echo "        type: integer"
+  echo "        example: 0"
+  echo "        Only output alignments with all bits set in INT present in the FLAG"
+  echo "        field. INT can be specified"
+  echo "        in hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/) or in octal by"
+  echo "        beginning with '0'"
+  echo "        (i.e. /^0[0-7]+/). Default: \`0\`."
+  echo ""
+  echo "    -F, --excl_flags"
+  echo "        type: string"
+  echo "        example: 0x900"
+  echo "        Do not output alignments with any bits set in INT present in the FLAG"
+  echo "        field. INT can be specified"
+  echo "        in hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/) or in octal by"
+  echo "        beginning with '0'"
+  echo "        (i.e. /^0[0-7]+/). This defaults to 0x900 representing filtering of"
+  echo "        secondary and"
+  echo "        supplementary alignments. Default: \`0x900\`."
+  echo ""
+  echo "    --rf, --incl_flags"
+  echo "        type: string"
+  echo "        example: 0"
+  echo "        Only output alignments with any bits set in INT present in the FLAG"
+  echo "        field. INT can be specified"
+  echo "        in hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/), in octal by"
+  echo "        beginning with '0'"
+  echo "        (i.e. /^0[0-7]+/), as a decimal number not beginning with '0' or as a"
+  echo "        comma-separated list of"
+  echo "        flag names. Default: \`0\`."
+  echo ""
+  echo "    -G, --excl_flags_all"
+  echo "        type: integer"
+  echo "        example: 0"
+  echo "        Only EXCLUDE reads with all of the bits set in INT present in the FLAG"
+  echo "        field. INT can be specified"
+  echo "        in hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/) or in octal by"
+  echo "        beginning with '0' (i.e. /^0[0-7]+/)."
+  echo "        Default: \`0\`."
+  echo ""
+  echo "    -d, --aux_tag"
+  echo "        type: string"
+  echo "        Only output alignments containing an auxiliary tag matching both TAG and"
+  echo "        VAL. If VAL is omitted"
+  echo "        then any value is accepted. The tag types supported are i, f, Z, A and"
+  echo "        H. \"B\" arrays are not"
+  echo "        supported. This is comparable to the method used in samtools view --tag."
+  echo "        The option may be specified"
+  echo "        multiple times and is equivalent to using the --aux_tag_file option."
+  echo ""
+  echo "    -D, --aux_tag_file"
+  echo "        type: string"
+  echo "        Only output alignments containing an auxiliary tag matching TAG and"
+  echo "        having a value listed in FILE."
+  echo "        The format of the file is one line per value. This is equivalent to"
+  echo "        specifying --aux_tag multiple times."
+  echo ""
+  echo "    -i, --casava"
+  echo "        type: boolean_true"
+  echo "        add Illumina Casava 1.8 format entry to header (eg 1:N:0:ATCACG)"
+  echo ""
+  echo "    -c, --compression"
+  echo "        type: integer"
+  echo "        example: 0"
+  echo "        set compression level when writing gz or bgzf fasta files."
+  echo ""
+  echo "    --i1, --index1"
+  echo "        type: file, file must exist"
+  echo "        write first index reads to FILE."
+  echo ""
+  echo "    --i2, --index2"
+  echo "        type: file, file must exist"
+  echo "        write second index reads to FILE."
+  echo ""
+  echo "    --barcode_tag"
+  echo "        type: string"
+  echo "        example: BC"
+  echo "        Auxiliary tag to find index reads in. Default: \`BC\`."
+  echo ""
+  echo "    --quality_tag"
+  echo "        type: string"
+  echo "        example: QT"
+  echo "        Auxiliary tag to find index quality in. Default: \`QT\`."
+  echo ""
+  echo "    --index_format"
+  echo "        type: string"
+  echo "        string to describe how to parse the barcode and quality tags. For"
+  echo "        example:"
+  echo "        * \`i14i8\`: the first 14 characters are index 1, the next 8 characters"
+  echo "        are index 2."
+  echo "        * \`n8i14\`: ignore the first 8 characters, and use the next 14 characters"
+  echo "        for index 1."
+  echo "        If the tag contains a separator, then the numeric part can be replaced"
+  echo "        with\`*\` to mean"
+  echo "        'read until the separator or end of tag', for example: \`n*i*\`."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/samtools/samtools_fastq/.config.vsh.yaml b/target/executable/samtools/samtools_fastq/.config.vsh.yaml
index 64d1ea21..a157fd0c 100644
--- a/target/executable/samtools/samtools_fastq/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_fastq/.config.vsh.yaml
@@ -328,6 +328,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -432,16 +435,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/samtools/samtools_fastq"
   executable: "target/executable/samtools/samtools_fastq/samtools_fastq"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/samtools/samtools_fastq/samtools_fastq b/target/executable/samtools/samtools_fastq/samtools_fastq
index f34a74ec..35a89d58 100755
--- a/target/executable/samtools/samtools_fastq/samtools_fastq
+++ b/target/executable/samtools/samtools_fastq/samtools_fastq
@@ -2,7 +2,7 @@
 
 # samtools_fastq main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,179 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "samtools_fastq main"
-  echo ""
-  echo "Converts a SAM, BAM or CRAM to FASTQ format."
-  echo ""
-  echo "Inputs:"
-  echo "    --input"
-  echo "        type: file, required parameter, file must exist"
-  echo "        input SAM/BAM/CRAM file"
-  echo ""
-  echo "Outputs:"
-  echo "    --output"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        output FASTQ file"
-  echo ""
-  echo "Options:"
-  echo "    -n, --no_suffix"
-  echo "        type: boolean_true"
-  echo "        By default, either '/1' or '/2' is added to the end of read names where"
-  echo "        the corresponding"
-  echo "        READ1 or READ2 FLAG bit is set. Using -n causes read names to be left as"
-  echo "        they are."
-  echo ""
-  echo "    -N, --suffix"
-  echo "        type: boolean_true"
-  echo "        Always add either '/1' or '/2' to the end of read names even when put"
-  echo "        into different files."
-  echo ""
-  echo "    -O, --use_oq"
-  echo "        type: boolean_true"
-  echo "        Use quality values from OQ tags in preference to standard quality string"
-  echo "        if available."
-  echo ""
-  echo "    -s, --singleton"
-  echo "        type: file, file must exist"
-  echo "        write singleton reads to FILE."
-  echo ""
-  echo "    -t, --copy_tags"
-  echo "        type: boolean_true"
-  echo "        Copy RG, BC and QT tags to the FASTQ header line, if they exist."
-  echo ""
-  echo "    -T, --copy_tags_list"
-  echo "        type: string"
-  echo "        Specify a comma-separated list of tags to copy to the FASTQ header line,"
-  echo "        if they exist."
-  echo "        TAGLIST can be blank or \`*\` to indicate all tags should be copied to the"
-  echo "        output. If using \`*\`,"
-  echo "        be careful to quote it to avoid unwanted shell expansion."
-  echo ""
-  echo "    -1, --read1"
-  echo "        type: file, output, file must exist"
-  echo "        Write reads with the READ1 FLAG set (and READ2 not set) to FILE instead"
-  echo "        of outputting them."
-  echo "        If the -s option is used, only paired reads will be written to this"
-  echo "        file."
-  echo ""
-  echo "    -2, --read2"
-  echo "        type: file, output, file must exist"
-  echo "        Write reads with the READ2 FLAG set (and READ1 not set) to FILE instead"
-  echo "        of outputting them."
-  echo "        If the -s option is used, only paired reads will be written to this"
-  echo "        file."
-  echo ""
-  echo "    -o, --output_reads"
-  echo "        type: file, output, file must exist"
-  echo "        Write reads with either READ1 FLAG or READ2 flag set to FILE instead of"
-  echo "        outputting them to stdout."
-  echo "        This is equivalent to -1 FILE -2 FILE."
-  echo ""
-  echo "    0, --output_reads_both"
-  echo "        type: file, output, file must exist"
-  echo "        Write reads where the READ1 and READ2 FLAG bits set are either both set"
-  echo "        or both unset to FILE"
-  echo "        instead of outputting them."
-  echo ""
-  echo "    -f, --filter_flags"
-  echo "        type: integer"
-  echo "        example: 0"
-  echo "        Only output alignments with all bits set in INT present in the FLAG"
-  echo "        field. INT can be specified"
-  echo "        in hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/) or in octal by"
-  echo "        beginning with '0'"
-  echo "        (i.e. /^0[0-7]+/). Default: \`0\`."
-  echo ""
-  echo "    -F, --excl_flags"
-  echo "        type: string"
-  echo "        example: 0x900"
-  echo "        Do not output alignments with any bits set in INT present in the FLAG"
-  echo "        field. INT can be specified"
-  echo "        in hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/) or in octal by"
-  echo "        beginning with '0'"
-  echo "        (i.e. /^0[0-7]+/). This defaults to 0x900 representing filtering of"
-  echo "        secondary and"
-  echo "        supplementary alignments. Default: \`0x900\`."
-  echo ""
-  echo "    --rf, --incl_flags"
-  echo "        type: string"
-  echo "        example: 0"
-  echo "        Only output alignments with any bits set in INT present in the FLAG"
-  echo "        field. INT can be specified"
-  echo "        in hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/), in octal by"
-  echo "        beginning with '0'"
-  echo "        (i.e. /^0[0-7]+/), as a decimal number not beginning with '0' or as a"
-  echo "        comma-separated list of"
-  echo "        flag names. Default: \`0\`."
-  echo ""
-  echo "    -G, --excl_flags_all"
-  echo "        type: integer"
-  echo "        example: 0"
-  echo "        Only EXCLUDE reads with all of the bits set in INT present in the FLAG"
-  echo "        field. INT can be specified"
-  echo "        in hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/) or in octal by"
-  echo "        beginning with '0' (i.e. /^0[0-7]+/)."
-  echo "        Default: \`0\`."
-  echo ""
-  echo "    -d, --aux_tag"
-  echo "        type: string"
-  echo "        Only output alignments containing an auxiliary tag matching both TAG and"
-  echo "        VAL. If VAL is omitted"
-  echo "        then any value is accepted. The tag types supported are i, f, Z, A and"
-  echo "        H. \"B\" arrays are not"
-  echo "        supported. This is comparable to the method used in samtools view --tag."
-  echo "        The option may be specified"
-  echo "        multiple times and is equivalent to using the --aux_tag_file option."
-  echo ""
-  echo "    -D, --aux_tag_file"
-  echo "        type: string"
-  echo "        Only output alignments containing an auxiliary tag matching TAG and"
-  echo "        having a value listed in FILE."
-  echo "        The format of the file is one line per value. This is equivalent to"
-  echo "        specifying --aux_tag multiple times."
-  echo ""
-  echo "    -i, --casava"
-  echo "        type: boolean_true"
-  echo "        Add Illumina Casava 1.8 format entry to header, for example:"
-  echo "        \`1:N:0:ATCACG\`."
-  echo ""
-  echo "    -c, --compression"
-  echo "        type: integer"
-  echo "        example: 0"
-  echo "        set compression level when writing gz or bgzf fastq files."
-  echo ""
-  echo "    --i1, --index1"
-  echo "        type: file, file must exist"
-  echo "        write first index reads to FILE."
-  echo ""
-  echo "    --i2, --index2"
-  echo "        type: file, file must exist"
-  echo "        write second index reads to FILE."
-  echo ""
-  echo "    --barcode_tag"
-  echo "        type: string"
-  echo "        example: BC"
-  echo "        Auxiliary tag to find index reads in. Default: \`BC\`."
-  echo ""
-  echo "    --quality_tag"
-  echo "        type: string"
-  echo "        example: QT"
-  echo "        Auxiliary tag to find index quality in. Default: \`QT\`."
-  echo ""
-  echo "    --index_format"
-  echo "        type: string"
-  echo "        string to describe how to parse the barcode and quality tags. For"
-  echo "        example:"
-  echo "        * \`i14i8\`: the first 14 characters are index 1, the next 8 characters"
-  echo "        are index 2."
-  echo "        * \`n8i14\`: ignore the first 8 characters, and use the next 14 characters"
-  echo "        for index 1."
-  echo "        If the tag contains a separator, then the numeric part can be replaced"
-  echo "        with '*' to mean"
-  echo "        'read until the separator or end of tag', for example: \`n*i*\`."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -626,9 +453,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_fastq"
-LABEL org.opencontainers.image.created="2024-12-03T10:33:57Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:37Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -743,6 +570,205 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "samtools_fastq main"
+  echo ""
+  echo "Converts a SAM, BAM or CRAM to FASTQ format."
+  echo ""
+  echo "Inputs:"
+  echo "    --input"
+  echo "        type: file, required parameter, file must exist"
+  echo "        input SAM/BAM/CRAM file"
+  echo ""
+  echo "Outputs:"
+  echo "    --output"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        output FASTQ file"
+  echo ""
+  echo "Options:"
+  echo "    -n, --no_suffix"
+  echo "        type: boolean_true"
+  echo "        By default, either '/1' or '/2' is added to the end of read names where"
+  echo "        the corresponding"
+  echo "        READ1 or READ2 FLAG bit is set. Using -n causes read names to be left as"
+  echo "        they are."
+  echo ""
+  echo "    -N, --suffix"
+  echo "        type: boolean_true"
+  echo "        Always add either '/1' or '/2' to the end of read names even when put"
+  echo "        into different files."
+  echo ""
+  echo "    -O, --use_oq"
+  echo "        type: boolean_true"
+  echo "        Use quality values from OQ tags in preference to standard quality string"
+  echo "        if available."
+  echo ""
+  echo "    -s, --singleton"
+  echo "        type: file, file must exist"
+  echo "        write singleton reads to FILE."
+  echo ""
+  echo "    -t, --copy_tags"
+  echo "        type: boolean_true"
+  echo "        Copy RG, BC and QT tags to the FASTQ header line, if they exist."
+  echo ""
+  echo "    -T, --copy_tags_list"
+  echo "        type: string"
+  echo "        Specify a comma-separated list of tags to copy to the FASTQ header line,"
+  echo "        if they exist."
+  echo "        TAGLIST can be blank or \`*\` to indicate all tags should be copied to the"
+  echo "        output. If using \`*\`,"
+  echo "        be careful to quote it to avoid unwanted shell expansion."
+  echo ""
+  echo "    -1, --read1"
+  echo "        type: file, output, file must exist"
+  echo "        Write reads with the READ1 FLAG set (and READ2 not set) to FILE instead"
+  echo "        of outputting them."
+  echo "        If the -s option is used, only paired reads will be written to this"
+  echo "        file."
+  echo ""
+  echo "    -2, --read2"
+  echo "        type: file, output, file must exist"
+  echo "        Write reads with the READ2 FLAG set (and READ1 not set) to FILE instead"
+  echo "        of outputting them."
+  echo "        If the -s option is used, only paired reads will be written to this"
+  echo "        file."
+  echo ""
+  echo "    -o, --output_reads"
+  echo "        type: file, output, file must exist"
+  echo "        Write reads with either READ1 FLAG or READ2 flag set to FILE instead of"
+  echo "        outputting them to stdout."
+  echo "        This is equivalent to -1 FILE -2 FILE."
+  echo ""
+  echo "    0, --output_reads_both"
+  echo "        type: file, output, file must exist"
+  echo "        Write reads where the READ1 and READ2 FLAG bits set are either both set"
+  echo "        or both unset to FILE"
+  echo "        instead of outputting them."
+  echo ""
+  echo "    -f, --filter_flags"
+  echo "        type: integer"
+  echo "        example: 0"
+  echo "        Only output alignments with all bits set in INT present in the FLAG"
+  echo "        field. INT can be specified"
+  echo "        in hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/) or in octal by"
+  echo "        beginning with '0'"
+  echo "        (i.e. /^0[0-7]+/). Default: \`0\`."
+  echo ""
+  echo "    -F, --excl_flags"
+  echo "        type: string"
+  echo "        example: 0x900"
+  echo "        Do not output alignments with any bits set in INT present in the FLAG"
+  echo "        field. INT can be specified"
+  echo "        in hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/) or in octal by"
+  echo "        beginning with '0'"
+  echo "        (i.e. /^0[0-7]+/). This defaults to 0x900 representing filtering of"
+  echo "        secondary and"
+  echo "        supplementary alignments. Default: \`0x900\`."
+  echo ""
+  echo "    --rf, --incl_flags"
+  echo "        type: string"
+  echo "        example: 0"
+  echo "        Only output alignments with any bits set in INT present in the FLAG"
+  echo "        field. INT can be specified"
+  echo "        in hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/), in octal by"
+  echo "        beginning with '0'"
+  echo "        (i.e. /^0[0-7]+/), as a decimal number not beginning with '0' or as a"
+  echo "        comma-separated list of"
+  echo "        flag names. Default: \`0\`."
+  echo ""
+  echo "    -G, --excl_flags_all"
+  echo "        type: integer"
+  echo "        example: 0"
+  echo "        Only EXCLUDE reads with all of the bits set in INT present in the FLAG"
+  echo "        field. INT can be specified"
+  echo "        in hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/) or in octal by"
+  echo "        beginning with '0' (i.e. /^0[0-7]+/)."
+  echo "        Default: \`0\`."
+  echo ""
+  echo "    -d, --aux_tag"
+  echo "        type: string"
+  echo "        Only output alignments containing an auxiliary tag matching both TAG and"
+  echo "        VAL. If VAL is omitted"
+  echo "        then any value is accepted. The tag types supported are i, f, Z, A and"
+  echo "        H. \"B\" arrays are not"
+  echo "        supported. This is comparable to the method used in samtools view --tag."
+  echo "        The option may be specified"
+  echo "        multiple times and is equivalent to using the --aux_tag_file option."
+  echo ""
+  echo "    -D, --aux_tag_file"
+  echo "        type: string"
+  echo "        Only output alignments containing an auxiliary tag matching TAG and"
+  echo "        having a value listed in FILE."
+  echo "        The format of the file is one line per value. This is equivalent to"
+  echo "        specifying --aux_tag multiple times."
+  echo ""
+  echo "    -i, --casava"
+  echo "        type: boolean_true"
+  echo "        Add Illumina Casava 1.8 format entry to header, for example:"
+  echo "        \`1:N:0:ATCACG\`."
+  echo ""
+  echo "    -c, --compression"
+  echo "        type: integer"
+  echo "        example: 0"
+  echo "        set compression level when writing gz or bgzf fastq files."
+  echo ""
+  echo "    --i1, --index1"
+  echo "        type: file, file must exist"
+  echo "        write first index reads to FILE."
+  echo ""
+  echo "    --i2, --index2"
+  echo "        type: file, file must exist"
+  echo "        write second index reads to FILE."
+  echo ""
+  echo "    --barcode_tag"
+  echo "        type: string"
+  echo "        example: BC"
+  echo "        Auxiliary tag to find index reads in. Default: \`BC\`."
+  echo ""
+  echo "    --quality_tag"
+  echo "        type: string"
+  echo "        example: QT"
+  echo "        Auxiliary tag to find index quality in. Default: \`QT\`."
+  echo ""
+  echo "    --index_format"
+  echo "        type: string"
+  echo "        string to describe how to parse the barcode and quality tags. For"
+  echo "        example:"
+  echo "        * \`i14i8\`: the first 14 characters are index 1, the next 8 characters"
+  echo "        are index 2."
+  echo "        * \`n8i14\`: ignore the first 8 characters, and use the next 14 characters"
+  echo "        for index 1."
+  echo "        If the tag contains a separator, then the numeric part can be replaced"
+  echo "        with '*' to mean"
+  echo "        'read until the separator or end of tag', for example: \`n*i*\`."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/samtools/samtools_flagstat/.config.vsh.yaml b/target/executable/samtools/samtools_flagstat/.config.vsh.yaml
index 532c5c1a..7be99a25 100644
--- a/target/executable/samtools/samtools_flagstat/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_flagstat/.config.vsh.yaml
@@ -66,6 +66,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -172,16 +175,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/samtools/samtools_flagstat"
   executable: "target/executable/samtools/samtools_flagstat/samtools_flagstat"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/samtools/samtools_flagstat/samtools_flagstat b/target/executable/samtools/samtools_flagstat/samtools_flagstat
index a9b1bfb2..67f28cab 100755
--- a/target/executable/samtools/samtools_flagstat/samtools_flagstat
+++ b/target/executable/samtools/samtools_flagstat/samtools_flagstat
@@ -2,7 +2,7 @@
 
 # samtools_flagstat main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,27 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "samtools_flagstat main"
-  echo ""
-  echo "Counts the number of alignments in SAM/BAM/CRAM files for each FLAG type."
-  echo ""
-  echo "Inputs:"
-  echo "    --bam"
-  echo "        type: file, file must exist"
-  echo "        BAM input files."
-  echo ""
-  echo "    --bai"
-  echo "        type: file, file must exist"
-  echo "        BAM index file."
-  echo ""
-  echo "Outputs:"
-  echo "    --output"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        example: output.flagstat"
-  echo "        File containing samtools stats output."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -474,9 +453,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_flagstat"
-LABEL org.opencontainers.image.created="2024-12-03T10:33:58Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:39Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -591,6 +570,53 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "samtools_flagstat main"
+  echo ""
+  echo "Counts the number of alignments in SAM/BAM/CRAM files for each FLAG type."
+  echo ""
+  echo "Inputs:"
+  echo "    --bam"
+  echo "        type: file, file must exist"
+  echo "        BAM input files."
+  echo ""
+  echo "    --bai"
+  echo "        type: file, file must exist"
+  echo "        BAM index file."
+  echo ""
+  echo "Outputs:"
+  echo "    --output"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        example: output.flagstat"
+  echo "        File containing samtools stats output."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/samtools/samtools_idxstats/.config.vsh.yaml b/target/executable/samtools/samtools_idxstats/.config.vsh.yaml
index c6981d2d..2f8322db 100644
--- a/target/executable/samtools/samtools_idxstats/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_idxstats/.config.vsh.yaml
@@ -75,6 +75,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -182,16 +185,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/samtools/samtools_idxstats"
   executable: "target/executable/samtools/samtools_idxstats/samtools_idxstats"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/samtools/samtools_idxstats/samtools_idxstats b/target/executable/samtools/samtools_idxstats/samtools_idxstats
index 95962259..76df52e4 100755
--- a/target/executable/samtools/samtools_idxstats/samtools_idxstats
+++ b/target/executable/samtools/samtools_idxstats/samtools_idxstats
@@ -2,7 +2,7 @@
 
 # samtools_idxstats main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,31 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "samtools_idxstats main"
-  echo ""
-  echo "Reports alignment summary statistics for a BAM file."
-  echo ""
-  echo "Inputs:"
-  echo "    --bam"
-  echo "        type: file, file must exist"
-  echo "        BAM input file."
-  echo ""
-  echo "    --bai"
-  echo "        type: file, file must exist"
-  echo "        BAM index file."
-  echo ""
-  echo "    --fasta"
-  echo "        type: file, file must exist"
-  echo "        Reference file the CRAM was created with (optional)."
-  echo ""
-  echo "Outputs:"
-  echo "    --output"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        example: output.idxstats"
-  echo "        File containing samtools stats output in tab-delimited format."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -478,9 +453,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_idxstats"
-LABEL org.opencontainers.image.created="2024-12-03T10:34:00Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:39Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -595,6 +570,57 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "samtools_idxstats main"
+  echo ""
+  echo "Reports alignment summary statistics for a BAM file."
+  echo ""
+  echo "Inputs:"
+  echo "    --bam"
+  echo "        type: file, file must exist"
+  echo "        BAM input file."
+  echo ""
+  echo "    --bai"
+  echo "        type: file, file must exist"
+  echo "        BAM index file."
+  echo ""
+  echo "    --fasta"
+  echo "        type: file, file must exist"
+  echo "        Reference file the CRAM was created with (optional)."
+  echo ""
+  echo "Outputs:"
+  echo "    --output"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        example: output.idxstats"
+  echo "        File containing samtools stats output in tab-delimited format."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/samtools/samtools_index/.config.vsh.yaml b/target/executable/samtools/samtools_index/.config.vsh.yaml
index 4cd45f17..40351902 100644
--- a/target/executable/samtools/samtools_index/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_index/.config.vsh.yaml
@@ -84,6 +84,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -188,16 +191,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/samtools/samtools_index"
   executable: "target/executable/samtools/samtools_index/samtools_index"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/samtools/samtools_index/samtools_index b/target/executable/samtools/samtools_index/samtools_index
index 946cc145..3d89c0d4 100755
--- a/target/executable/samtools/samtools_index/samtools_index
+++ b/target/executable/samtools/samtools_index/samtools_index
@@ -2,7 +2,7 @@
 
 # samtools_index main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,38 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "samtools_index main"
-  echo ""
-  echo "Index SAM/BAM/CRAM files."
-  echo ""
-  echo "Inputs:"
-  echo "    --input"
-  echo "        type: file, required parameter, file must exist"
-  echo "        Input file name"
-  echo ""
-  echo "Outputs:"
-  echo "    -o, --output"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        example: out.bam.bai"
-  echo "        Output file name"
-  echo ""
-  echo "Options:"
-  echo "    -b, --bai"
-  echo "        type: boolean_true"
-  echo "        Generate BAM index"
-  echo ""
-  echo "    -c, --csi"
-  echo "        type: boolean_true"
-  echo "        Create a CSI index for BAM files instead of the traditional BAI"
-  echo "        index. This will be required for genomes with larger chromosome"
-  echo "        sizes."
-  echo ""
-  echo "    -m, --min_shift"
-  echo "        type: integer"
-  echo "        Create a CSI index, with a minimum interval size of 2^INT."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -485,9 +453,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_index"
-LABEL org.opencontainers.image.created="2024-12-03T10:33:59Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:38Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -602,6 +570,64 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "samtools_index main"
+  echo ""
+  echo "Index SAM/BAM/CRAM files."
+  echo ""
+  echo "Inputs:"
+  echo "    --input"
+  echo "        type: file, required parameter, file must exist"
+  echo "        Input file name"
+  echo ""
+  echo "Outputs:"
+  echo "    -o, --output"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        example: out.bam.bai"
+  echo "        Output file name"
+  echo ""
+  echo "Options:"
+  echo "    -b, --bai"
+  echo "        type: boolean_true"
+  echo "        Generate BAM index"
+  echo ""
+  echo "    -c, --csi"
+  echo "        type: boolean_true"
+  echo "        Create a CSI index for BAM files instead of the traditional BAI"
+  echo "        index. This will be required for genomes with larger chromosome"
+  echo "        sizes."
+  echo ""
+  echo "    -m, --min_shift"
+  echo "        type: integer"
+  echo "        Create a CSI index, with a minimum interval size of 2^INT."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/samtools/samtools_sort/.config.vsh.yaml b/target/executable/samtools/samtools_sort/.config.vsh.yaml
index 092019df..5487ae1e 100644
--- a/target/executable/samtools/samtools_sort/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_sort/.config.vsh.yaml
@@ -227,6 +227,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -331,16 +334,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/samtools/samtools_sort"
   executable: "target/executable/samtools/samtools_sort/samtools_sort"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/samtools/samtools_sort/samtools_sort b/target/executable/samtools/samtools_sort/samtools_sort
index 311a300f..24b4b039 100755
--- a/target/executable/samtools/samtools_sort/samtools_sort
+++ b/target/executable/samtools/samtools_sort/samtools_sort
@@ -2,7 +2,7 @@
 
 # samtools_sort main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,109 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "samtools_sort main"
-  echo ""
-  echo "Sort SAM/BAM/CRAM file."
-  echo ""
-  echo "Inputs:"
-  echo "    --input"
-  echo "        type: file, required parameter, file must exist"
-  echo "        SAM/BAM/CRAM input file."
-  echo ""
-  echo "Outputs:"
-  echo "    --output"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        example: out.bam"
-  echo "        Write final output to file."
-  echo ""
-  echo "    -O, --output_fmt"
-  echo "        type: string"
-  echo "        example: BAM"
-  echo "        Specify output format (SAM, BAM, CRAM)."
-  echo ""
-  echo "    --output_fmt_option"
-  echo "        type: string"
-  echo "        Specify a single output file format option in the form"
-  echo "        of OPTION or OPTION=VALUE."
-  echo ""
-  echo "    --reference"
-  echo "        type: file, file must exist"
-  echo "        example: ref.fa"
-  echo "        Reference sequence FASTA FILE."
-  echo ""
-  echo "    --write_index"
-  echo "        type: boolean_true"
-  echo "        Automatically index the output files."
-  echo ""
-  echo "    -T, --prefix"
-  echo "        type: string"
-  echo "        Write temporary files to PREFIX.nnnn.bam."
-  echo ""
-  echo "    --no_PG"
-  echo "        type: boolean_true"
-  echo "        Do not add a PG line."
-  echo ""
-  echo "    --template_coordinate"
-  echo "        type: boolean_true"
-  echo "        Sort by template-coordinate."
-  echo ""
-  echo "    --input_fmt_option"
-  echo "        type: string"
-  echo "        Specify a single input file format option in the form"
-  echo "        of OPTION or OPTION=VALUE."
-  echo ""
-  echo "Options:"
-  echo "    -l, --compression"
-  echo "        type: integer"
-  echo "        default: 0"
-  echo "        Set compression level, from 0 (uncompressed) to 9 (best)."
-  echo ""
-  echo "    -u, --uncompressed"
-  echo "        type: boolean_true"
-  echo "        Output uncompressed data (equivalent to --compression 0)."
-  echo ""
-  echo "    -M, --minimiser"
-  echo "        type: boolean_true"
-  echo "        Use minimiser for clustering unaligned/unplaced reads."
-  echo ""
-  echo "    -R, --not_reverse"
-  echo "        type: boolean_true"
-  echo "        Do not use reverse strand (only compatible with --minimiser)"
-  echo ""
-  echo "    -K, --kmer_size"
-  echo "        type: integer"
-  echo "        example: 20"
-  echo "        Kmer size to use for minimiser."
-  echo ""
-  echo "    -I, --order"
-  echo "        type: file, file must exist"
-  echo "        example: ref.fa"
-  echo "        Order minimisers by their position in FILE FASTA."
-  echo ""
-  echo "    -w, --window"
-  echo "        type: integer"
-  echo "        example: 100"
-  echo "        Window size for minimiser INDEXING VIA --order REF.FA."
-  echo ""
-  echo "    -H, --homopolymers"
-  echo "        type: boolean_true"
-  echo "        Squash homopolymers when computing minimiser."
-  echo ""
-  echo "    -n, --natural_sort"
-  echo "        type: boolean_true"
-  echo "        Sort by read name (natural): cannot be used with samtools index."
-  echo ""
-  echo "    -N, --ascii_sort"
-  echo "        type: boolean_true"
-  echo "        Sort by read name (ASCII): cannot be used with samtools index."
-  echo ""
-  echo "    -t, --tag"
-  echo "        type: string"
-  echo "        Sort by value of TAG. Uses position as secondary index"
-  echo "        (or read name if --natural_sort is set)."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -556,9 +453,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_sort"
-LABEL org.opencontainers.image.created="2024-12-03T10:33:59Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:38Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -673,6 +570,135 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "samtools_sort main"
+  echo ""
+  echo "Sort SAM/BAM/CRAM file."
+  echo ""
+  echo "Inputs:"
+  echo "    --input"
+  echo "        type: file, required parameter, file must exist"
+  echo "        SAM/BAM/CRAM input file."
+  echo ""
+  echo "Outputs:"
+  echo "    --output"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        example: out.bam"
+  echo "        Write final output to file."
+  echo ""
+  echo "    -O, --output_fmt"
+  echo "        type: string"
+  echo "        example: BAM"
+  echo "        Specify output format (SAM, BAM, CRAM)."
+  echo ""
+  echo "    --output_fmt_option"
+  echo "        type: string"
+  echo "        Specify a single output file format option in the form"
+  echo "        of OPTION or OPTION=VALUE."
+  echo ""
+  echo "    --reference"
+  echo "        type: file, file must exist"
+  echo "        example: ref.fa"
+  echo "        Reference sequence FASTA FILE."
+  echo ""
+  echo "    --write_index"
+  echo "        type: boolean_true"
+  echo "        Automatically index the output files."
+  echo ""
+  echo "    -T, --prefix"
+  echo "        type: string"
+  echo "        Write temporary files to PREFIX.nnnn.bam."
+  echo ""
+  echo "    --no_PG"
+  echo "        type: boolean_true"
+  echo "        Do not add a PG line."
+  echo ""
+  echo "    --template_coordinate"
+  echo "        type: boolean_true"
+  echo "        Sort by template-coordinate."
+  echo ""
+  echo "    --input_fmt_option"
+  echo "        type: string"
+  echo "        Specify a single input file format option in the form"
+  echo "        of OPTION or OPTION=VALUE."
+  echo ""
+  echo "Options:"
+  echo "    -l, --compression"
+  echo "        type: integer"
+  echo "        default: 0"
+  echo "        Set compression level, from 0 (uncompressed) to 9 (best)."
+  echo ""
+  echo "    -u, --uncompressed"
+  echo "        type: boolean_true"
+  echo "        Output uncompressed data (equivalent to --compression 0)."
+  echo ""
+  echo "    -M, --minimiser"
+  echo "        type: boolean_true"
+  echo "        Use minimiser for clustering unaligned/unplaced reads."
+  echo ""
+  echo "    -R, --not_reverse"
+  echo "        type: boolean_true"
+  echo "        Do not use reverse strand (only compatible with --minimiser)"
+  echo ""
+  echo "    -K, --kmer_size"
+  echo "        type: integer"
+  echo "        example: 20"
+  echo "        Kmer size to use for minimiser."
+  echo ""
+  echo "    -I, --order"
+  echo "        type: file, file must exist"
+  echo "        example: ref.fa"
+  echo "        Order minimisers by their position in FILE FASTA."
+  echo ""
+  echo "    -w, --window"
+  echo "        type: integer"
+  echo "        example: 100"
+  echo "        Window size for minimiser INDEXING VIA --order REF.FA."
+  echo ""
+  echo "    -H, --homopolymers"
+  echo "        type: boolean_true"
+  echo "        Squash homopolymers when computing minimiser."
+  echo ""
+  echo "    -n, --natural_sort"
+  echo "        type: boolean_true"
+  echo "        Sort by read name (natural): cannot be used with samtools index."
+  echo ""
+  echo "    -N, --ascii_sort"
+  echo "        type: boolean_true"
+  echo "        Sort by read name (ASCII): cannot be used with samtools index."
+  echo ""
+  echo "    -t, --tag"
+  echo "        type: string"
+  echo "        Sort by value of TAG. Uses position as secondary index"
+  echo "        (or read name if --natural_sort is set)."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/samtools/samtools_stats/.config.vsh.yaml b/target/executable/samtools/samtools_stats/.config.vsh.yaml
index 46bc1acb..208337de 100644
--- a/target/executable/samtools/samtools_stats/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_stats/.config.vsh.yaml
@@ -295,6 +295,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -400,16 +403,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/samtools/samtools_stats"
   executable: "target/executable/samtools/samtools_stats/samtools_stats"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/samtools/samtools_stats/samtools_stats b/target/executable/samtools/samtools_stats/samtools_stats
index 42ef5bae..84ba3d2c 100755
--- a/target/executable/samtools/samtools_stats/samtools_stats
+++ b/target/executable/samtools/samtools_stats/samtools_stats
@@ -2,7 +2,7 @@
 
 # samtools_stats main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,128 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "samtools_stats main"
-  echo ""
-  echo "Reports alignment summary statistics for a BAM file."
-  echo ""
-  echo "Inputs:"
-  echo "    --input"
-  echo "        type: file, required parameter, file must exist"
-  echo "        Input file."
-  echo ""
-  echo "    --bai"
-  echo "        type: file, file must exist"
-  echo "        Index file."
-  echo ""
-  echo "    --fasta"
-  echo "        type: file, file must exist"
-  echo "        Reference file the CRAM was created with."
-  echo ""
-  echo "    -c, --coverage"
-  echo "        type: integer, multiple values allowed"
-  echo "        example: 1;1000;1"
-  echo "        Coverage distribution min;max;step. Default: [1, 1000, 1]."
-  echo ""
-  echo "    -d, --remove_dups"
-  echo "        type: boolean_true"
-  echo "        Exclude from statistics reads marked as duplicates."
-  echo ""
-  echo "    -X, --customized_index_file"
-  echo "        type: boolean_true"
-  echo "        Use a customized index file."
-  echo ""
-  echo "    -f, --required_flag"
-  echo "        type: string"
-  echo "        example: 0"
-  echo "        Required flag, 0 for unset. See also \`samtools flags\`. Default: \`\"0\"\`."
-  echo ""
-  echo "    -F, --filtering_flag"
-  echo "        type: string"
-  echo "        example: 0"
-  echo "        Filtering flag, 0 for unset. See also \`samtools flags\`. Default: \`0\`."
-  echo ""
-  echo "    --GC_depth"
-  echo "        type: double"
-  echo "        example: 20000.0"
-  echo "        The size of GC-depth bins (decreasing bin size increases memory"
-  echo "        requirement). Default: \`20000\`."
-  echo ""
-  echo "    -i, --insert_size"
-  echo "        type: integer"
-  echo "        example: 8000"
-  echo "        Maximum insert size. Default: \`8000\`."
-  echo ""
-  echo "    -I, --id"
-  echo "        type: string"
-  echo "        Include only listed read group or sample name."
-  echo ""
-  echo "    -l, --read_length"
-  echo "        type: integer"
-  echo "        example: -1"
-  echo "        Include in the statistics only reads with the given read length."
-  echo "        Default: \`-1\`."
-  echo ""
-  echo "    -m, --most_inserts"
-  echo "        type: double"
-  echo "        example: 0.99"
-  echo "        Report only the main part of inserts. Default: \`0.99\`."
-  echo ""
-  echo "    -P, --split_prefix"
-  echo "        type: string"
-  echo "        Path or string prefix for filepaths output by --split (default is input"
-  echo "        filename)."
-  echo ""
-  echo "    -q, --trim_quality"
-  echo "        type: integer"
-  echo "        example: 0"
-  echo "        The BWA trimming parameter. Default: \`0\`."
-  echo ""
-  echo "    -r, --ref_seq"
-  echo "        type: file, file must exist"
-  echo "        Reference sequence (required for GC-depth and mismatches-per-cycle"
-  echo "        calculation)."
-  echo ""
-  echo "    -S, --split"
-  echo "        type: string"
-  echo "        Also write statistics to separate files split by tagged field."
-  echo ""
-  echo "    -t, --target_regions"
-  echo "        type: file, file must exist"
-  echo "        Do stats in these regions only. Tab-delimited file chr,from,to, 1-based,"
-  echo "        inclusive."
-  echo ""
-  echo "    -x, --sparse"
-  echo "        type: boolean_true"
-  echo "        Suppress outputting IS rows where there are no insertions."
-  echo ""
-  echo "    -p, --remove_overlaps"
-  echo "        type: boolean_true"
-  echo "        Remove overlaps of paired-end reads from coverage and base count"
-  echo "        computations."
-  echo ""
-  echo "    -g, --cov_threshold"
-  echo "        type: integer"
-  echo "        example: 0"
-  echo "        Only bases with coverage above this value will be included in the target"
-  echo "        percentage computation. Default: \`0\`."
-  echo ""
-  echo "    --input_fmt_option"
-  echo "        type: string"
-  echo "        Specify a single input file format option in the form of OPTION or"
-  echo "        OPTION=VALUE."
-  echo ""
-  echo "    --reference"
-  echo "        type: file, file must exist"
-  echo "        Reference sequence FASTA FILE."
-  echo ""
-  echo "Outputs:"
-  echo "    -o, --output"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        example: out.txt"
-  echo "        Output file."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -575,9 +453,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_stats"
-LABEL org.opencontainers.image.created="2024-12-03T10:33:59Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:38Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -692,6 +570,154 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "samtools_stats main"
+  echo ""
+  echo "Reports alignment summary statistics for a BAM file."
+  echo ""
+  echo "Inputs:"
+  echo "    --input"
+  echo "        type: file, required parameter, file must exist"
+  echo "        Input file."
+  echo ""
+  echo "    --bai"
+  echo "        type: file, file must exist"
+  echo "        Index file."
+  echo ""
+  echo "    --fasta"
+  echo "        type: file, file must exist"
+  echo "        Reference file the CRAM was created with."
+  echo ""
+  echo "    -c, --coverage"
+  echo "        type: integer, multiple values allowed"
+  echo "        example: 1;1000;1"
+  echo "        Coverage distribution min;max;step. Default: [1, 1000, 1]."
+  echo ""
+  echo "    -d, --remove_dups"
+  echo "        type: boolean_true"
+  echo "        Exclude from statistics reads marked as duplicates."
+  echo ""
+  echo "    -X, --customized_index_file"
+  echo "        type: boolean_true"
+  echo "        Use a customized index file."
+  echo ""
+  echo "    -f, --required_flag"
+  echo "        type: string"
+  echo "        example: 0"
+  echo "        Required flag, 0 for unset. See also \`samtools flags\`. Default: \`\"0\"\`."
+  echo ""
+  echo "    -F, --filtering_flag"
+  echo "        type: string"
+  echo "        example: 0"
+  echo "        Filtering flag, 0 for unset. See also \`samtools flags\`. Default: \`0\`."
+  echo ""
+  echo "    --GC_depth"
+  echo "        type: double"
+  echo "        example: 20000.0"
+  echo "        The size of GC-depth bins (decreasing bin size increases memory"
+  echo "        requirement). Default: \`20000\`."
+  echo ""
+  echo "    -i, --insert_size"
+  echo "        type: integer"
+  echo "        example: 8000"
+  echo "        Maximum insert size. Default: \`8000\`."
+  echo ""
+  echo "    -I, --id"
+  echo "        type: string"
+  echo "        Include only listed read group or sample name."
+  echo ""
+  echo "    -l, --read_length"
+  echo "        type: integer"
+  echo "        example: -1"
+  echo "        Include in the statistics only reads with the given read length."
+  echo "        Default: \`-1\`."
+  echo ""
+  echo "    -m, --most_inserts"
+  echo "        type: double"
+  echo "        example: 0.99"
+  echo "        Report only the main part of inserts. Default: \`0.99\`."
+  echo ""
+  echo "    -P, --split_prefix"
+  echo "        type: string"
+  echo "        Path or string prefix for filepaths output by --split (default is input"
+  echo "        filename)."
+  echo ""
+  echo "    -q, --trim_quality"
+  echo "        type: integer"
+  echo "        example: 0"
+  echo "        The BWA trimming parameter. Default: \`0\`."
+  echo ""
+  echo "    -r, --ref_seq"
+  echo "        type: file, file must exist"
+  echo "        Reference sequence (required for GC-depth and mismatches-per-cycle"
+  echo "        calculation)."
+  echo ""
+  echo "    -S, --split"
+  echo "        type: string"
+  echo "        Also write statistics to separate files split by tagged field."
+  echo ""
+  echo "    -t, --target_regions"
+  echo "        type: file, file must exist"
+  echo "        Do stats in these regions only. Tab-delimited file chr,from,to, 1-based,"
+  echo "        inclusive."
+  echo ""
+  echo "    -x, --sparse"
+  echo "        type: boolean_true"
+  echo "        Suppress outputting IS rows where there are no insertions."
+  echo ""
+  echo "    -p, --remove_overlaps"
+  echo "        type: boolean_true"
+  echo "        Remove overlaps of paired-end reads from coverage and base count"
+  echo "        computations."
+  echo ""
+  echo "    -g, --cov_threshold"
+  echo "        type: integer"
+  echo "        example: 0"
+  echo "        Only bases with coverage above this value will be included in the target"
+  echo "        percentage computation. Default: \`0\`."
+  echo ""
+  echo "    --input_fmt_option"
+  echo "        type: string"
+  echo "        Specify a single input file format option in the form of OPTION or"
+  echo "        OPTION=VALUE."
+  echo ""
+  echo "    --reference"
+  echo "        type: file, file must exist"
+  echo "        Reference sequence FASTA FILE."
+  echo ""
+  echo "Outputs:"
+  echo "    -o, --output"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        example: out.txt"
+  echo "        Output file."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/samtools/samtools_view/.config.vsh.yaml b/target/executable/samtools/samtools_view/.config.vsh.yaml
index a8bce0fb..8cb7b649 100644
--- a/target/executable/samtools/samtools_view/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_view/.config.vsh.yaml
@@ -559,6 +559,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -664,16 +667,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/samtools/samtools_view"
   executable: "target/executable/samtools/samtools_view/samtools_view"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/samtools/samtools_view/samtools_view b/target/executable/samtools/samtools_view/samtools_view
index 510371d6..c13166de 100755
--- a/target/executable/samtools/samtools_view/samtools_view
+++ b/target/executable/samtools/samtools_view/samtools_view
@@ -2,7 +2,7 @@
 
 # samtools_view main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,6 +172,405 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
+
+# initialise variables
+VIASH_MODE='run'
+VIASH_ENGINE_ID='docker'
+
+######## Helper functions for setting up Docker images for viash ########
+# expects: ViashDockerBuild
+
+# ViashDockerInstallationCheck: check whether Docker is installed correctly
+#
+# examples:
+#   ViashDockerInstallationCheck
+function ViashDockerInstallationCheck {
+  ViashDebug "Checking whether Docker is installed"
+  if [ ! command -v docker &> /dev/null ]; then
+    ViashCritical "Docker doesn't seem to be installed. See 'https://docs.docker.com/get-docker/' for instructions."
+    exit 1
+  fi
+
+  ViashDebug "Checking whether the Docker daemon is running"
+  local save=$-; set +e
+  local docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
+  local out=$?
+  [[ $save =~ e ]] && set -e
+  if [ $out -ne 0 ]; then
+    ViashCritical "Docker daemon does not seem to be running. Try one of the following:"
+    ViashCritical "- Try running 'dockerd' in the command line"
+    ViashCritical "- See https://docs.docker.com/config/daemon/"
+    exit 1
+  fi
+}
+
+# ViashDockerRemoteTagCheck: check whether a Docker image is available 
+# on a remote. Assumes `docker login` has been performed, if relevant.
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   ViashDockerRemoteTagCheck python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerRemoteTagCheck sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerRemoteTagCheck {
+  docker manifest inspect $1 > /dev/null 2> /dev/null
+}
+
+# ViashDockerLocalTagCheck: check whether a Docker image is available locally
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   docker pull python:latest
+#   ViashDockerLocalTagCheck python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerLocalTagCheck sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerLocalTagCheck {
+  [ -n "$(docker images -q $1)" ]
+}
+
+# ViashDockerPull: pull a Docker image
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   ViashDockerPull python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerPull sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerPull {
+  ViashNotice "Checking if Docker image is available at '$1'"
+  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
+    docker pull $1 && return 0 || return 1
+  else
+    local save=$-; set +e
+    docker pull $1 2> /dev/null > /dev/null
+    local out=$?
+    [[ $save =~ e ]] && set -e
+    if [ $out -ne 0 ]; then
+      ViashWarning "Could not pull from '$1'. Docker image doesn't exist or is not accessible."
+    fi
+    return $out
+  fi
+}
+
+# ViashDockerPush: push a Docker image
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   ViashDockerPush python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerPush sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerPush {
+  ViashNotice "Pushing image to '$1'"
+  local save=$-; set +e
+  local out
+  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
+    docker push $1
+    out=$?
+  else
+    docker push $1 2> /dev/null > /dev/null
+    out=$?
+  fi
+  [[ $save =~ e ]] && set -e
+  if [ $out -eq 0 ]; then
+    ViashNotice "Container '$1' push succeeded."
+  else
+    ViashError "Container '$1' push errored. You might not be logged in or have the necessary permissions."
+  fi
+  return $out
+}
+
+# ViashDockerPullElseBuild: pull a Docker image, else build it
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# ViashDockerBuild    : a Bash function which builds a docker image, takes image identifier as argument.
+# examples:
+#   ViashDockerPullElseBuild mynewcomponent
+function ViashDockerPullElseBuild {
+  local save=$-; set +e
+  ViashDockerPull $1
+  local out=$?
+  [[ $save =~ e ]] && set -e
+  if [ $out -ne 0 ]; then
+    ViashDockerBuild $@
+  fi
+}
+
+# ViashDockerSetup: create a Docker image, according to specified docker setup strategy
+#
+# $1          : image identifier with format `[registry/]image[:tag]`
+# $2          : docker setup strategy, see DockerSetupStrategy.scala
+# examples:
+#   ViashDockerSetup mynewcomponent alwaysbuild
+function ViashDockerSetup {
+  local image_id="$1"
+  local setup_strategy="$2"
+  if [ "$setup_strategy" == "alwaysbuild" -o "$setup_strategy" == "build" -o "$setup_strategy" == "b" ]; then
+    ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+  elif [ "$setup_strategy" == "alwayspull" -o "$setup_strategy" == "pull" -o "$setup_strategy" == "p" ]; then
+    ViashDockerPull $image_id
+  elif [ "$setup_strategy" == "alwayspullelsebuild" -o "$setup_strategy" == "pullelsebuild" ]; then
+    ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+  elif [ "$setup_strategy" == "alwayspullelsecachedbuild" -o "$setup_strategy" == "pullelsecachedbuild" ]; then
+    ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+  elif [ "$setup_strategy" == "alwayscachedbuild" -o "$setup_strategy" == "cachedbuild" -o "$setup_strategy" == "cb" ]; then
+    ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+  elif [[ "$setup_strategy" =~ ^ifneedbe ]]; then
+    local save=$-; set +e
+    ViashDockerLocalTagCheck $image_id
+    local outCheck=$?
+    [[ $save =~ e ]] && set -e
+    if [ $outCheck -eq 0 ]; then
+      ViashInfo "Image $image_id already exists"
+    elif [ "$setup_strategy" == "ifneedbebuild" ]; then
+      ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+    elif [ "$setup_strategy" == "ifneedbecachedbuild" ]; then
+      ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+    elif [ "$setup_strategy" == "ifneedbepull" ]; then
+      ViashDockerPull $image_id
+    elif [ "$setup_strategy" == "ifneedbepullelsebuild" ]; then
+      ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+    elif [ "$setup_strategy" == "ifneedbepullelsecachedbuild" ]; then
+      ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+    else
+      ViashError "Unrecognised Docker strategy: $setup_strategy"
+      exit 1
+    fi
+  elif [ "$setup_strategy" == "push" -o "$setup_strategy" == "forcepush" -o "$setup_strategy" == "alwayspush" ]; then
+    ViashDockerPush "$image_id"
+  elif [ "$setup_strategy" == "pushifnotpresent" -o "$setup_strategy" == "gentlepush" -o "$setup_strategy" == "maybepush" ]; then
+    local save=$-; set +e
+    ViashDockerRemoteTagCheck $image_id
+    local outCheck=$?
+    [[ $save =~ e ]] && set -e
+    if [ $outCheck -eq 0 ]; then
+      ViashNotice "Container '$image_id' exists, doing nothing."
+    else
+      ViashNotice "Container '$image_id' does not yet exist."
+      ViashDockerPush "$image_id"
+    fi
+  elif [ "$setup_strategy" == "donothing" -o "$setup_strategy" == "meh" ]; then
+    ViashNotice "Skipping setup."
+  else
+    ViashError "Unrecognised Docker strategy: $setup_strategy"
+    exit 1
+  fi
+}
+
+# ViashDockerCheckCommands: Check whether a docker container has the required commands
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# $@                  : commands to verify being present
+# examples:
+#   ViashDockerCheckCommands bash:4.0 bash ps foo
+function ViashDockerCheckCommands {
+  local image_id="$1"
+  shift 1
+  local commands="$@"
+  local save=$-; set +e
+  local missing # mark 'missing' as local in advance, otherwise the exit code of the command will be missing and always be '0'
+  missing=$(docker run --rm --entrypoint=sh "$image_id" -c "for command in $commands; do command -v \$command >/dev/null 2>&1; if [ \$? -ne 0 ]; then echo \$command; exit 1; fi; done")
+  local outCheck=$?
+  [[ $save =~ e ]] && set -e
+  if [ $outCheck -ne 0 ]; then
+  	ViashError "Docker container '$image_id' does not contain command '$missing'."
+  	exit 1
+  fi
+}
+
+# ViashDockerBuild: build a docker image
+# $1                               : image identifier with format `[registry/]image[:tag]`
+# $...                             : additional arguments to pass to docker build
+# $VIASH_META_TEMP_DIR             : temporary directory to store dockerfile & optional resources in
+# $VIASH_META_NAME                 : name of the component
+# $VIASH_META_RESOURCES_DIR        : directory containing the resources
+# $VIASH_VERBOSITY                 : verbosity level
+# exit code $?                     : whether or not the image was built successfully
+function ViashDockerBuild {
+  local image_id="$1"
+  shift 1
+
+  # create temporary directory to store dockerfile & optional resources in
+  local tmpdir=$(mktemp -d "$VIASH_META_TEMP_DIR/dockerbuild-$VIASH_META_NAME-XXXXXX")
+  local dockerfile="$tmpdir/Dockerfile"
+  function clean_up {
+    rm -rf "$tmpdir"
+  }
+  trap clean_up EXIT
+
+  # store dockerfile and resources
+  ViashDockerfile "$VIASH_ENGINE_ID" > "$dockerfile"
+
+  # generate the build command
+  local docker_build_cmd="docker build -t '$image_id' $@ '$VIASH_META_RESOURCES_DIR' -f '$dockerfile'"
+
+  # build the container
+  ViashNotice "Building container '$image_id' with Dockerfile"
+  ViashInfo "$docker_build_cmd"
+  local save=$-; set +e
+  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
+    eval $docker_build_cmd
+  else
+    eval $docker_build_cmd &> "$tmpdir/docker_build.log"
+  fi
+
+  # check exit code
+  local out=$?
+  [[ $save =~ e ]] && set -e
+  if [ $out -ne 0 ]; then
+    ViashError "Error occurred while building container '$image_id'"
+    if [ $VIASH_VERBOSITY -lt $VIASH_LOGCODE_INFO ]; then
+      ViashError "Transcript: --------------------------------"
+      cat "$tmpdir/docker_build.log"
+      ViashError "End of transcript --------------------------"
+    fi
+    exit 1
+  fi
+}
+
+######## End of helper functions for setting up Docker images for viash ########
+
+# ViashDockerFile: print the dockerfile to stdout
+# $1    : engine identifier
+# return : dockerfile required to run this component
+# examples:
+#   ViashDockerFile
+function ViashDockerfile {
+  local engine_id="$1"
+
+  if [[ "$engine_id" == "docker" ]]; then
+    cat << 'VIASHDOCKER'
+FROM quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1
+ENTRYPOINT []
+RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \
+sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
+
+LABEL org.opencontainers.image.authors="Emma Rousseau"
+LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_view"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:38Z"
+LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+LABEL org.opencontainers.image.version="main"
+
+VIASHDOCKER
+  fi
+}
+
+# ViashDockerBuildArgs: return the arguments to pass to docker build
+# $1    : engine identifier
+# return : arguments to pass to docker build
+function ViashDockerBuildArgs {
+  local engine_id="$1"
+
+  if [[ "$engine_id" == "docker" ]]; then
+    echo ""
+  fi
+}
+
+# ViashAbsolutePath: generate absolute path from relative path
+# borrowed from https://stackoverflow.com/a/21951256
+# $1     : relative filename
+# return : absolute path
+# examples:
+#   ViashAbsolutePath some_file.txt   # returns /path/to/some_file.txt
+#   ViashAbsolutePath /foo/bar/..     # returns /foo
+function ViashAbsolutePath {
+  local thePath
+  local parr
+  local outp
+  local len
+  if [[ ! "$1" =~ ^/ ]]; then
+    thePath="$PWD/$1"
+  else
+    thePath="$1"
+  fi
+  echo "$thePath" | (
+    IFS=/
+    read -a parr
+    declare -a outp
+    for i in "${parr[@]}"; do
+      case "$i" in
+      ''|.) continue ;;
+      ..)
+        len=${#outp[@]}
+        if ((len==0)); then
+          continue
+        else
+          unset outp[$((len-1))]
+        fi
+        ;;
+      *)
+        len=${#outp[@]}
+        outp[$len]="$i"
+      ;;
+      esac
+    done
+    echo /"${outp[*]}"
+  )
+}
+# ViashDockerAutodetectMount: auto configuring docker mounts from parameters
+# $1                             : The parameter value
+# returns                        : New parameter
+# $VIASH_DIRECTORY_MOUNTS        : Added another parameter to be passed to docker
+# $VIASH_DOCKER_AUTOMOUNT_PREFIX : The prefix to be used for the automounts
+# examples:
+#   ViashDockerAutodetectMount /path/to/bar      # returns '/viash_automount/path/to/bar'
+#   ViashDockerAutodetectMountArg /path/to/bar   # returns '--volume="/path/to:/viash_automount/path/to"'
+function ViashDockerAutodetectMount {
+  local abs_path=$(ViashAbsolutePath "$1")
+  local mount_source
+  local base_name
+  if [ -d "$abs_path" ]; then
+    mount_source="$abs_path"
+    base_name=""
+  else
+    mount_source=`dirname "$abs_path"`
+    base_name=`basename "$abs_path"`
+  fi
+  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
+  if [ -z "$base_name" ]; then
+    echo "$mount_target"
+  else
+    echo "$mount_target/$base_name"
+  fi
+}
+function ViashDockerAutodetectMountArg {
+  local abs_path=$(ViashAbsolutePath "$1")
+  local mount_source
+  local base_name
+  if [ -d "$abs_path" ]; then
+    mount_source="$abs_path"
+    base_name=""
+  else
+    mount_source=`dirname "$abs_path"`
+    base_name=`basename "$abs_path"`
+  fi
+  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
+  ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target"
+  echo "--volume=\"$mount_source:$mount_target\""
+}
+function ViashDockerStripAutomount {
+  local abs_path=$(ViashAbsolutePath "$1")
+  echo "${abs_path#$VIASH_DOCKER_AUTOMOUNT_PREFIX}"
+}
+# initialise variables
+VIASH_DIRECTORY_MOUNTS=()
+
+# configure default docker automount prefix if it is unset
+if [ -z "${VIASH_DOCKER_AUTOMOUNT_PREFIX+x}" ]; then
+  VIASH_DOCKER_AUTOMOUNT_PREFIX="/viash_automount"
+fi
+
+# initialise docker variables
+VIASH_DOCKER_RUN_ARGS=(-i --rm)
+
+
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
   echo "samtools_view main"
@@ -543,405 +942,32 @@ function ViashHelp {
   echo "    --write_index"
   echo "        type: boolean_true"
   echo "        Automatically index the output files."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
 }
 
-# initialise variables
-VIASH_MODE='run'
-VIASH_ENGINE_ID='docker'
-
-######## Helper functions for setting up Docker images for viash ########
-# expects: ViashDockerBuild
-
-# ViashDockerInstallationCheck: check whether Docker is installed correctly
-#
-# examples:
-#   ViashDockerInstallationCheck
-function ViashDockerInstallationCheck {
-  ViashDebug "Checking whether Docker is installed"
-  if [ ! command -v docker &> /dev/null ]; then
-    ViashCritical "Docker doesn't seem to be installed. See 'https://docs.docker.com/get-docker/' for instructions."
-    exit 1
-  fi
-
-  ViashDebug "Checking whether the Docker daemon is running"
-  local save=$-; set +e
-  local docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
-  local out=$?
-  [[ $save =~ e ]] && set -e
-  if [ $out -ne 0 ]; then
-    ViashCritical "Docker daemon does not seem to be running. Try one of the following:"
-    ViashCritical "- Try running 'dockerd' in the command line"
-    ViashCritical "- See https://docs.docker.com/config/daemon/"
-    exit 1
-  fi
-}
-
-# ViashDockerRemoteTagCheck: check whether a Docker image is available 
-# on a remote. Assumes `docker login` has been performed, if relevant.
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   ViashDockerRemoteTagCheck python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerRemoteTagCheck sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerRemoteTagCheck {
-  docker manifest inspect $1 > /dev/null 2> /dev/null
-}
-
-# ViashDockerLocalTagCheck: check whether a Docker image is available locally
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   docker pull python:latest
-#   ViashDockerLocalTagCheck python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerLocalTagCheck sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerLocalTagCheck {
-  [ -n "$(docker images -q $1)" ]
-}
-
-# ViashDockerPull: pull a Docker image
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   ViashDockerPull python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerPull sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerPull {
-  ViashNotice "Checking if Docker image is available at '$1'"
-  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
-    docker pull $1 && return 0 || return 1
-  else
-    local save=$-; set +e
-    docker pull $1 2> /dev/null > /dev/null
-    local out=$?
-    [[ $save =~ e ]] && set -e
-    if [ $out -ne 0 ]; then
-      ViashWarning "Could not pull from '$1'. Docker image doesn't exist or is not accessible."
-    fi
-    return $out
-  fi
-}
-
-# ViashDockerPush: push a Docker image
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   ViashDockerPush python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerPush sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerPush {
-  ViashNotice "Pushing image to '$1'"
-  local save=$-; set +e
-  local out
-  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
-    docker push $1
-    out=$?
-  else
-    docker push $1 2> /dev/null > /dev/null
-    out=$?
-  fi
-  [[ $save =~ e ]] && set -e
-  if [ $out -eq 0 ]; then
-    ViashNotice "Container '$1' push succeeded."
-  else
-    ViashError "Container '$1' push errored. You might not be logged in or have the necessary permissions."
-  fi
-  return $out
-}
-
-# ViashDockerPullElseBuild: pull a Docker image, else build it
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# ViashDockerBuild    : a Bash function which builds a docker image, takes image identifier as argument.
-# examples:
-#   ViashDockerPullElseBuild mynewcomponent
-function ViashDockerPullElseBuild {
-  local save=$-; set +e
-  ViashDockerPull $1
-  local out=$?
-  [[ $save =~ e ]] && set -e
-  if [ $out -ne 0 ]; then
-    ViashDockerBuild $@
-  fi
-}
-
-# ViashDockerSetup: create a Docker image, according to specified docker setup strategy
-#
-# $1          : image identifier with format `[registry/]image[:tag]`
-# $2          : docker setup strategy, see DockerSetupStrategy.scala
-# examples:
-#   ViashDockerSetup mynewcomponent alwaysbuild
-function ViashDockerSetup {
-  local image_id="$1"
-  local setup_strategy="$2"
-  if [ "$setup_strategy" == "alwaysbuild" -o "$setup_strategy" == "build" -o "$setup_strategy" == "b" ]; then
-    ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-  elif [ "$setup_strategy" == "alwayspull" -o "$setup_strategy" == "pull" -o "$setup_strategy" == "p" ]; then
-    ViashDockerPull $image_id
-  elif [ "$setup_strategy" == "alwayspullelsebuild" -o "$setup_strategy" == "pullelsebuild" ]; then
-    ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-  elif [ "$setup_strategy" == "alwayspullelsecachedbuild" -o "$setup_strategy" == "pullelsecachedbuild" ]; then
-    ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-  elif [ "$setup_strategy" == "alwayscachedbuild" -o "$setup_strategy" == "cachedbuild" -o "$setup_strategy" == "cb" ]; then
-    ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-  elif [[ "$setup_strategy" =~ ^ifneedbe ]]; then
-    local save=$-; set +e
-    ViashDockerLocalTagCheck $image_id
-    local outCheck=$?
-    [[ $save =~ e ]] && set -e
-    if [ $outCheck -eq 0 ]; then
-      ViashInfo "Image $image_id already exists"
-    elif [ "$setup_strategy" == "ifneedbebuild" ]; then
-      ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-    elif [ "$setup_strategy" == "ifneedbecachedbuild" ]; then
-      ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-    elif [ "$setup_strategy" == "ifneedbepull" ]; then
-      ViashDockerPull $image_id
-    elif [ "$setup_strategy" == "ifneedbepullelsebuild" ]; then
-      ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-    elif [ "$setup_strategy" == "ifneedbepullelsecachedbuild" ]; then
-      ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-    else
-      ViashError "Unrecognised Docker strategy: $setup_strategy"
-      exit 1
-    fi
-  elif [ "$setup_strategy" == "push" -o "$setup_strategy" == "forcepush" -o "$setup_strategy" == "alwayspush" ]; then
-    ViashDockerPush "$image_id"
-  elif [ "$setup_strategy" == "pushifnotpresent" -o "$setup_strategy" == "gentlepush" -o "$setup_strategy" == "maybepush" ]; then
-    local save=$-; set +e
-    ViashDockerRemoteTagCheck $image_id
-    local outCheck=$?
-    [[ $save =~ e ]] && set -e
-    if [ $outCheck -eq 0 ]; then
-      ViashNotice "Container '$image_id' exists, doing nothing."
-    else
-      ViashNotice "Container '$image_id' does not yet exist."
-      ViashDockerPush "$image_id"
-    fi
-  elif [ "$setup_strategy" == "donothing" -o "$setup_strategy" == "meh" ]; then
-    ViashNotice "Skipping setup."
-  else
-    ViashError "Unrecognised Docker strategy: $setup_strategy"
-    exit 1
-  fi
-}
-
-# ViashDockerCheckCommands: Check whether a docker container has the required commands
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# $@                  : commands to verify being present
-# examples:
-#   ViashDockerCheckCommands bash:4.0 bash ps foo
-function ViashDockerCheckCommands {
-  local image_id="$1"
-  shift 1
-  local commands="$@"
-  local save=$-; set +e
-  local missing # mark 'missing' as local in advance, otherwise the exit code of the command will be missing and always be '0'
-  missing=$(docker run --rm --entrypoint=sh "$image_id" -c "for command in $commands; do command -v \$command >/dev/null 2>&1; if [ \$? -ne 0 ]; then echo \$command; exit 1; fi; done")
-  local outCheck=$?
-  [[ $save =~ e ]] && set -e
-  if [ $outCheck -ne 0 ]; then
-  	ViashError "Docker container '$image_id' does not contain command '$missing'."
-  	exit 1
-  fi
-}
-
-# ViashDockerBuild: build a docker image
-# $1                               : image identifier with format `[registry/]image[:tag]`
-# $...                             : additional arguments to pass to docker build
-# $VIASH_META_TEMP_DIR             : temporary directory to store dockerfile & optional resources in
-# $VIASH_META_NAME                 : name of the component
-# $VIASH_META_RESOURCES_DIR        : directory containing the resources
-# $VIASH_VERBOSITY                 : verbosity level
-# exit code $?                     : whether or not the image was built successfully
-function ViashDockerBuild {
-  local image_id="$1"
-  shift 1
-
-  # create temporary directory to store dockerfile & optional resources in
-  local tmpdir=$(mktemp -d "$VIASH_META_TEMP_DIR/dockerbuild-$VIASH_META_NAME-XXXXXX")
-  local dockerfile="$tmpdir/Dockerfile"
-  function clean_up {
-    rm -rf "$tmpdir"
-  }
-  trap clean_up EXIT
-
-  # store dockerfile and resources
-  ViashDockerfile "$VIASH_ENGINE_ID" > "$dockerfile"
-
-  # generate the build command
-  local docker_build_cmd="docker build -t '$image_id' $@ '$VIASH_META_RESOURCES_DIR' -f '$dockerfile'"
-
-  # build the container
-  ViashNotice "Building container '$image_id' with Dockerfile"
-  ViashInfo "$docker_build_cmd"
-  local save=$-; set +e
-  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
-    eval $docker_build_cmd
-  else
-    eval $docker_build_cmd &> "$tmpdir/docker_build.log"
-  fi
-
-  # check exit code
-  local out=$?
-  [[ $save =~ e ]] && set -e
-  if [ $out -ne 0 ]; then
-    ViashError "Error occurred while building container '$image_id'"
-    if [ $VIASH_VERBOSITY -lt $VIASH_LOGCODE_INFO ]; then
-      ViashError "Transcript: --------------------------------"
-      cat "$tmpdir/docker_build.log"
-      ViashError "End of transcript --------------------------"
-    fi
-    exit 1
-  fi
-}
-
-######## End of helper functions for setting up Docker images for viash ########
-
-# ViashDockerFile: print the dockerfile to stdout
-# $1    : engine identifier
-# return : dockerfile required to run this component
-# examples:
-#   ViashDockerFile
-function ViashDockerfile {
-  local engine_id="$1"
-
-  if [[ "$engine_id" == "docker" ]]; then
-    cat << 'VIASHDOCKER'
-FROM quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1
-ENTRYPOINT []
-RUN samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \
-sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
-
-LABEL org.opencontainers.image.authors="Emma Rousseau"
-LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_view"
-LABEL org.opencontainers.image.created="2024-12-03T10:33:58Z"
-LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-LABEL org.opencontainers.image.version="main"
-
-VIASHDOCKER
-  fi
-}
-
-# ViashDockerBuildArgs: return the arguments to pass to docker build
-# $1    : engine identifier
-# return : arguments to pass to docker build
-function ViashDockerBuildArgs {
-  local engine_id="$1"
-
-  if [[ "$engine_id" == "docker" ]]; then
-    echo ""
-  fi
-}
-
-# ViashAbsolutePath: generate absolute path from relative path
-# borrowed from https://stackoverflow.com/a/21951256
-# $1     : relative filename
-# return : absolute path
-# examples:
-#   ViashAbsolutePath some_file.txt   # returns /path/to/some_file.txt
-#   ViashAbsolutePath /foo/bar/..     # returns /foo
-function ViashAbsolutePath {
-  local thePath
-  local parr
-  local outp
-  local len
-  if [[ ! "$1" =~ ^/ ]]; then
-    thePath="$PWD/$1"
-  else
-    thePath="$1"
-  fi
-  echo "$thePath" | (
-    IFS=/
-    read -a parr
-    declare -a outp
-    for i in "${parr[@]}"; do
-      case "$i" in
-      ''|.) continue ;;
-      ..)
-        len=${#outp[@]}
-        if ((len==0)); then
-          continue
-        else
-          unset outp[$((len-1))]
-        fi
-        ;;
-      *)
-        len=${#outp[@]}
-        outp[$len]="$i"
-      ;;
-      esac
-    done
-    echo /"${outp[*]}"
-  )
-}
-# ViashDockerAutodetectMount: auto configuring docker mounts from parameters
-# $1                             : The parameter value
-# returns                        : New parameter
-# $VIASH_DIRECTORY_MOUNTS        : Added another parameter to be passed to docker
-# $VIASH_DOCKER_AUTOMOUNT_PREFIX : The prefix to be used for the automounts
-# examples:
-#   ViashDockerAutodetectMount /path/to/bar      # returns '/viash_automount/path/to/bar'
-#   ViashDockerAutodetectMountArg /path/to/bar   # returns '--volume="/path/to:/viash_automount/path/to"'
-function ViashDockerAutodetectMount {
-  local abs_path=$(ViashAbsolutePath "$1")
-  local mount_source
-  local base_name
-  if [ -d "$abs_path" ]; then
-    mount_source="$abs_path"
-    base_name=""
-  else
-    mount_source=`dirname "$abs_path"`
-    base_name=`basename "$abs_path"`
-  fi
-  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
-  if [ -z "$base_name" ]; then
-    echo "$mount_target"
-  else
-    echo "$mount_target/$base_name"
-  fi
-}
-function ViashDockerAutodetectMountArg {
-  local abs_path=$(ViashAbsolutePath "$1")
-  local mount_source
-  local base_name
-  if [ -d "$abs_path" ]; then
-    mount_source="$abs_path"
-    base_name=""
-  else
-    mount_source=`dirname "$abs_path"`
-    base_name=`basename "$abs_path"`
-  fi
-  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
-  ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target"
-  echo "--volume=\"$mount_source:$mount_target\""
-}
-function ViashDockerStripAutomount {
-  local abs_path=$(ViashAbsolutePath "$1")
-  echo "${abs_path#$VIASH_DOCKER_AUTOMOUNT_PREFIX}"
-}
-# initialise variables
-VIASH_DIRECTORY_MOUNTS=()
-
-# configure default docker automount prefix if it is unset
-if [ -z "${VIASH_DOCKER_AUTOMOUNT_PREFIX+x}" ]; then
-  VIASH_DOCKER_AUTOMOUNT_PREFIX="/viash_automount"
-fi
-
-# initialise docker variables
-VIASH_DOCKER_RUN_ARGS=(-i --rm)
-
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/seqtk/seqtk_sample/.config.vsh.yaml b/target/executable/seqtk/seqtk_sample/.config.vsh.yaml
index 2b9094cb..334cdbd4 100644
--- a/target/executable/seqtk/seqtk_sample/.config.vsh.yaml
+++ b/target/executable/seqtk/seqtk_sample/.config.vsh.yaml
@@ -80,6 +80,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -172,16 +175,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/seqtk/seqtk_sample"
   executable: "target/executable/seqtk/seqtk_sample/seqtk_sample"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/seqtk/seqtk_sample/seqtk_sample b/target/executable/seqtk/seqtk_sample/seqtk_sample
index d478abc7..84f4eeb3 100755
--- a/target/executable/seqtk/seqtk_sample/seqtk_sample
+++ b/target/executable/seqtk/seqtk_sample/seqtk_sample
@@ -2,7 +2,7 @@
 
 # seqtk_sample main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,37 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "seqtk_sample main"
-  echo ""
-  echo "Subsamples sequences from FASTA/Q files."
-  echo ""
-  echo "Inputs:"
-  echo "    --input"
-  echo "        type: file, required parameter, file must exist"
-  echo "        The input FASTA/Q file."
-  echo ""
-  echo "Outputs:"
-  echo "    --output"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        The output FASTA/Q file."
-  echo ""
-  echo "Options:"
-  echo "    --seed"
-  echo "        type: integer"
-  echo "        example: 42"
-  echo "        Seed for random generator."
-  echo ""
-  echo "    --fraction_number"
-  echo "        type: double, required parameter"
-  echo "        example: 0.1"
-  echo "        Fraction or number of sequences to sample."
-  echo ""
-  echo "    --two_pass_mode"
-  echo "        type: boolean_true"
-  echo "        Twice as slow but with much reduced memory"
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -481,9 +450,9 @@ FROM quay.io/biocontainers/seqtk:1.4--he4a0461_2
 ENTRYPOINT []
 LABEL org.opencontainers.image.authors="Jakub Majercik"
 LABEL org.opencontainers.image.description="Companion container for running component seqtk seqtk_sample"
-LABEL org.opencontainers.image.created="2024-12-03T10:33:56Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:45Z"
 LABEL org.opencontainers.image.source="https://github.com/lh3/seqtk/tree/v1.4"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -598,6 +567,63 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "seqtk_sample main"
+  echo ""
+  echo "Subsamples sequences from FASTA/Q files."
+  echo ""
+  echo "Inputs:"
+  echo "    --input"
+  echo "        type: file, required parameter, file must exist"
+  echo "        The input FASTA/Q file."
+  echo ""
+  echo "Outputs:"
+  echo "    --output"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        The output FASTA/Q file."
+  echo ""
+  echo "Options:"
+  echo "    --seed"
+  echo "        type: integer"
+  echo "        example: 42"
+  echo "        Seed for random generator."
+  echo ""
+  echo "    --fraction_number"
+  echo "        type: double, required parameter"
+  echo "        example: 0.1"
+  echo "        Fraction or number of sequences to sample."
+  echo ""
+  echo "    --two_pass_mode"
+  echo "        type: boolean_true"
+  echo "        Twice as slow but with much reduced memory"
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml b/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml
index e1a1a416..cbf68a9c 100644
--- a/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml
+++ b/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml
@@ -99,6 +99,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -195,16 +198,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/seqtk/seqtk_subseq"
   executable: "target/executable/seqtk/seqtk_subseq/seqtk_subseq"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/seqtk/seqtk_subseq/seqtk_subseq b/target/executable/seqtk/seqtk_subseq/seqtk_subseq
index 2fd70a48..61feebcb 100755
--- a/target/executable/seqtk/seqtk_subseq/seqtk_subseq
+++ b/target/executable/seqtk/seqtk_subseq/seqtk_subseq
@@ -2,7 +2,7 @@
 
 # seqtk_subseq main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,45 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "seqtk_subseq main"
-  echo ""
-  echo "Extract subsequences from FASTA/Q files. Takes as input a FASTA/Q file and a"
-  echo "name.lst (sequence ids file) or a reg.bed (genomic regions file)."
-  echo ""
-  echo "Inputs:"
-  echo "    --input"
-  echo "        type: file, required parameter, file must exist"
-  echo "        example: input.fa"
-  echo "        The input FASTA/Q file."
-  echo ""
-  echo "    --name_list"
-  echo "        type: file, required parameter, file must exist"
-  echo "        example: list.lst"
-  echo "        List of sequence names (name.lst) or genomic regions (reg.bed) to"
-  echo "        extract."
-  echo ""
-  echo "Outputs:"
-  echo "    -o, --output"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        default: output.fa"
-  echo "        The output FASTA/Q file."
-  echo ""
-  echo "Options:"
-  echo "    -t, --tab"
-  echo "        type: boolean_true"
-  echo "        TAB delimited output."
-  echo ""
-  echo "    -s, --strand_aware"
-  echo "        type: boolean_true"
-  echo "        Strand aware."
-  echo ""
-  echo "    -l, --sequence_line_length"
-  echo "        type: integer"
-  echo "        example: 0"
-  echo "        Sequence line length of input fasta file. Default: 0."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -491,9 +452,9 @@ RUN echo $(echo $(seqtk 2>&1) | sed -n 's/.*\(Version: [^ ]*\).*/\1/p') > /var/s
 
 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component seqtk seqtk_subseq"
-LABEL org.opencontainers.image.created="2024-12-03T10:33:56Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:45Z"
 LABEL org.opencontainers.image.source="https://github.com/lh3/seqtk/tree/v1.4"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -608,6 +569,71 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "seqtk_subseq main"
+  echo ""
+  echo "Extract subsequences from FASTA/Q files. Takes as input a FASTA/Q file and a"
+  echo "name.lst (sequence ids file) or a reg.bed (genomic regions file)."
+  echo ""
+  echo "Inputs:"
+  echo "    --input"
+  echo "        type: file, required parameter, file must exist"
+  echo "        example: input.fa"
+  echo "        The input FASTA/Q file."
+  echo ""
+  echo "    --name_list"
+  echo "        type: file, required parameter, file must exist"
+  echo "        example: list.lst"
+  echo "        List of sequence names (name.lst) or genomic regions (reg.bed) to"
+  echo "        extract."
+  echo ""
+  echo "Outputs:"
+  echo "    -o, --output"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        default: output.fa"
+  echo "        The output FASTA/Q file."
+  echo ""
+  echo "Options:"
+  echo "    -t, --tab"
+  echo "        type: boolean_true"
+  echo "        TAB delimited output."
+  echo ""
+  echo "    -s, --strand_aware"
+  echo "        type: boolean_true"
+  echo "        Strand aware."
+  echo ""
+  echo "    -l, --sequence_line_length"
+  echo "        type: integer"
+  echo "        example: 0"
+  echo "        Sequence line length of input fasta file. Default: 0."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/sgdemux/.config.vsh.yaml b/target/executable/sgdemux/.config.vsh.yaml
index 6519f639..8d567451 100644
--- a/target/executable/sgdemux/.config.vsh.yaml
+++ b/target/executable/sgdemux/.config.vsh.yaml
@@ -328,6 +328,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -428,16 +431,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/sgdemux"
   executable: "target/executable/sgdemux/sgdemux"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/sgdemux/sgdemux b/target/executable/sgdemux/sgdemux
index f0605c73..e959903b 100755
--- a/target/executable/sgdemux/sgdemux
+++ b/target/executable/sgdemux/sgdemux
@@ -2,7 +2,7 @@
 
 # sgdemux main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,180 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "sgdemux main"
-  echo ""
-  echo "Demultiplex sequence data generated on Singular Genomics' sequencing"
-  echo "instruments."
-  echo ""
-  echo "Input:"
-  echo "    -f, --fastqs"
-  echo "        type: file, required parameter, multiple values allowed, file must exist"
-  echo "        example: sample1_r1.fq;sample1_r2.fq;sample2_r1.fq;sample2_r2.fq"
-  echo "        Path to the input FASTQs, or path prefix if not a file"
-  echo ""
-  echo "    -s, --sample_metadata"
-  echo "        type: file, required parameter, file must exist"
-  echo "        Path to the sample metadata CSV file including sample names and barcode"
-  echo "        sequences"
-  echo ""
-  echo "Output:"
-  echo "    --sample_fastq"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        example: output"
-  echo "        The directory containing demultiplexed sample FASTQ files."
-  echo ""
-  echo "    --metrics"
-  echo "        type: file, output, file must exist"
-  echo "        example: metrics.tsv"
-  echo "        Demultiplexing summary statisitcs:"
-  echo "          - control_reads_omitted: The number of reads that were omitted for"
-  echo "        being control reads."
-  echo "          - failing_reads_omitted: The number of reads that were omitted for"
-  echo "        having failed QC."
-  echo "          - total_templates: The total number of template reads that were"
-  echo "        output."
-  echo ""
-  echo "    --most_frequent_unmatched"
-  echo "        type: file, output, file must exist"
-  echo "        example: most_frequent_unmatched.tsv"
-  echo "        It contains the (approximate) counts of the most prevelant observed"
-  echo "        barcode sequences"
-  echo "        that did not match to one of the expected barcodes. Can only be created"
-  echo "        when 'most_unmatched_to_output'"
-  echo "        is not set to 0."
-  echo ""
-  echo "    --sample_barcode_hop_metrics"
-  echo "        type: file, output, file must exist"
-  echo "        example: sample_barcode_hop_metrics.tsv"
-  echo "        File containing the frequently observed barcodes that are unexpected"
-  echo "        combinations of expected barcodes in a dual-indexed run."
-  echo ""
-  echo "    --per_project_metrics"
-  echo "        type: file, output, file must exist"
-  echo "        example: per_project_metrics.tsv"
-  echo "        Aggregates the metrics by project (aggregates the metrics across samples"
-  echo "        with the same project) and"
-  echo "        has the same columns as \`--metrics\`. In this case, sample_ID will"
-  echo "        contain the project name (or None if no project is given)."
-  echo "        THe barcode will contain all Ns. The undetermined sample will not be"
-  echo "        aggregated with any other sample."
-  echo ""
-  echo "    --per_sample_metrics"
-  echo "        type: file, output, file must exist"
-  echo "        example: per_sample_metrics.tsv"
-  echo "        Tab-separated file containing statistics per sample."
-  echo ""
-  echo "Arguments:"
-  echo "    -r, --read_structures"
-  echo "        type: string, multiple values allowed"
-  echo "        Read structures, one per input FASTQ. Do not provide when using a path"
-  echo "        prefix for FASTQs"
-  echo ""
-  echo "    -m, --allowed_mismatches"
-  echo "        type: integer"
-  echo "        example: 1"
-  echo "        Number of allowed mismatches between the observed barcode and the"
-  echo "        expected barcode"
-  echo ""
-  echo "    -d, --min_delta"
-  echo "        type: integer"
-  echo "        example: 2"
-  echo "        The minimum allowed difference between an observed barcode and the"
-  echo "        second closest expected barcode"
-  echo ""
-  echo "    -F, --free_ns"
-  echo "        type: integer"
-  echo "        example: 1"
-  echo "        Number of N's to allow in a barcode without counting against the"
-  echo "        allowed_mismatches"
-  echo ""
-  echo "    -N, --max_no_calls"
-  echo "        type: integer"
-  echo "        Max no-calls (N's) in a barcode before it is considered unmatchable."
-  echo "        A barcode with total N's greater than 'max_no_call' will be considered"
-  echo "        unmatchable."
-  echo ""
-  echo "    -M, --quality_mask_threshold"
-  echo "        type: integer, multiple values allowed"
-  echo "        Mask template bases with quality scores less than specified value(s)."
-  echo "        Sample barcode/index and UMI bases are never masked. If provided either"
-  echo "        a single value,"
-  echo "        or one value per FASTQ must be provided."
-  echo ""
-  echo "    -C, --filter_control_reads"
-  echo "        type: boolean_true"
-  echo "        Filter out control reads"
-  echo ""
-  echo "    -Q, --filter_failing_quality"
-  echo "        type: boolean_true"
-  echo "        Filter reads failing quality filter"
-  echo ""
-  echo "    -T, --output_types"
-  echo "        type: string, multiple values allowed"
-  echo "        example: T"
-  echo "        choices: [ T, B, S, M ]"
-  echo "        The types of output FASTQs to write."
-  echo "        For each read structure, all segment types listed will be output to a"
-  echo "        FASTQ file."
-  echo "        These may be any of the following:"
-  echo "         - \`T\` - Template bases"
-  echo "         - \`B\` - Sample barcode bases"
-  echo "         - \`M\` - Molecular barcode bases"
-  echo "         - \`S\` - Skip bases"
-  echo ""
-  echo "    -u, --undetermined_sample_name"
-  echo "        type: string"
-  echo "        example: Undetermined"
-  echo "        The sample name for undetermined reads (reads that do not match an"
-  echo "        expected barcode)"
-  echo ""
-  echo "    -U, --most_unmatched_to_output"
-  echo "        type: integer"
-  echo "        example: 1000"
-  echo "        Output the most frequent \"unmatched\" barcodes up to this number."
-  echo "        If set to 0 unmatched barcodes will not be collected, improving overall"
-  echo "        performance."
-  echo ""
-  echo "    --override_matcher"
-  echo "        type: string"
-  echo "        choices: [ cached-hamming-distance, pre-compute ]"
-  echo "        If the sample barcodes are > 12 bp long, a cached hamming distance"
-  echo "        matcher is used."
-  echo "        If the barcodes are less than or equal to 12 bp long, all possible"
-  echo "        matches are precomputed."
-  echo "        This option allows for overriding that heuristic."
-  echo ""
-  echo "    --skip_read_name_check"
-  echo "        type: boolean_true"
-  echo "        If this is true, then all the read names across FASTQs will not be"
-  echo "        enforced to be the same."
-  echo "        This may be useful when the read names are known to be the same and"
-  echo "        performance matters."
-  echo "        Regardless, the first read name in each FASTQ will always be checked."
-  echo ""
-  echo "    --sample_barcode_in_fastq_header"
-  echo "        type: boolean_true"
-  echo "        If this is true, then the sample barcode is expected to be in the FASTQ"
-  echo "        read header."
-  echo "        For dual indexed data, the barcodes must be \`+\` (plus) delimited."
-  echo "        Additionally, if true,"
-  echo "        then neither index FASTQ files nor sample barcode segments in the read"
-  echo "        structure may be specified."
-  echo ""
-  echo "    --metric_prefix"
-  echo "        type: string"
-  echo "        Prepend this prefix to all output metric file names"
-  echo ""
-  echo "    -l, --lane"
-  echo "        type: integer, multiple values allowed"
-  echo "        Select a subset of lanes to demultiplex.  Will cause only samples and"
-  echo "        input FASTQs with"
-  echo "        the given \`Lane\`(s) to be demultiplexed. Samples without a lane will be"
-  echo "        ignored, and"
-  echo "        FASTQs without lane information will be ignored"
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -631,9 +457,9 @@ echo "sgdemux: $(sgdemux --version | cut -d' ' -f2)" > /var/software_versions.tx
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component sgdemux"
-LABEL org.opencontainers.image.created="2024-12-03T10:34:00Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:45Z"
 LABEL org.opencontainers.image.source="https://github.com/Singular-Genomics/singular-demux"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -748,6 +574,206 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "sgdemux main"
+  echo ""
+  echo "Demultiplex sequence data generated on Singular Genomics' sequencing"
+  echo "instruments."
+  echo ""
+  echo "Input:"
+  echo "    -f, --fastqs"
+  echo "        type: file, required parameter, multiple values allowed, file must exist"
+  echo "        example: sample1_r1.fq;sample1_r2.fq;sample2_r1.fq;sample2_r2.fq"
+  echo "        Path to the input FASTQs, or path prefix if not a file"
+  echo ""
+  echo "    -s, --sample_metadata"
+  echo "        type: file, required parameter, file must exist"
+  echo "        Path to the sample metadata CSV file including sample names and barcode"
+  echo "        sequences"
+  echo ""
+  echo "Output:"
+  echo "    --sample_fastq"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        example: output"
+  echo "        The directory containing demultiplexed sample FASTQ files."
+  echo ""
+  echo "    --metrics"
+  echo "        type: file, output, file must exist"
+  echo "        example: metrics.tsv"
+  echo "        Demultiplexing summary statisitcs:"
+  echo "          - control_reads_omitted: The number of reads that were omitted for"
+  echo "        being control reads."
+  echo "          - failing_reads_omitted: The number of reads that were omitted for"
+  echo "        having failed QC."
+  echo "          - total_templates: The total number of template reads that were"
+  echo "        output."
+  echo ""
+  echo "    --most_frequent_unmatched"
+  echo "        type: file, output, file must exist"
+  echo "        example: most_frequent_unmatched.tsv"
+  echo "        It contains the (approximate) counts of the most prevelant observed"
+  echo "        barcode sequences"
+  echo "        that did not match to one of the expected barcodes. Can only be created"
+  echo "        when 'most_unmatched_to_output'"
+  echo "        is not set to 0."
+  echo ""
+  echo "    --sample_barcode_hop_metrics"
+  echo "        type: file, output, file must exist"
+  echo "        example: sample_barcode_hop_metrics.tsv"
+  echo "        File containing the frequently observed barcodes that are unexpected"
+  echo "        combinations of expected barcodes in a dual-indexed run."
+  echo ""
+  echo "    --per_project_metrics"
+  echo "        type: file, output, file must exist"
+  echo "        example: per_project_metrics.tsv"
+  echo "        Aggregates the metrics by project (aggregates the metrics across samples"
+  echo "        with the same project) and"
+  echo "        has the same columns as \`--metrics\`. In this case, sample_ID will"
+  echo "        contain the project name (or None if no project is given)."
+  echo "        THe barcode will contain all Ns. The undetermined sample will not be"
+  echo "        aggregated with any other sample."
+  echo ""
+  echo "    --per_sample_metrics"
+  echo "        type: file, output, file must exist"
+  echo "        example: per_sample_metrics.tsv"
+  echo "        Tab-separated file containing statistics per sample."
+  echo ""
+  echo "Arguments:"
+  echo "    -r, --read_structures"
+  echo "        type: string, multiple values allowed"
+  echo "        Read structures, one per input FASTQ. Do not provide when using a path"
+  echo "        prefix for FASTQs"
+  echo ""
+  echo "    -m, --allowed_mismatches"
+  echo "        type: integer"
+  echo "        example: 1"
+  echo "        Number of allowed mismatches between the observed barcode and the"
+  echo "        expected barcode"
+  echo ""
+  echo "    -d, --min_delta"
+  echo "        type: integer"
+  echo "        example: 2"
+  echo "        The minimum allowed difference between an observed barcode and the"
+  echo "        second closest expected barcode"
+  echo ""
+  echo "    -F, --free_ns"
+  echo "        type: integer"
+  echo "        example: 1"
+  echo "        Number of N's to allow in a barcode without counting against the"
+  echo "        allowed_mismatches"
+  echo ""
+  echo "    -N, --max_no_calls"
+  echo "        type: integer"
+  echo "        Max no-calls (N's) in a barcode before it is considered unmatchable."
+  echo "        A barcode with total N's greater than 'max_no_call' will be considered"
+  echo "        unmatchable."
+  echo ""
+  echo "    -M, --quality_mask_threshold"
+  echo "        type: integer, multiple values allowed"
+  echo "        Mask template bases with quality scores less than specified value(s)."
+  echo "        Sample barcode/index and UMI bases are never masked. If provided either"
+  echo "        a single value,"
+  echo "        or one value per FASTQ must be provided."
+  echo ""
+  echo "    -C, --filter_control_reads"
+  echo "        type: boolean_true"
+  echo "        Filter out control reads"
+  echo ""
+  echo "    -Q, --filter_failing_quality"
+  echo "        type: boolean_true"
+  echo "        Filter reads failing quality filter"
+  echo ""
+  echo "    -T, --output_types"
+  echo "        type: string, multiple values allowed"
+  echo "        example: T"
+  echo "        choices: [ T, B, S, M ]"
+  echo "        The types of output FASTQs to write."
+  echo "        For each read structure, all segment types listed will be output to a"
+  echo "        FASTQ file."
+  echo "        These may be any of the following:"
+  echo "         - \`T\` - Template bases"
+  echo "         - \`B\` - Sample barcode bases"
+  echo "         - \`M\` - Molecular barcode bases"
+  echo "         - \`S\` - Skip bases"
+  echo ""
+  echo "    -u, --undetermined_sample_name"
+  echo "        type: string"
+  echo "        example: Undetermined"
+  echo "        The sample name for undetermined reads (reads that do not match an"
+  echo "        expected barcode)"
+  echo ""
+  echo "    -U, --most_unmatched_to_output"
+  echo "        type: integer"
+  echo "        example: 1000"
+  echo "        Output the most frequent \"unmatched\" barcodes up to this number."
+  echo "        If set to 0 unmatched barcodes will not be collected, improving overall"
+  echo "        performance."
+  echo ""
+  echo "    --override_matcher"
+  echo "        type: string"
+  echo "        choices: [ cached-hamming-distance, pre-compute ]"
+  echo "        If the sample barcodes are > 12 bp long, a cached hamming distance"
+  echo "        matcher is used."
+  echo "        If the barcodes are less than or equal to 12 bp long, all possible"
+  echo "        matches are precomputed."
+  echo "        This option allows for overriding that heuristic."
+  echo ""
+  echo "    --skip_read_name_check"
+  echo "        type: boolean_true"
+  echo "        If this is true, then all the read names across FASTQs will not be"
+  echo "        enforced to be the same."
+  echo "        This may be useful when the read names are known to be the same and"
+  echo "        performance matters."
+  echo "        Regardless, the first read name in each FASTQ will always be checked."
+  echo ""
+  echo "    --sample_barcode_in_fastq_header"
+  echo "        type: boolean_true"
+  echo "        If this is true, then the sample barcode is expected to be in the FASTQ"
+  echo "        read header."
+  echo "        For dual indexed data, the barcodes must be \`+\` (plus) delimited."
+  echo "        Additionally, if true,"
+  echo "        then neither index FASTQ files nor sample barcode segments in the read"
+  echo "        structure may be specified."
+  echo ""
+  echo "    --metric_prefix"
+  echo "        type: string"
+  echo "        Prepend this prefix to all output metric file names"
+  echo ""
+  echo "    -l, --lane"
+  echo "        type: integer, multiple values allowed"
+  echo "        Select a subset of lanes to demultiplex.  Will cause only samples and"
+  echo "        input FASTQs with"
+  echo "        the given \`Lane\`(s) to be demultiplexed. Samples without a lane will be"
+  echo "        ignored, and"
+  echo "        FASTQs without lane information will be ignored"
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/snpeff/.config.vsh.yaml b/target/executable/snpeff/.config.vsh.yaml
index f2e67d56..6d014463 100644
--- a/target/executable/snpeff/.config.vsh.yaml
+++ b/target/executable/snpeff/.config.vsh.yaml
@@ -523,6 +523,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -627,16 +630,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/snpeff"
   executable: "target/executable/snpeff/snpeff"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/snpeff/snpeff b/target/executable/snpeff/snpeff
index d03aed8d..4c58c84d 100755
--- a/target/executable/snpeff/snpeff
+++ b/target/executable/snpeff/snpeff
@@ -2,7 +2,7 @@
 
 # snpeff main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -169,6 +169,405 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
+
+# initialise variables
+VIASH_MODE='run'
+VIASH_ENGINE_ID='docker'
+
+######## Helper functions for setting up Docker images for viash ########
+# expects: ViashDockerBuild
+
+# ViashDockerInstallationCheck: check whether Docker is installed correctly
+#
+# examples:
+#   ViashDockerInstallationCheck
+function ViashDockerInstallationCheck {
+  ViashDebug "Checking whether Docker is installed"
+  if [ ! command -v docker &> /dev/null ]; then
+    ViashCritical "Docker doesn't seem to be installed. See 'https://docs.docker.com/get-docker/' for instructions."
+    exit 1
+  fi
+
+  ViashDebug "Checking whether the Docker daemon is running"
+  local save=$-; set +e
+  local docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
+  local out=$?
+  [[ $save =~ e ]] && set -e
+  if [ $out -ne 0 ]; then
+    ViashCritical "Docker daemon does not seem to be running. Try one of the following:"
+    ViashCritical "- Try running 'dockerd' in the command line"
+    ViashCritical "- See https://docs.docker.com/config/daemon/"
+    exit 1
+  fi
+}
+
+# ViashDockerRemoteTagCheck: check whether a Docker image is available 
+# on a remote. Assumes `docker login` has been performed, if relevant.
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   ViashDockerRemoteTagCheck python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerRemoteTagCheck sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerRemoteTagCheck {
+  docker manifest inspect $1 > /dev/null 2> /dev/null
+}
+
+# ViashDockerLocalTagCheck: check whether a Docker image is available locally
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   docker pull python:latest
+#   ViashDockerLocalTagCheck python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerLocalTagCheck sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerLocalTagCheck {
+  [ -n "$(docker images -q $1)" ]
+}
+
+# ViashDockerPull: pull a Docker image
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   ViashDockerPull python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerPull sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerPull {
+  ViashNotice "Checking if Docker image is available at '$1'"
+  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
+    docker pull $1 && return 0 || return 1
+  else
+    local save=$-; set +e
+    docker pull $1 2> /dev/null > /dev/null
+    local out=$?
+    [[ $save =~ e ]] && set -e
+    if [ $out -ne 0 ]; then
+      ViashWarning "Could not pull from '$1'. Docker image doesn't exist or is not accessible."
+    fi
+    return $out
+  fi
+}
+
+# ViashDockerPush: push a Docker image
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   ViashDockerPush python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerPush sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerPush {
+  ViashNotice "Pushing image to '$1'"
+  local save=$-; set +e
+  local out
+  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
+    docker push $1
+    out=$?
+  else
+    docker push $1 2> /dev/null > /dev/null
+    out=$?
+  fi
+  [[ $save =~ e ]] && set -e
+  if [ $out -eq 0 ]; then
+    ViashNotice "Container '$1' push succeeded."
+  else
+    ViashError "Container '$1' push errored. You might not be logged in or have the necessary permissions."
+  fi
+  return $out
+}
+
+# ViashDockerPullElseBuild: pull a Docker image, else build it
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# ViashDockerBuild    : a Bash function which builds a docker image, takes image identifier as argument.
+# examples:
+#   ViashDockerPullElseBuild mynewcomponent
+function ViashDockerPullElseBuild {
+  local save=$-; set +e
+  ViashDockerPull $1
+  local out=$?
+  [[ $save =~ e ]] && set -e
+  if [ $out -ne 0 ]; then
+    ViashDockerBuild $@
+  fi
+}
+
+# ViashDockerSetup: create a Docker image, according to specified docker setup strategy
+#
+# $1          : image identifier with format `[registry/]image[:tag]`
+# $2          : docker setup strategy, see DockerSetupStrategy.scala
+# examples:
+#   ViashDockerSetup mynewcomponent alwaysbuild
+function ViashDockerSetup {
+  local image_id="$1"
+  local setup_strategy="$2"
+  if [ "$setup_strategy" == "alwaysbuild" -o "$setup_strategy" == "build" -o "$setup_strategy" == "b" ]; then
+    ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+  elif [ "$setup_strategy" == "alwayspull" -o "$setup_strategy" == "pull" -o "$setup_strategy" == "p" ]; then
+    ViashDockerPull $image_id
+  elif [ "$setup_strategy" == "alwayspullelsebuild" -o "$setup_strategy" == "pullelsebuild" ]; then
+    ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+  elif [ "$setup_strategy" == "alwayspullelsecachedbuild" -o "$setup_strategy" == "pullelsecachedbuild" ]; then
+    ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+  elif [ "$setup_strategy" == "alwayscachedbuild" -o "$setup_strategy" == "cachedbuild" -o "$setup_strategy" == "cb" ]; then
+    ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+  elif [[ "$setup_strategy" =~ ^ifneedbe ]]; then
+    local save=$-; set +e
+    ViashDockerLocalTagCheck $image_id
+    local outCheck=$?
+    [[ $save =~ e ]] && set -e
+    if [ $outCheck -eq 0 ]; then
+      ViashInfo "Image $image_id already exists"
+    elif [ "$setup_strategy" == "ifneedbebuild" ]; then
+      ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+    elif [ "$setup_strategy" == "ifneedbecachedbuild" ]; then
+      ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+    elif [ "$setup_strategy" == "ifneedbepull" ]; then
+      ViashDockerPull $image_id
+    elif [ "$setup_strategy" == "ifneedbepullelsebuild" ]; then
+      ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+    elif [ "$setup_strategy" == "ifneedbepullelsecachedbuild" ]; then
+      ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+    else
+      ViashError "Unrecognised Docker strategy: $setup_strategy"
+      exit 1
+    fi
+  elif [ "$setup_strategy" == "push" -o "$setup_strategy" == "forcepush" -o "$setup_strategy" == "alwayspush" ]; then
+    ViashDockerPush "$image_id"
+  elif [ "$setup_strategy" == "pushifnotpresent" -o "$setup_strategy" == "gentlepush" -o "$setup_strategy" == "maybepush" ]; then
+    local save=$-; set +e
+    ViashDockerRemoteTagCheck $image_id
+    local outCheck=$?
+    [[ $save =~ e ]] && set -e
+    if [ $outCheck -eq 0 ]; then
+      ViashNotice "Container '$image_id' exists, doing nothing."
+    else
+      ViashNotice "Container '$image_id' does not yet exist."
+      ViashDockerPush "$image_id"
+    fi
+  elif [ "$setup_strategy" == "donothing" -o "$setup_strategy" == "meh" ]; then
+    ViashNotice "Skipping setup."
+  else
+    ViashError "Unrecognised Docker strategy: $setup_strategy"
+    exit 1
+  fi
+}
+
+# ViashDockerCheckCommands: Check whether a docker container has the required commands
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# $@                  : commands to verify being present
+# examples:
+#   ViashDockerCheckCommands bash:4.0 bash ps foo
+function ViashDockerCheckCommands {
+  local image_id="$1"
+  shift 1
+  local commands="$@"
+  local save=$-; set +e
+  local missing # mark 'missing' as local in advance, otherwise the exit code of the command will be missing and always be '0'
+  missing=$(docker run --rm --entrypoint=sh "$image_id" -c "for command in $commands; do command -v \$command >/dev/null 2>&1; if [ \$? -ne 0 ]; then echo \$command; exit 1; fi; done")
+  local outCheck=$?
+  [[ $save =~ e ]] && set -e
+  if [ $outCheck -ne 0 ]; then
+  	ViashError "Docker container '$image_id' does not contain command '$missing'."
+  	exit 1
+  fi
+}
+
+# ViashDockerBuild: build a docker image
+# $1                               : image identifier with format `[registry/]image[:tag]`
+# $...                             : additional arguments to pass to docker build
+# $VIASH_META_TEMP_DIR             : temporary directory to store dockerfile & optional resources in
+# $VIASH_META_NAME                 : name of the component
+# $VIASH_META_RESOURCES_DIR        : directory containing the resources
+# $VIASH_VERBOSITY                 : verbosity level
+# exit code $?                     : whether or not the image was built successfully
+function ViashDockerBuild {
+  local image_id="$1"
+  shift 1
+
+  # create temporary directory to store dockerfile & optional resources in
+  local tmpdir=$(mktemp -d "$VIASH_META_TEMP_DIR/dockerbuild-$VIASH_META_NAME-XXXXXX")
+  local dockerfile="$tmpdir/Dockerfile"
+  function clean_up {
+    rm -rf "$tmpdir"
+  }
+  trap clean_up EXIT
+
+  # store dockerfile and resources
+  ViashDockerfile "$VIASH_ENGINE_ID" > "$dockerfile"
+
+  # generate the build command
+  local docker_build_cmd="docker build -t '$image_id' $@ '$VIASH_META_RESOURCES_DIR' -f '$dockerfile'"
+
+  # build the container
+  ViashNotice "Building container '$image_id' with Dockerfile"
+  ViashInfo "$docker_build_cmd"
+  local save=$-; set +e
+  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
+    eval $docker_build_cmd
+  else
+    eval $docker_build_cmd &> "$tmpdir/docker_build.log"
+  fi
+
+  # check exit code
+  local out=$?
+  [[ $save =~ e ]] && set -e
+  if [ $out -ne 0 ]; then
+    ViashError "Error occurred while building container '$image_id'"
+    if [ $VIASH_VERBOSITY -lt $VIASH_LOGCODE_INFO ]; then
+      ViashError "Transcript: --------------------------------"
+      cat "$tmpdir/docker_build.log"
+      ViashError "End of transcript --------------------------"
+    fi
+    exit 1
+  fi
+}
+
+######## End of helper functions for setting up Docker images for viash ########
+
+# ViashDockerFile: print the dockerfile to stdout
+# $1    : engine identifier
+# return : dockerfile required to run this component
+# examples:
+#   ViashDockerFile
+function ViashDockerfile {
+  local engine_id="$1"
+
+  if [[ "$engine_id" == "docker" ]]; then
+    cat << 'VIASHDOCKER'
+FROM quay.io/staphb/snpeff:5.2a
+ENTRYPOINT []
+RUN version=$(snpEff -version) && \
+version_trimmed=$(echo "$version" | awk '{print $1, $2}') && \
+echo "$version_trimmed" > /var/software_versions.txt
+
+LABEL org.opencontainers.image.description="Companion container for running component snpeff"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:42Z"
+LABEL org.opencontainers.image.source="https://github.com/pcingola/SnpEff"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+LABEL org.opencontainers.image.version="main"
+
+VIASHDOCKER
+  fi
+}
+
+# ViashDockerBuildArgs: return the arguments to pass to docker build
+# $1    : engine identifier
+# return : arguments to pass to docker build
+function ViashDockerBuildArgs {
+  local engine_id="$1"
+
+  if [[ "$engine_id" == "docker" ]]; then
+    echo ""
+  fi
+}
+
+# ViashAbsolutePath: generate absolute path from relative path
+# borrowed from https://stackoverflow.com/a/21951256
+# $1     : relative filename
+# return : absolute path
+# examples:
+#   ViashAbsolutePath some_file.txt   # returns /path/to/some_file.txt
+#   ViashAbsolutePath /foo/bar/..     # returns /foo
+function ViashAbsolutePath {
+  local thePath
+  local parr
+  local outp
+  local len
+  if [[ ! "$1" =~ ^/ ]]; then
+    thePath="$PWD/$1"
+  else
+    thePath="$1"
+  fi
+  echo "$thePath" | (
+    IFS=/
+    read -a parr
+    declare -a outp
+    for i in "${parr[@]}"; do
+      case "$i" in
+      ''|.) continue ;;
+      ..)
+        len=${#outp[@]}
+        if ((len==0)); then
+          continue
+        else
+          unset outp[$((len-1))]
+        fi
+        ;;
+      *)
+        len=${#outp[@]}
+        outp[$len]="$i"
+      ;;
+      esac
+    done
+    echo /"${outp[*]}"
+  )
+}
+# ViashDockerAutodetectMount: auto configuring docker mounts from parameters
+# $1                             : The parameter value
+# returns                        : New parameter
+# $VIASH_DIRECTORY_MOUNTS        : Added another parameter to be passed to docker
+# $VIASH_DOCKER_AUTOMOUNT_PREFIX : The prefix to be used for the automounts
+# examples:
+#   ViashDockerAutodetectMount /path/to/bar      # returns '/viash_automount/path/to/bar'
+#   ViashDockerAutodetectMountArg /path/to/bar   # returns '--volume="/path/to:/viash_automount/path/to"'
+function ViashDockerAutodetectMount {
+  local abs_path=$(ViashAbsolutePath "$1")
+  local mount_source
+  local base_name
+  if [ -d "$abs_path" ]; then
+    mount_source="$abs_path"
+    base_name=""
+  else
+    mount_source=`dirname "$abs_path"`
+    base_name=`basename "$abs_path"`
+  fi
+  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
+  if [ -z "$base_name" ]; then
+    echo "$mount_target"
+  else
+    echo "$mount_target/$base_name"
+  fi
+}
+function ViashDockerAutodetectMountArg {
+  local abs_path=$(ViashAbsolutePath "$1")
+  local mount_source
+  local base_name
+  if [ -d "$abs_path" ]; then
+    mount_source="$abs_path"
+    base_name=""
+  else
+    mount_source=`dirname "$abs_path"`
+    base_name=`basename "$abs_path"`
+  fi
+  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
+  ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target"
+  echo "--volume=\"$mount_source:$mount_target\""
+}
+function ViashDockerStripAutomount {
+  local abs_path=$(ViashAbsolutePath "$1")
+  echo "${abs_path#$VIASH_DOCKER_AUTOMOUNT_PREFIX}"
+}
+# initialise variables
+VIASH_DIRECTORY_MOUNTS=()
+
+# configure default docker automount prefix if it is unset
+if [ -z "${VIASH_DOCKER_AUTOMOUNT_PREFIX+x}" ]; then
+  VIASH_DOCKER_AUTOMOUNT_PREFIX="/viash_automount"
+fi
+
+# initialise docker variables
+VIASH_DOCKER_RUN_ARGS=(-i --rm)
+
+
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
   echo "snpeff main"
@@ -474,405 +873,32 @@ function ViashHelp {
   echo "    --upDownStreamLen, --ud"
   echo "        type: integer"
   echo "        Set upstream downstream interval length (in bases)."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
 }
 
-# initialise variables
-VIASH_MODE='run'
-VIASH_ENGINE_ID='docker'
-
-######## Helper functions for setting up Docker images for viash ########
-# expects: ViashDockerBuild
-
-# ViashDockerInstallationCheck: check whether Docker is installed correctly
-#
-# examples:
-#   ViashDockerInstallationCheck
-function ViashDockerInstallationCheck {
-  ViashDebug "Checking whether Docker is installed"
-  if [ ! command -v docker &> /dev/null ]; then
-    ViashCritical "Docker doesn't seem to be installed. See 'https://docs.docker.com/get-docker/' for instructions."
-    exit 1
-  fi
-
-  ViashDebug "Checking whether the Docker daemon is running"
-  local save=$-; set +e
-  local docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
-  local out=$?
-  [[ $save =~ e ]] && set -e
-  if [ $out -ne 0 ]; then
-    ViashCritical "Docker daemon does not seem to be running. Try one of the following:"
-    ViashCritical "- Try running 'dockerd' in the command line"
-    ViashCritical "- See https://docs.docker.com/config/daemon/"
-    exit 1
-  fi
-}
-
-# ViashDockerRemoteTagCheck: check whether a Docker image is available 
-# on a remote. Assumes `docker login` has been performed, if relevant.
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   ViashDockerRemoteTagCheck python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerRemoteTagCheck sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerRemoteTagCheck {
-  docker manifest inspect $1 > /dev/null 2> /dev/null
-}
-
-# ViashDockerLocalTagCheck: check whether a Docker image is available locally
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   docker pull python:latest
-#   ViashDockerLocalTagCheck python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerLocalTagCheck sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerLocalTagCheck {
-  [ -n "$(docker images -q $1)" ]
-}
-
-# ViashDockerPull: pull a Docker image
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   ViashDockerPull python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerPull sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerPull {
-  ViashNotice "Checking if Docker image is available at '$1'"
-  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
-    docker pull $1 && return 0 || return 1
-  else
-    local save=$-; set +e
-    docker pull $1 2> /dev/null > /dev/null
-    local out=$?
-    [[ $save =~ e ]] && set -e
-    if [ $out -ne 0 ]; then
-      ViashWarning "Could not pull from '$1'. Docker image doesn't exist or is not accessible."
-    fi
-    return $out
-  fi
-}
-
-# ViashDockerPush: push a Docker image
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   ViashDockerPush python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerPush sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerPush {
-  ViashNotice "Pushing image to '$1'"
-  local save=$-; set +e
-  local out
-  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
-    docker push $1
-    out=$?
-  else
-    docker push $1 2> /dev/null > /dev/null
-    out=$?
-  fi
-  [[ $save =~ e ]] && set -e
-  if [ $out -eq 0 ]; then
-    ViashNotice "Container '$1' push succeeded."
-  else
-    ViashError "Container '$1' push errored. You might not be logged in or have the necessary permissions."
-  fi
-  return $out
-}
-
-# ViashDockerPullElseBuild: pull a Docker image, else build it
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# ViashDockerBuild    : a Bash function which builds a docker image, takes image identifier as argument.
-# examples:
-#   ViashDockerPullElseBuild mynewcomponent
-function ViashDockerPullElseBuild {
-  local save=$-; set +e
-  ViashDockerPull $1
-  local out=$?
-  [[ $save =~ e ]] && set -e
-  if [ $out -ne 0 ]; then
-    ViashDockerBuild $@
-  fi
-}
-
-# ViashDockerSetup: create a Docker image, according to specified docker setup strategy
-#
-# $1          : image identifier with format `[registry/]image[:tag]`
-# $2          : docker setup strategy, see DockerSetupStrategy.scala
-# examples:
-#   ViashDockerSetup mynewcomponent alwaysbuild
-function ViashDockerSetup {
-  local image_id="$1"
-  local setup_strategy="$2"
-  if [ "$setup_strategy" == "alwaysbuild" -o "$setup_strategy" == "build" -o "$setup_strategy" == "b" ]; then
-    ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-  elif [ "$setup_strategy" == "alwayspull" -o "$setup_strategy" == "pull" -o "$setup_strategy" == "p" ]; then
-    ViashDockerPull $image_id
-  elif [ "$setup_strategy" == "alwayspullelsebuild" -o "$setup_strategy" == "pullelsebuild" ]; then
-    ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-  elif [ "$setup_strategy" == "alwayspullelsecachedbuild" -o "$setup_strategy" == "pullelsecachedbuild" ]; then
-    ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-  elif [ "$setup_strategy" == "alwayscachedbuild" -o "$setup_strategy" == "cachedbuild" -o "$setup_strategy" == "cb" ]; then
-    ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-  elif [[ "$setup_strategy" =~ ^ifneedbe ]]; then
-    local save=$-; set +e
-    ViashDockerLocalTagCheck $image_id
-    local outCheck=$?
-    [[ $save =~ e ]] && set -e
-    if [ $outCheck -eq 0 ]; then
-      ViashInfo "Image $image_id already exists"
-    elif [ "$setup_strategy" == "ifneedbebuild" ]; then
-      ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-    elif [ "$setup_strategy" == "ifneedbecachedbuild" ]; then
-      ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-    elif [ "$setup_strategy" == "ifneedbepull" ]; then
-      ViashDockerPull $image_id
-    elif [ "$setup_strategy" == "ifneedbepullelsebuild" ]; then
-      ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-    elif [ "$setup_strategy" == "ifneedbepullelsecachedbuild" ]; then
-      ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-    else
-      ViashError "Unrecognised Docker strategy: $setup_strategy"
-      exit 1
-    fi
-  elif [ "$setup_strategy" == "push" -o "$setup_strategy" == "forcepush" -o "$setup_strategy" == "alwayspush" ]; then
-    ViashDockerPush "$image_id"
-  elif [ "$setup_strategy" == "pushifnotpresent" -o "$setup_strategy" == "gentlepush" -o "$setup_strategy" == "maybepush" ]; then
-    local save=$-; set +e
-    ViashDockerRemoteTagCheck $image_id
-    local outCheck=$?
-    [[ $save =~ e ]] && set -e
-    if [ $outCheck -eq 0 ]; then
-      ViashNotice "Container '$image_id' exists, doing nothing."
-    else
-      ViashNotice "Container '$image_id' does not yet exist."
-      ViashDockerPush "$image_id"
-    fi
-  elif [ "$setup_strategy" == "donothing" -o "$setup_strategy" == "meh" ]; then
-    ViashNotice "Skipping setup."
-  else
-    ViashError "Unrecognised Docker strategy: $setup_strategy"
-    exit 1
-  fi
-}
-
-# ViashDockerCheckCommands: Check whether a docker container has the required commands
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# $@                  : commands to verify being present
-# examples:
-#   ViashDockerCheckCommands bash:4.0 bash ps foo
-function ViashDockerCheckCommands {
-  local image_id="$1"
-  shift 1
-  local commands="$@"
-  local save=$-; set +e
-  local missing # mark 'missing' as local in advance, otherwise the exit code of the command will be missing and always be '0'
-  missing=$(docker run --rm --entrypoint=sh "$image_id" -c "for command in $commands; do command -v \$command >/dev/null 2>&1; if [ \$? -ne 0 ]; then echo \$command; exit 1; fi; done")
-  local outCheck=$?
-  [[ $save =~ e ]] && set -e
-  if [ $outCheck -ne 0 ]; then
-  	ViashError "Docker container '$image_id' does not contain command '$missing'."
-  	exit 1
-  fi
-}
-
-# ViashDockerBuild: build a docker image
-# $1                               : image identifier with format `[registry/]image[:tag]`
-# $...                             : additional arguments to pass to docker build
-# $VIASH_META_TEMP_DIR             : temporary directory to store dockerfile & optional resources in
-# $VIASH_META_NAME                 : name of the component
-# $VIASH_META_RESOURCES_DIR        : directory containing the resources
-# $VIASH_VERBOSITY                 : verbosity level
-# exit code $?                     : whether or not the image was built successfully
-function ViashDockerBuild {
-  local image_id="$1"
-  shift 1
-
-  # create temporary directory to store dockerfile & optional resources in
-  local tmpdir=$(mktemp -d "$VIASH_META_TEMP_DIR/dockerbuild-$VIASH_META_NAME-XXXXXX")
-  local dockerfile="$tmpdir/Dockerfile"
-  function clean_up {
-    rm -rf "$tmpdir"
-  }
-  trap clean_up EXIT
-
-  # store dockerfile and resources
-  ViashDockerfile "$VIASH_ENGINE_ID" > "$dockerfile"
-
-  # generate the build command
-  local docker_build_cmd="docker build -t '$image_id' $@ '$VIASH_META_RESOURCES_DIR' -f '$dockerfile'"
-
-  # build the container
-  ViashNotice "Building container '$image_id' with Dockerfile"
-  ViashInfo "$docker_build_cmd"
-  local save=$-; set +e
-  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
-    eval $docker_build_cmd
-  else
-    eval $docker_build_cmd &> "$tmpdir/docker_build.log"
-  fi
-
-  # check exit code
-  local out=$?
-  [[ $save =~ e ]] && set -e
-  if [ $out -ne 0 ]; then
-    ViashError "Error occurred while building container '$image_id'"
-    if [ $VIASH_VERBOSITY -lt $VIASH_LOGCODE_INFO ]; then
-      ViashError "Transcript: --------------------------------"
-      cat "$tmpdir/docker_build.log"
-      ViashError "End of transcript --------------------------"
-    fi
-    exit 1
-  fi
-}
-
-######## End of helper functions for setting up Docker images for viash ########
-
-# ViashDockerFile: print the dockerfile to stdout
-# $1    : engine identifier
-# return : dockerfile required to run this component
-# examples:
-#   ViashDockerFile
-function ViashDockerfile {
-  local engine_id="$1"
-
-  if [[ "$engine_id" == "docker" ]]; then
-    cat << 'VIASHDOCKER'
-FROM quay.io/staphb/snpeff:5.2a
-ENTRYPOINT []
-RUN version=$(snpEff -version) && \
-version_trimmed=$(echo "$version" | awk '{print $1, $2}') && \
-echo "$version_trimmed" > /var/software_versions.txt
-
-LABEL org.opencontainers.image.description="Companion container for running component snpeff"
-LABEL org.opencontainers.image.created="2024-12-03T10:33:55Z"
-LABEL org.opencontainers.image.source="https://github.com/pcingola/SnpEff"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-LABEL org.opencontainers.image.version="main"
-
-VIASHDOCKER
-  fi
-}
-
-# ViashDockerBuildArgs: return the arguments to pass to docker build
-# $1    : engine identifier
-# return : arguments to pass to docker build
-function ViashDockerBuildArgs {
-  local engine_id="$1"
-
-  if [[ "$engine_id" == "docker" ]]; then
-    echo ""
-  fi
-}
-
-# ViashAbsolutePath: generate absolute path from relative path
-# borrowed from https://stackoverflow.com/a/21951256
-# $1     : relative filename
-# return : absolute path
-# examples:
-#   ViashAbsolutePath some_file.txt   # returns /path/to/some_file.txt
-#   ViashAbsolutePath /foo/bar/..     # returns /foo
-function ViashAbsolutePath {
-  local thePath
-  local parr
-  local outp
-  local len
-  if [[ ! "$1" =~ ^/ ]]; then
-    thePath="$PWD/$1"
-  else
-    thePath="$1"
-  fi
-  echo "$thePath" | (
-    IFS=/
-    read -a parr
-    declare -a outp
-    for i in "${parr[@]}"; do
-      case "$i" in
-      ''|.) continue ;;
-      ..)
-        len=${#outp[@]}
-        if ((len==0)); then
-          continue
-        else
-          unset outp[$((len-1))]
-        fi
-        ;;
-      *)
-        len=${#outp[@]}
-        outp[$len]="$i"
-      ;;
-      esac
-    done
-    echo /"${outp[*]}"
-  )
-}
-# ViashDockerAutodetectMount: auto configuring docker mounts from parameters
-# $1                             : The parameter value
-# returns                        : New parameter
-# $VIASH_DIRECTORY_MOUNTS        : Added another parameter to be passed to docker
-# $VIASH_DOCKER_AUTOMOUNT_PREFIX : The prefix to be used for the automounts
-# examples:
-#   ViashDockerAutodetectMount /path/to/bar      # returns '/viash_automount/path/to/bar'
-#   ViashDockerAutodetectMountArg /path/to/bar   # returns '--volume="/path/to:/viash_automount/path/to"'
-function ViashDockerAutodetectMount {
-  local abs_path=$(ViashAbsolutePath "$1")
-  local mount_source
-  local base_name
-  if [ -d "$abs_path" ]; then
-    mount_source="$abs_path"
-    base_name=""
-  else
-    mount_source=`dirname "$abs_path"`
-    base_name=`basename "$abs_path"`
-  fi
-  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
-  if [ -z "$base_name" ]; then
-    echo "$mount_target"
-  else
-    echo "$mount_target/$base_name"
-  fi
-}
-function ViashDockerAutodetectMountArg {
-  local abs_path=$(ViashAbsolutePath "$1")
-  local mount_source
-  local base_name
-  if [ -d "$abs_path" ]; then
-    mount_source="$abs_path"
-    base_name=""
-  else
-    mount_source=`dirname "$abs_path"`
-    base_name=`basename "$abs_path"`
-  fi
-  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
-  ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target"
-  echo "--volume=\"$mount_source:$mount_target\""
-}
-function ViashDockerStripAutomount {
-  local abs_path=$(ViashAbsolutePath "$1")
-  echo "${abs_path#$VIASH_DOCKER_AUTOMOUNT_PREFIX}"
-}
-# initialise variables
-VIASH_DIRECTORY_MOUNTS=()
-
-# configure default docker automount prefix if it is unset
-if [ -z "${VIASH_DOCKER_AUTOMOUNT_PREFIX+x}" ]; then
-  VIASH_DOCKER_AUTOMOUNT_PREFIX="/viash_automount"
-fi
-
-# initialise docker variables
-VIASH_DOCKER_RUN_ARGS=(-i --rm)
-
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/sortmerna/.config.vsh.yaml b/target/executable/sortmerna/.config.vsh.yaml
index 46c03ed7..eaeb0e9c 100644
--- a/target/executable/sortmerna/.config.vsh.yaml
+++ b/target/executable/sortmerna/.config.vsh.yaml
@@ -487,6 +487,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -593,16 +596,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/sortmerna"
   executable: "target/executable/sortmerna/sortmerna"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/sortmerna/sortmerna b/target/executable/sortmerna/sortmerna
index 05ea8108..b4f0cc71 100755
--- a/target/executable/sortmerna/sortmerna
+++ b/target/executable/sortmerna/sortmerna
@@ -2,7 +2,7 @@
 
 # sortmerna main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -169,6 +169,403 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
+
+# initialise variables
+VIASH_MODE='run'
+VIASH_ENGINE_ID='docker'
+
+######## Helper functions for setting up Docker images for viash ########
+# expects: ViashDockerBuild
+
+# ViashDockerInstallationCheck: check whether Docker is installed correctly
+#
+# examples:
+#   ViashDockerInstallationCheck
+function ViashDockerInstallationCheck {
+  ViashDebug "Checking whether Docker is installed"
+  if [ ! command -v docker &> /dev/null ]; then
+    ViashCritical "Docker doesn't seem to be installed. See 'https://docs.docker.com/get-docker/' for instructions."
+    exit 1
+  fi
+
+  ViashDebug "Checking whether the Docker daemon is running"
+  local save=$-; set +e
+  local docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
+  local out=$?
+  [[ $save =~ e ]] && set -e
+  if [ $out -ne 0 ]; then
+    ViashCritical "Docker daemon does not seem to be running. Try one of the following:"
+    ViashCritical "- Try running 'dockerd' in the command line"
+    ViashCritical "- See https://docs.docker.com/config/daemon/"
+    exit 1
+  fi
+}
+
+# ViashDockerRemoteTagCheck: check whether a Docker image is available 
+# on a remote. Assumes `docker login` has been performed, if relevant.
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   ViashDockerRemoteTagCheck python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerRemoteTagCheck sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerRemoteTagCheck {
+  docker manifest inspect $1 > /dev/null 2> /dev/null
+}
+
+# ViashDockerLocalTagCheck: check whether a Docker image is available locally
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   docker pull python:latest
+#   ViashDockerLocalTagCheck python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerLocalTagCheck sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerLocalTagCheck {
+  [ -n "$(docker images -q $1)" ]
+}
+
+# ViashDockerPull: pull a Docker image
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   ViashDockerPull python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerPull sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerPull {
+  ViashNotice "Checking if Docker image is available at '$1'"
+  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
+    docker pull $1 && return 0 || return 1
+  else
+    local save=$-; set +e
+    docker pull $1 2> /dev/null > /dev/null
+    local out=$?
+    [[ $save =~ e ]] && set -e
+    if [ $out -ne 0 ]; then
+      ViashWarning "Could not pull from '$1'. Docker image doesn't exist or is not accessible."
+    fi
+    return $out
+  fi
+}
+
+# ViashDockerPush: push a Docker image
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   ViashDockerPush python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerPush sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerPush {
+  ViashNotice "Pushing image to '$1'"
+  local save=$-; set +e
+  local out
+  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
+    docker push $1
+    out=$?
+  else
+    docker push $1 2> /dev/null > /dev/null
+    out=$?
+  fi
+  [[ $save =~ e ]] && set -e
+  if [ $out -eq 0 ]; then
+    ViashNotice "Container '$1' push succeeded."
+  else
+    ViashError "Container '$1' push errored. You might not be logged in or have the necessary permissions."
+  fi
+  return $out
+}
+
+# ViashDockerPullElseBuild: pull a Docker image, else build it
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# ViashDockerBuild    : a Bash function which builds a docker image, takes image identifier as argument.
+# examples:
+#   ViashDockerPullElseBuild mynewcomponent
+function ViashDockerPullElseBuild {
+  local save=$-; set +e
+  ViashDockerPull $1
+  local out=$?
+  [[ $save =~ e ]] && set -e
+  if [ $out -ne 0 ]; then
+    ViashDockerBuild $@
+  fi
+}
+
+# ViashDockerSetup: create a Docker image, according to specified docker setup strategy
+#
+# $1          : image identifier with format `[registry/]image[:tag]`
+# $2          : docker setup strategy, see DockerSetupStrategy.scala
+# examples:
+#   ViashDockerSetup mynewcomponent alwaysbuild
+function ViashDockerSetup {
+  local image_id="$1"
+  local setup_strategy="$2"
+  if [ "$setup_strategy" == "alwaysbuild" -o "$setup_strategy" == "build" -o "$setup_strategy" == "b" ]; then
+    ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+  elif [ "$setup_strategy" == "alwayspull" -o "$setup_strategy" == "pull" -o "$setup_strategy" == "p" ]; then
+    ViashDockerPull $image_id
+  elif [ "$setup_strategy" == "alwayspullelsebuild" -o "$setup_strategy" == "pullelsebuild" ]; then
+    ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+  elif [ "$setup_strategy" == "alwayspullelsecachedbuild" -o "$setup_strategy" == "pullelsecachedbuild" ]; then
+    ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+  elif [ "$setup_strategy" == "alwayscachedbuild" -o "$setup_strategy" == "cachedbuild" -o "$setup_strategy" == "cb" ]; then
+    ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+  elif [[ "$setup_strategy" =~ ^ifneedbe ]]; then
+    local save=$-; set +e
+    ViashDockerLocalTagCheck $image_id
+    local outCheck=$?
+    [[ $save =~ e ]] && set -e
+    if [ $outCheck -eq 0 ]; then
+      ViashInfo "Image $image_id already exists"
+    elif [ "$setup_strategy" == "ifneedbebuild" ]; then
+      ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+    elif [ "$setup_strategy" == "ifneedbecachedbuild" ]; then
+      ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+    elif [ "$setup_strategy" == "ifneedbepull" ]; then
+      ViashDockerPull $image_id
+    elif [ "$setup_strategy" == "ifneedbepullelsebuild" ]; then
+      ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+    elif [ "$setup_strategy" == "ifneedbepullelsecachedbuild" ]; then
+      ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+    else
+      ViashError "Unrecognised Docker strategy: $setup_strategy"
+      exit 1
+    fi
+  elif [ "$setup_strategy" == "push" -o "$setup_strategy" == "forcepush" -o "$setup_strategy" == "alwayspush" ]; then
+    ViashDockerPush "$image_id"
+  elif [ "$setup_strategy" == "pushifnotpresent" -o "$setup_strategy" == "gentlepush" -o "$setup_strategy" == "maybepush" ]; then
+    local save=$-; set +e
+    ViashDockerRemoteTagCheck $image_id
+    local outCheck=$?
+    [[ $save =~ e ]] && set -e
+    if [ $outCheck -eq 0 ]; then
+      ViashNotice "Container '$image_id' exists, doing nothing."
+    else
+      ViashNotice "Container '$image_id' does not yet exist."
+      ViashDockerPush "$image_id"
+    fi
+  elif [ "$setup_strategy" == "donothing" -o "$setup_strategy" == "meh" ]; then
+    ViashNotice "Skipping setup."
+  else
+    ViashError "Unrecognised Docker strategy: $setup_strategy"
+    exit 1
+  fi
+}
+
+# ViashDockerCheckCommands: Check whether a docker container has the required commands
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# $@                  : commands to verify being present
+# examples:
+#   ViashDockerCheckCommands bash:4.0 bash ps foo
+function ViashDockerCheckCommands {
+  local image_id="$1"
+  shift 1
+  local commands="$@"
+  local save=$-; set +e
+  local missing # mark 'missing' as local in advance, otherwise the exit code of the command will be missing and always be '0'
+  missing=$(docker run --rm --entrypoint=sh "$image_id" -c "for command in $commands; do command -v \$command >/dev/null 2>&1; if [ \$? -ne 0 ]; then echo \$command; exit 1; fi; done")
+  local outCheck=$?
+  [[ $save =~ e ]] && set -e
+  if [ $outCheck -ne 0 ]; then
+  	ViashError "Docker container '$image_id' does not contain command '$missing'."
+  	exit 1
+  fi
+}
+
+# ViashDockerBuild: build a docker image
+# $1                               : image identifier with format `[registry/]image[:tag]`
+# $...                             : additional arguments to pass to docker build
+# $VIASH_META_TEMP_DIR             : temporary directory to store dockerfile & optional resources in
+# $VIASH_META_NAME                 : name of the component
+# $VIASH_META_RESOURCES_DIR        : directory containing the resources
+# $VIASH_VERBOSITY                 : verbosity level
+# exit code $?                     : whether or not the image was built successfully
+function ViashDockerBuild {
+  local image_id="$1"
+  shift 1
+
+  # create temporary directory to store dockerfile & optional resources in
+  local tmpdir=$(mktemp -d "$VIASH_META_TEMP_DIR/dockerbuild-$VIASH_META_NAME-XXXXXX")
+  local dockerfile="$tmpdir/Dockerfile"
+  function clean_up {
+    rm -rf "$tmpdir"
+  }
+  trap clean_up EXIT
+
+  # store dockerfile and resources
+  ViashDockerfile "$VIASH_ENGINE_ID" > "$dockerfile"
+
+  # generate the build command
+  local docker_build_cmd="docker build -t '$image_id' $@ '$VIASH_META_RESOURCES_DIR' -f '$dockerfile'"
+
+  # build the container
+  ViashNotice "Building container '$image_id' with Dockerfile"
+  ViashInfo "$docker_build_cmd"
+  local save=$-; set +e
+  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
+    eval $docker_build_cmd
+  else
+    eval $docker_build_cmd &> "$tmpdir/docker_build.log"
+  fi
+
+  # check exit code
+  local out=$?
+  [[ $save =~ e ]] && set -e
+  if [ $out -ne 0 ]; then
+    ViashError "Error occurred while building container '$image_id'"
+    if [ $VIASH_VERBOSITY -lt $VIASH_LOGCODE_INFO ]; then
+      ViashError "Transcript: --------------------------------"
+      cat "$tmpdir/docker_build.log"
+      ViashError "End of transcript --------------------------"
+    fi
+    exit 1
+  fi
+}
+
+######## End of helper functions for setting up Docker images for viash ########
+
+# ViashDockerFile: print the dockerfile to stdout
+# $1    : engine identifier
+# return : dockerfile required to run this component
+# examples:
+#   ViashDockerFile
+function ViashDockerfile {
+  local engine_id="$1"
+
+  if [[ "$engine_id" == "docker" ]]; then
+    cat << 'VIASHDOCKER'
+FROM quay.io/biocontainers/sortmerna:4.3.6--h9ee0642_0
+ENTRYPOINT []
+RUN echo SortMeRNA: `sortmerna --version | sed -n 's/.*version \([0-9]\+\.[0-9]\+\.[0-9]\+\).*/\1/p'`
+
+LABEL org.opencontainers.image.description="Companion container for running component sortmerna"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:43Z"
+LABEL org.opencontainers.image.source="https://github.com/sortmerna/sortmerna"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+LABEL org.opencontainers.image.version="main"
+
+VIASHDOCKER
+  fi
+}
+
+# ViashDockerBuildArgs: return the arguments to pass to docker build
+# $1    : engine identifier
+# return : arguments to pass to docker build
+function ViashDockerBuildArgs {
+  local engine_id="$1"
+
+  if [[ "$engine_id" == "docker" ]]; then
+    echo ""
+  fi
+}
+
+# ViashAbsolutePath: generate absolute path from relative path
+# borrowed from https://stackoverflow.com/a/21951256
+# $1     : relative filename
+# return : absolute path
+# examples:
+#   ViashAbsolutePath some_file.txt   # returns /path/to/some_file.txt
+#   ViashAbsolutePath /foo/bar/..     # returns /foo
+function ViashAbsolutePath {
+  local thePath
+  local parr
+  local outp
+  local len
+  if [[ ! "$1" =~ ^/ ]]; then
+    thePath="$PWD/$1"
+  else
+    thePath="$1"
+  fi
+  echo "$thePath" | (
+    IFS=/
+    read -a parr
+    declare -a outp
+    for i in "${parr[@]}"; do
+      case "$i" in
+      ''|.) continue ;;
+      ..)
+        len=${#outp[@]}
+        if ((len==0)); then
+          continue
+        else
+          unset outp[$((len-1))]
+        fi
+        ;;
+      *)
+        len=${#outp[@]}
+        outp[$len]="$i"
+      ;;
+      esac
+    done
+    echo /"${outp[*]}"
+  )
+}
+# ViashDockerAutodetectMount: auto configuring docker mounts from parameters
+# $1                             : The parameter value
+# returns                        : New parameter
+# $VIASH_DIRECTORY_MOUNTS        : Added another parameter to be passed to docker
+# $VIASH_DOCKER_AUTOMOUNT_PREFIX : The prefix to be used for the automounts
+# examples:
+#   ViashDockerAutodetectMount /path/to/bar      # returns '/viash_automount/path/to/bar'
+#   ViashDockerAutodetectMountArg /path/to/bar   # returns '--volume="/path/to:/viash_automount/path/to"'
+function ViashDockerAutodetectMount {
+  local abs_path=$(ViashAbsolutePath "$1")
+  local mount_source
+  local base_name
+  if [ -d "$abs_path" ]; then
+    mount_source="$abs_path"
+    base_name=""
+  else
+    mount_source=`dirname "$abs_path"`
+    base_name=`basename "$abs_path"`
+  fi
+  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
+  if [ -z "$base_name" ]; then
+    echo "$mount_target"
+  else
+    echo "$mount_target/$base_name"
+  fi
+}
+function ViashDockerAutodetectMountArg {
+  local abs_path=$(ViashAbsolutePath "$1")
+  local mount_source
+  local base_name
+  if [ -d "$abs_path" ]; then
+    mount_source="$abs_path"
+    base_name=""
+  else
+    mount_source=`dirname "$abs_path"`
+    base_name=`basename "$abs_path"`
+  fi
+  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
+  ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target"
+  echo "--volume=\"$mount_source:$mount_target\""
+}
+function ViashDockerStripAutomount {
+  local abs_path=$(ViashAbsolutePath "$1")
+  echo "${abs_path#$VIASH_DOCKER_AUTOMOUNT_PREFIX}"
+}
+# initialise variables
+VIASH_DIRECTORY_MOUNTS=()
+
+# configure default docker automount prefix if it is unset
+if [ -z "${VIASH_DOCKER_AUTOMOUNT_PREFIX+x}" ]; then
+  VIASH_DOCKER_AUTOMOUNT_PREFIX="/viash_automount"
+fi
+
+# initialise docker variables
+VIASH_DOCKER_RUN_ARGS=(-i --rm)
+
+
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
   echo "sortmerna main"
@@ -460,403 +857,32 @@ function ViashHelp {
   echo "        example: 1000"
   echo "        Maximum number of positions to store for each unique L-mer. Set to 0 to"
   echo "        store all positions. Default: '1000'"
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
 }
 
-# initialise variables
-VIASH_MODE='run'
-VIASH_ENGINE_ID='docker'
-
-######## Helper functions for setting up Docker images for viash ########
-# expects: ViashDockerBuild
-
-# ViashDockerInstallationCheck: check whether Docker is installed correctly
-#
-# examples:
-#   ViashDockerInstallationCheck
-function ViashDockerInstallationCheck {
-  ViashDebug "Checking whether Docker is installed"
-  if [ ! command -v docker &> /dev/null ]; then
-    ViashCritical "Docker doesn't seem to be installed. See 'https://docs.docker.com/get-docker/' for instructions."
-    exit 1
-  fi
-
-  ViashDebug "Checking whether the Docker daemon is running"
-  local save=$-; set +e
-  local docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
-  local out=$?
-  [[ $save =~ e ]] && set -e
-  if [ $out -ne 0 ]; then
-    ViashCritical "Docker daemon does not seem to be running. Try one of the following:"
-    ViashCritical "- Try running 'dockerd' in the command line"
-    ViashCritical "- See https://docs.docker.com/config/daemon/"
-    exit 1
-  fi
-}
-
-# ViashDockerRemoteTagCheck: check whether a Docker image is available 
-# on a remote. Assumes `docker login` has been performed, if relevant.
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   ViashDockerRemoteTagCheck python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerRemoteTagCheck sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerRemoteTagCheck {
-  docker manifest inspect $1 > /dev/null 2> /dev/null
-}
-
-# ViashDockerLocalTagCheck: check whether a Docker image is available locally
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   docker pull python:latest
-#   ViashDockerLocalTagCheck python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerLocalTagCheck sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerLocalTagCheck {
-  [ -n "$(docker images -q $1)" ]
-}
-
-# ViashDockerPull: pull a Docker image
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   ViashDockerPull python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerPull sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerPull {
-  ViashNotice "Checking if Docker image is available at '$1'"
-  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
-    docker pull $1 && return 0 || return 1
-  else
-    local save=$-; set +e
-    docker pull $1 2> /dev/null > /dev/null
-    local out=$?
-    [[ $save =~ e ]] && set -e
-    if [ $out -ne 0 ]; then
-      ViashWarning "Could not pull from '$1'. Docker image doesn't exist or is not accessible."
-    fi
-    return $out
-  fi
-}
-
-# ViashDockerPush: push a Docker image
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   ViashDockerPush python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerPush sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerPush {
-  ViashNotice "Pushing image to '$1'"
-  local save=$-; set +e
-  local out
-  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
-    docker push $1
-    out=$?
-  else
-    docker push $1 2> /dev/null > /dev/null
-    out=$?
-  fi
-  [[ $save =~ e ]] && set -e
-  if [ $out -eq 0 ]; then
-    ViashNotice "Container '$1' push succeeded."
-  else
-    ViashError "Container '$1' push errored. You might not be logged in or have the necessary permissions."
-  fi
-  return $out
-}
-
-# ViashDockerPullElseBuild: pull a Docker image, else build it
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# ViashDockerBuild    : a Bash function which builds a docker image, takes image identifier as argument.
-# examples:
-#   ViashDockerPullElseBuild mynewcomponent
-function ViashDockerPullElseBuild {
-  local save=$-; set +e
-  ViashDockerPull $1
-  local out=$?
-  [[ $save =~ e ]] && set -e
-  if [ $out -ne 0 ]; then
-    ViashDockerBuild $@
-  fi
-}
-
-# ViashDockerSetup: create a Docker image, according to specified docker setup strategy
-#
-# $1          : image identifier with format `[registry/]image[:tag]`
-# $2          : docker setup strategy, see DockerSetupStrategy.scala
-# examples:
-#   ViashDockerSetup mynewcomponent alwaysbuild
-function ViashDockerSetup {
-  local image_id="$1"
-  local setup_strategy="$2"
-  if [ "$setup_strategy" == "alwaysbuild" -o "$setup_strategy" == "build" -o "$setup_strategy" == "b" ]; then
-    ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-  elif [ "$setup_strategy" == "alwayspull" -o "$setup_strategy" == "pull" -o "$setup_strategy" == "p" ]; then
-    ViashDockerPull $image_id
-  elif [ "$setup_strategy" == "alwayspullelsebuild" -o "$setup_strategy" == "pullelsebuild" ]; then
-    ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-  elif [ "$setup_strategy" == "alwayspullelsecachedbuild" -o "$setup_strategy" == "pullelsecachedbuild" ]; then
-    ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-  elif [ "$setup_strategy" == "alwayscachedbuild" -o "$setup_strategy" == "cachedbuild" -o "$setup_strategy" == "cb" ]; then
-    ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-  elif [[ "$setup_strategy" =~ ^ifneedbe ]]; then
-    local save=$-; set +e
-    ViashDockerLocalTagCheck $image_id
-    local outCheck=$?
-    [[ $save =~ e ]] && set -e
-    if [ $outCheck -eq 0 ]; then
-      ViashInfo "Image $image_id already exists"
-    elif [ "$setup_strategy" == "ifneedbebuild" ]; then
-      ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-    elif [ "$setup_strategy" == "ifneedbecachedbuild" ]; then
-      ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-    elif [ "$setup_strategy" == "ifneedbepull" ]; then
-      ViashDockerPull $image_id
-    elif [ "$setup_strategy" == "ifneedbepullelsebuild" ]; then
-      ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-    elif [ "$setup_strategy" == "ifneedbepullelsecachedbuild" ]; then
-      ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-    else
-      ViashError "Unrecognised Docker strategy: $setup_strategy"
-      exit 1
-    fi
-  elif [ "$setup_strategy" == "push" -o "$setup_strategy" == "forcepush" -o "$setup_strategy" == "alwayspush" ]; then
-    ViashDockerPush "$image_id"
-  elif [ "$setup_strategy" == "pushifnotpresent" -o "$setup_strategy" == "gentlepush" -o "$setup_strategy" == "maybepush" ]; then
-    local save=$-; set +e
-    ViashDockerRemoteTagCheck $image_id
-    local outCheck=$?
-    [[ $save =~ e ]] && set -e
-    if [ $outCheck -eq 0 ]; then
-      ViashNotice "Container '$image_id' exists, doing nothing."
-    else
-      ViashNotice "Container '$image_id' does not yet exist."
-      ViashDockerPush "$image_id"
-    fi
-  elif [ "$setup_strategy" == "donothing" -o "$setup_strategy" == "meh" ]; then
-    ViashNotice "Skipping setup."
-  else
-    ViashError "Unrecognised Docker strategy: $setup_strategy"
-    exit 1
-  fi
-}
-
-# ViashDockerCheckCommands: Check whether a docker container has the required commands
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# $@                  : commands to verify being present
-# examples:
-#   ViashDockerCheckCommands bash:4.0 bash ps foo
-function ViashDockerCheckCommands {
-  local image_id="$1"
-  shift 1
-  local commands="$@"
-  local save=$-; set +e
-  local missing # mark 'missing' as local in advance, otherwise the exit code of the command will be missing and always be '0'
-  missing=$(docker run --rm --entrypoint=sh "$image_id" -c "for command in $commands; do command -v \$command >/dev/null 2>&1; if [ \$? -ne 0 ]; then echo \$command; exit 1; fi; done")
-  local outCheck=$?
-  [[ $save =~ e ]] && set -e
-  if [ $outCheck -ne 0 ]; then
-  	ViashError "Docker container '$image_id' does not contain command '$missing'."
-  	exit 1
-  fi
-}
-
-# ViashDockerBuild: build a docker image
-# $1                               : image identifier with format `[registry/]image[:tag]`
-# $...                             : additional arguments to pass to docker build
-# $VIASH_META_TEMP_DIR             : temporary directory to store dockerfile & optional resources in
-# $VIASH_META_NAME                 : name of the component
-# $VIASH_META_RESOURCES_DIR        : directory containing the resources
-# $VIASH_VERBOSITY                 : verbosity level
-# exit code $?                     : whether or not the image was built successfully
-function ViashDockerBuild {
-  local image_id="$1"
-  shift 1
-
-  # create temporary directory to store dockerfile & optional resources in
-  local tmpdir=$(mktemp -d "$VIASH_META_TEMP_DIR/dockerbuild-$VIASH_META_NAME-XXXXXX")
-  local dockerfile="$tmpdir/Dockerfile"
-  function clean_up {
-    rm -rf "$tmpdir"
-  }
-  trap clean_up EXIT
-
-  # store dockerfile and resources
-  ViashDockerfile "$VIASH_ENGINE_ID" > "$dockerfile"
-
-  # generate the build command
-  local docker_build_cmd="docker build -t '$image_id' $@ '$VIASH_META_RESOURCES_DIR' -f '$dockerfile'"
-
-  # build the container
-  ViashNotice "Building container '$image_id' with Dockerfile"
-  ViashInfo "$docker_build_cmd"
-  local save=$-; set +e
-  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
-    eval $docker_build_cmd
-  else
-    eval $docker_build_cmd &> "$tmpdir/docker_build.log"
-  fi
-
-  # check exit code
-  local out=$?
-  [[ $save =~ e ]] && set -e
-  if [ $out -ne 0 ]; then
-    ViashError "Error occurred while building container '$image_id'"
-    if [ $VIASH_VERBOSITY -lt $VIASH_LOGCODE_INFO ]; then
-      ViashError "Transcript: --------------------------------"
-      cat "$tmpdir/docker_build.log"
-      ViashError "End of transcript --------------------------"
-    fi
-    exit 1
-  fi
-}
-
-######## End of helper functions for setting up Docker images for viash ########
-
-# ViashDockerFile: print the dockerfile to stdout
-# $1    : engine identifier
-# return : dockerfile required to run this component
-# examples:
-#   ViashDockerFile
-function ViashDockerfile {
-  local engine_id="$1"
-
-  if [[ "$engine_id" == "docker" ]]; then
-    cat << 'VIASHDOCKER'
-FROM quay.io/biocontainers/sortmerna:4.3.6--h9ee0642_0
-ENTRYPOINT []
-RUN echo SortMeRNA: `sortmerna --version | sed -n 's/.*version \([0-9]\+\.[0-9]\+\.[0-9]\+\).*/\1/p'`
-
-LABEL org.opencontainers.image.description="Companion container for running component sortmerna"
-LABEL org.opencontainers.image.created="2024-12-03T10:33:57Z"
-LABEL org.opencontainers.image.source="https://github.com/sortmerna/sortmerna"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-LABEL org.opencontainers.image.version="main"
-
-VIASHDOCKER
-  fi
-}
-
-# ViashDockerBuildArgs: return the arguments to pass to docker build
-# $1    : engine identifier
-# return : arguments to pass to docker build
-function ViashDockerBuildArgs {
-  local engine_id="$1"
-
-  if [[ "$engine_id" == "docker" ]]; then
-    echo ""
-  fi
-}
-
-# ViashAbsolutePath: generate absolute path from relative path
-# borrowed from https://stackoverflow.com/a/21951256
-# $1     : relative filename
-# return : absolute path
-# examples:
-#   ViashAbsolutePath some_file.txt   # returns /path/to/some_file.txt
-#   ViashAbsolutePath /foo/bar/..     # returns /foo
-function ViashAbsolutePath {
-  local thePath
-  local parr
-  local outp
-  local len
-  if [[ ! "$1" =~ ^/ ]]; then
-    thePath="$PWD/$1"
-  else
-    thePath="$1"
-  fi
-  echo "$thePath" | (
-    IFS=/
-    read -a parr
-    declare -a outp
-    for i in "${parr[@]}"; do
-      case "$i" in
-      ''|.) continue ;;
-      ..)
-        len=${#outp[@]}
-        if ((len==0)); then
-          continue
-        else
-          unset outp[$((len-1))]
-        fi
-        ;;
-      *)
-        len=${#outp[@]}
-        outp[$len]="$i"
-      ;;
-      esac
-    done
-    echo /"${outp[*]}"
-  )
-}
-# ViashDockerAutodetectMount: auto configuring docker mounts from parameters
-# $1                             : The parameter value
-# returns                        : New parameter
-# $VIASH_DIRECTORY_MOUNTS        : Added another parameter to be passed to docker
-# $VIASH_DOCKER_AUTOMOUNT_PREFIX : The prefix to be used for the automounts
-# examples:
-#   ViashDockerAutodetectMount /path/to/bar      # returns '/viash_automount/path/to/bar'
-#   ViashDockerAutodetectMountArg /path/to/bar   # returns '--volume="/path/to:/viash_automount/path/to"'
-function ViashDockerAutodetectMount {
-  local abs_path=$(ViashAbsolutePath "$1")
-  local mount_source
-  local base_name
-  if [ -d "$abs_path" ]; then
-    mount_source="$abs_path"
-    base_name=""
-  else
-    mount_source=`dirname "$abs_path"`
-    base_name=`basename "$abs_path"`
-  fi
-  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
-  if [ -z "$base_name" ]; then
-    echo "$mount_target"
-  else
-    echo "$mount_target/$base_name"
-  fi
-}
-function ViashDockerAutodetectMountArg {
-  local abs_path=$(ViashAbsolutePath "$1")
-  local mount_source
-  local base_name
-  if [ -d "$abs_path" ]; then
-    mount_source="$abs_path"
-    base_name=""
-  else
-    mount_source=`dirname "$abs_path"`
-    base_name=`basename "$abs_path"`
-  fi
-  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
-  ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target"
-  echo "--volume=\"$mount_source:$mount_target\""
-}
-function ViashDockerStripAutomount {
-  local abs_path=$(ViashAbsolutePath "$1")
-  echo "${abs_path#$VIASH_DOCKER_AUTOMOUNT_PREFIX}"
-}
-# initialise variables
-VIASH_DIRECTORY_MOUNTS=()
-
-# configure default docker automount prefix if it is unset
-if [ -z "${VIASH_DOCKER_AUTOMOUNT_PREFIX+x}" ]; then
-  VIASH_DOCKER_AUTOMOUNT_PREFIX="/viash_automount"
-fi
-
-# initialise docker variables
-VIASH_DOCKER_RUN_ARGS=(-i --rm)
-
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/star/star_align_reads/.config.vsh.yaml b/target/executable/star/star_align_reads/.config.vsh.yaml
index 3289059c..17a13890 100644
--- a/target/executable/star/star_align_reads/.config.vsh.yaml
+++ b/target/executable/star/star_align_reads/.config.vsh.yaml
@@ -2540,6 +2540,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -2662,16 +2665,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/star/star_align_reads"
   executable: "target/executable/star/star_align_reads/star_align_reads"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/star/star_align_reads/star_align_reads b/target/executable/star/star_align_reads/star_align_reads
index c650db18..f9e3d04b 100755
--- a/target/executable/star/star_align_reads/star_align_reads
+++ b/target/executable/star/star_align_reads/star_align_reads
@@ -2,7 +2,7 @@
 
 # star_align_reads main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -173,6 +173,426 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
+
+# initialise variables
+VIASH_MODE='run'
+VIASH_ENGINE_ID='docker'
+
+######## Helper functions for setting up Docker images for viash ########
+# expects: ViashDockerBuild
+
+# ViashDockerInstallationCheck: check whether Docker is installed correctly
+#
+# examples:
+#   ViashDockerInstallationCheck
+function ViashDockerInstallationCheck {
+  ViashDebug "Checking whether Docker is installed"
+  if [ ! command -v docker &> /dev/null ]; then
+    ViashCritical "Docker doesn't seem to be installed. See 'https://docs.docker.com/get-docker/' for instructions."
+    exit 1
+  fi
+
+  ViashDebug "Checking whether the Docker daemon is running"
+  local save=$-; set +e
+  local docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
+  local out=$?
+  [[ $save =~ e ]] && set -e
+  if [ $out -ne 0 ]; then
+    ViashCritical "Docker daemon does not seem to be running. Try one of the following:"
+    ViashCritical "- Try running 'dockerd' in the command line"
+    ViashCritical "- See https://docs.docker.com/config/daemon/"
+    exit 1
+  fi
+}
+
+# ViashDockerRemoteTagCheck: check whether a Docker image is available 
+# on a remote. Assumes `docker login` has been performed, if relevant.
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   ViashDockerRemoteTagCheck python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerRemoteTagCheck sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerRemoteTagCheck {
+  docker manifest inspect $1 > /dev/null 2> /dev/null
+}
+
+# ViashDockerLocalTagCheck: check whether a Docker image is available locally
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   docker pull python:latest
+#   ViashDockerLocalTagCheck python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerLocalTagCheck sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerLocalTagCheck {
+  [ -n "$(docker images -q $1)" ]
+}
+
+# ViashDockerPull: pull a Docker image
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   ViashDockerPull python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerPull sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerPull {
+  ViashNotice "Checking if Docker image is available at '$1'"
+  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
+    docker pull $1 && return 0 || return 1
+  else
+    local save=$-; set +e
+    docker pull $1 2> /dev/null > /dev/null
+    local out=$?
+    [[ $save =~ e ]] && set -e
+    if [ $out -ne 0 ]; then
+      ViashWarning "Could not pull from '$1'. Docker image doesn't exist or is not accessible."
+    fi
+    return $out
+  fi
+}
+
+# ViashDockerPush: push a Docker image
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   ViashDockerPush python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerPush sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerPush {
+  ViashNotice "Pushing image to '$1'"
+  local save=$-; set +e
+  local out
+  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
+    docker push $1
+    out=$?
+  else
+    docker push $1 2> /dev/null > /dev/null
+    out=$?
+  fi
+  [[ $save =~ e ]] && set -e
+  if [ $out -eq 0 ]; then
+    ViashNotice "Container '$1' push succeeded."
+  else
+    ViashError "Container '$1' push errored. You might not be logged in or have the necessary permissions."
+  fi
+  return $out
+}
+
+# ViashDockerPullElseBuild: pull a Docker image, else build it
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# ViashDockerBuild    : a Bash function which builds a docker image, takes image identifier as argument.
+# examples:
+#   ViashDockerPullElseBuild mynewcomponent
+function ViashDockerPullElseBuild {
+  local save=$-; set +e
+  ViashDockerPull $1
+  local out=$?
+  [[ $save =~ e ]] && set -e
+  if [ $out -ne 0 ]; then
+    ViashDockerBuild $@
+  fi
+}
+
+# ViashDockerSetup: create a Docker image, according to specified docker setup strategy
+#
+# $1          : image identifier with format `[registry/]image[:tag]`
+# $2          : docker setup strategy, see DockerSetupStrategy.scala
+# examples:
+#   ViashDockerSetup mynewcomponent alwaysbuild
+function ViashDockerSetup {
+  local image_id="$1"
+  local setup_strategy="$2"
+  if [ "$setup_strategy" == "alwaysbuild" -o "$setup_strategy" == "build" -o "$setup_strategy" == "b" ]; then
+    ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+  elif [ "$setup_strategy" == "alwayspull" -o "$setup_strategy" == "pull" -o "$setup_strategy" == "p" ]; then
+    ViashDockerPull $image_id
+  elif [ "$setup_strategy" == "alwayspullelsebuild" -o "$setup_strategy" == "pullelsebuild" ]; then
+    ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+  elif [ "$setup_strategy" == "alwayspullelsecachedbuild" -o "$setup_strategy" == "pullelsecachedbuild" ]; then
+    ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+  elif [ "$setup_strategy" == "alwayscachedbuild" -o "$setup_strategy" == "cachedbuild" -o "$setup_strategy" == "cb" ]; then
+    ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+  elif [[ "$setup_strategy" =~ ^ifneedbe ]]; then
+    local save=$-; set +e
+    ViashDockerLocalTagCheck $image_id
+    local outCheck=$?
+    [[ $save =~ e ]] && set -e
+    if [ $outCheck -eq 0 ]; then
+      ViashInfo "Image $image_id already exists"
+    elif [ "$setup_strategy" == "ifneedbebuild" ]; then
+      ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+    elif [ "$setup_strategy" == "ifneedbecachedbuild" ]; then
+      ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+    elif [ "$setup_strategy" == "ifneedbepull" ]; then
+      ViashDockerPull $image_id
+    elif [ "$setup_strategy" == "ifneedbepullelsebuild" ]; then
+      ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+    elif [ "$setup_strategy" == "ifneedbepullelsecachedbuild" ]; then
+      ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+    else
+      ViashError "Unrecognised Docker strategy: $setup_strategy"
+      exit 1
+    fi
+  elif [ "$setup_strategy" == "push" -o "$setup_strategy" == "forcepush" -o "$setup_strategy" == "alwayspush" ]; then
+    ViashDockerPush "$image_id"
+  elif [ "$setup_strategy" == "pushifnotpresent" -o "$setup_strategy" == "gentlepush" -o "$setup_strategy" == "maybepush" ]; then
+    local save=$-; set +e
+    ViashDockerRemoteTagCheck $image_id
+    local outCheck=$?
+    [[ $save =~ e ]] && set -e
+    if [ $outCheck -eq 0 ]; then
+      ViashNotice "Container '$image_id' exists, doing nothing."
+    else
+      ViashNotice "Container '$image_id' does not yet exist."
+      ViashDockerPush "$image_id"
+    fi
+  elif [ "$setup_strategy" == "donothing" -o "$setup_strategy" == "meh" ]; then
+    ViashNotice "Skipping setup."
+  else
+    ViashError "Unrecognised Docker strategy: $setup_strategy"
+    exit 1
+  fi
+}
+
+# ViashDockerCheckCommands: Check whether a docker container has the required commands
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# $@                  : commands to verify being present
+# examples:
+#   ViashDockerCheckCommands bash:4.0 bash ps foo
+function ViashDockerCheckCommands {
+  local image_id="$1"
+  shift 1
+  local commands="$@"
+  local save=$-; set +e
+  local missing # mark 'missing' as local in advance, otherwise the exit code of the command will be missing and always be '0'
+  missing=$(docker run --rm --entrypoint=sh "$image_id" -c "for command in $commands; do command -v \$command >/dev/null 2>&1; if [ \$? -ne 0 ]; then echo \$command; exit 1; fi; done")
+  local outCheck=$?
+  [[ $save =~ e ]] && set -e
+  if [ $outCheck -ne 0 ]; then
+  	ViashError "Docker container '$image_id' does not contain command '$missing'."
+  	exit 1
+  fi
+}
+
+# ViashDockerBuild: build a docker image
+# $1                               : image identifier with format `[registry/]image[:tag]`
+# $...                             : additional arguments to pass to docker build
+# $VIASH_META_TEMP_DIR             : temporary directory to store dockerfile & optional resources in
+# $VIASH_META_NAME                 : name of the component
+# $VIASH_META_RESOURCES_DIR        : directory containing the resources
+# $VIASH_VERBOSITY                 : verbosity level
+# exit code $?                     : whether or not the image was built successfully
+function ViashDockerBuild {
+  local image_id="$1"
+  shift 1
+
+  # create temporary directory to store dockerfile & optional resources in
+  local tmpdir=$(mktemp -d "$VIASH_META_TEMP_DIR/dockerbuild-$VIASH_META_NAME-XXXXXX")
+  local dockerfile="$tmpdir/Dockerfile"
+  function clean_up {
+    rm -rf "$tmpdir"
+  }
+  trap clean_up EXIT
+
+  # store dockerfile and resources
+  ViashDockerfile "$VIASH_ENGINE_ID" > "$dockerfile"
+
+  # generate the build command
+  local docker_build_cmd="docker build -t '$image_id' $@ '$VIASH_META_RESOURCES_DIR' -f '$dockerfile'"
+
+  # build the container
+  ViashNotice "Building container '$image_id' with Dockerfile"
+  ViashInfo "$docker_build_cmd"
+  local save=$-; set +e
+  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
+    eval $docker_build_cmd
+  else
+    eval $docker_build_cmd &> "$tmpdir/docker_build.log"
+  fi
+
+  # check exit code
+  local out=$?
+  [[ $save =~ e ]] && set -e
+  if [ $out -ne 0 ]; then
+    ViashError "Error occurred while building container '$image_id'"
+    if [ $VIASH_VERBOSITY -lt $VIASH_LOGCODE_INFO ]; then
+      ViashError "Transcript: --------------------------------"
+      cat "$tmpdir/docker_build.log"
+      ViashError "End of transcript --------------------------"
+    fi
+    exit 1
+  fi
+}
+
+######## End of helper functions for setting up Docker images for viash ########
+
+# ViashDockerFile: print the dockerfile to stdout
+# $1    : engine identifier
+# return : dockerfile required to run this component
+# examples:
+#   ViashDockerFile
+function ViashDockerfile {
+  local engine_id="$1"
+
+  if [[ "$engine_id" == "docker" ]]; then
+    cat << 'VIASHDOCKER'
+FROM python:3.12-slim
+ENTRYPOINT []
+RUN apt-get update && \
+  DEBIAN_FRONTEND=noninteractive apt-get install -y procps gzip bzip2 && \
+  rm -rf /var/lib/apt/lists/*
+
+ENV STAR_VERSION 2.7.11b
+ENV PACKAGES gcc g++ make wget zlib1g-dev unzip xxd
+RUN apt-get update && \
+  apt-get install -y --no-install-recommends ${PACKAGES} && \
+  cd /tmp && \
+  wget --no-check-certificate https://github.com/alexdobin/STAR/archive/refs/tags/${STAR_VERSION}.zip && \
+  unzip ${STAR_VERSION}.zip && \
+  cd STAR-${STAR_VERSION}/source && \
+  make STARstatic CXXFLAGS_SIMD=-std=c++11 && \
+  cp STAR /usr/local/bin && \
+  cd / && \
+  rm -rf /tmp/STAR-${STAR_VERSION} /tmp/${STAR_VERSION}.zip && \
+  apt-get --purge autoremove -y ${PACKAGES} && \
+  apt-get clean
+
+RUN pip install --upgrade pip && \
+  pip install --upgrade --no-cache-dir "pyyaml"
+
+RUN STAR --version | sed 's#\(.*\)#star: "\1"#' > /var/software_versions.txt
+
+LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Robrecht Cannoodt"
+LABEL org.opencontainers.image.description="Companion container for running component star star_align_reads"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:35Z"
+LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+LABEL org.opencontainers.image.version="main"
+
+VIASHDOCKER
+  fi
+}
+
+# ViashDockerBuildArgs: return the arguments to pass to docker build
+# $1    : engine identifier
+# return : arguments to pass to docker build
+function ViashDockerBuildArgs {
+  local engine_id="$1"
+
+  if [[ "$engine_id" == "docker" ]]; then
+    echo ""
+  fi
+}
+
+# ViashAbsolutePath: generate absolute path from relative path
+# borrowed from https://stackoverflow.com/a/21951256
+# $1     : relative filename
+# return : absolute path
+# examples:
+#   ViashAbsolutePath some_file.txt   # returns /path/to/some_file.txt
+#   ViashAbsolutePath /foo/bar/..     # returns /foo
+function ViashAbsolutePath {
+  local thePath
+  local parr
+  local outp
+  local len
+  if [[ ! "$1" =~ ^/ ]]; then
+    thePath="$PWD/$1"
+  else
+    thePath="$1"
+  fi
+  echo "$thePath" | (
+    IFS=/
+    read -a parr
+    declare -a outp
+    for i in "${parr[@]}"; do
+      case "$i" in
+      ''|.) continue ;;
+      ..)
+        len=${#outp[@]}
+        if ((len==0)); then
+          continue
+        else
+          unset outp[$((len-1))]
+        fi
+        ;;
+      *)
+        len=${#outp[@]}
+        outp[$len]="$i"
+      ;;
+      esac
+    done
+    echo /"${outp[*]}"
+  )
+}
+# ViashDockerAutodetectMount: auto configuring docker mounts from parameters
+# $1                             : The parameter value
+# returns                        : New parameter
+# $VIASH_DIRECTORY_MOUNTS        : Added another parameter to be passed to docker
+# $VIASH_DOCKER_AUTOMOUNT_PREFIX : The prefix to be used for the automounts
+# examples:
+#   ViashDockerAutodetectMount /path/to/bar      # returns '/viash_automount/path/to/bar'
+#   ViashDockerAutodetectMountArg /path/to/bar   # returns '--volume="/path/to:/viash_automount/path/to"'
+function ViashDockerAutodetectMount {
+  local abs_path=$(ViashAbsolutePath "$1")
+  local mount_source
+  local base_name
+  if [ -d "$abs_path" ]; then
+    mount_source="$abs_path"
+    base_name=""
+  else
+    mount_source=`dirname "$abs_path"`
+    base_name=`basename "$abs_path"`
+  fi
+  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
+  if [ -z "$base_name" ]; then
+    echo "$mount_target"
+  else
+    echo "$mount_target/$base_name"
+  fi
+}
+function ViashDockerAutodetectMountArg {
+  local abs_path=$(ViashAbsolutePath "$1")
+  local mount_source
+  local base_name
+  if [ -d "$abs_path" ]; then
+    mount_source="$abs_path"
+    base_name=""
+  else
+    mount_source=`dirname "$abs_path"`
+    base_name=`basename "$abs_path"`
+  fi
+  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
+  ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target"
+  echo "--volume=\"$mount_source:$mount_target\""
+}
+function ViashDockerStripAutomount {
+  local abs_path=$(ViashAbsolutePath "$1")
+  echo "${abs_path#$VIASH_DOCKER_AUTOMOUNT_PREFIX}"
+}
+# initialise variables
+VIASH_DIRECTORY_MOUNTS=()
+
+# configure default docker automount prefix if it is unset
+if [ -z "${VIASH_DOCKER_AUTOMOUNT_PREFIX+x}" ]; then
+  VIASH_DOCKER_AUTOMOUNT_PREFIX="/viash_automount"
+fi
+
+# initialise docker variables
+VIASH_DOCKER_RUN_ARGS=(-i --rm)
+
+
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
   echo "star_align_reads main"
@@ -1617,426 +2037,32 @@ function ViashHelp {
   echo "        The output file containing the alignments to transcriptome in BAM"
   echo "        formats. This file is generated when --quantMode is set to"
   echo "        TranscriptomeSAM."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
 }
 
-# initialise variables
-VIASH_MODE='run'
-VIASH_ENGINE_ID='docker'
-
-######## Helper functions for setting up Docker images for viash ########
-# expects: ViashDockerBuild
-
-# ViashDockerInstallationCheck: check whether Docker is installed correctly
-#
-# examples:
-#   ViashDockerInstallationCheck
-function ViashDockerInstallationCheck {
-  ViashDebug "Checking whether Docker is installed"
-  if [ ! command -v docker &> /dev/null ]; then
-    ViashCritical "Docker doesn't seem to be installed. See 'https://docs.docker.com/get-docker/' for instructions."
-    exit 1
-  fi
-
-  ViashDebug "Checking whether the Docker daemon is running"
-  local save=$-; set +e
-  local docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
-  local out=$?
-  [[ $save =~ e ]] && set -e
-  if [ $out -ne 0 ]; then
-    ViashCritical "Docker daemon does not seem to be running. Try one of the following:"
-    ViashCritical "- Try running 'dockerd' in the command line"
-    ViashCritical "- See https://docs.docker.com/config/daemon/"
-    exit 1
-  fi
-}
-
-# ViashDockerRemoteTagCheck: check whether a Docker image is available 
-# on a remote. Assumes `docker login` has been performed, if relevant.
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   ViashDockerRemoteTagCheck python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerRemoteTagCheck sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerRemoteTagCheck {
-  docker manifest inspect $1 > /dev/null 2> /dev/null
-}
-
-# ViashDockerLocalTagCheck: check whether a Docker image is available locally
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   docker pull python:latest
-#   ViashDockerLocalTagCheck python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerLocalTagCheck sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerLocalTagCheck {
-  [ -n "$(docker images -q $1)" ]
-}
-
-# ViashDockerPull: pull a Docker image
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   ViashDockerPull python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerPull sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerPull {
-  ViashNotice "Checking if Docker image is available at '$1'"
-  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
-    docker pull $1 && return 0 || return 1
-  else
-    local save=$-; set +e
-    docker pull $1 2> /dev/null > /dev/null
-    local out=$?
-    [[ $save =~ e ]] && set -e
-    if [ $out -ne 0 ]; then
-      ViashWarning "Could not pull from '$1'. Docker image doesn't exist or is not accessible."
-    fi
-    return $out
-  fi
-}
-
-# ViashDockerPush: push a Docker image
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   ViashDockerPush python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerPush sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerPush {
-  ViashNotice "Pushing image to '$1'"
-  local save=$-; set +e
-  local out
-  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
-    docker push $1
-    out=$?
-  else
-    docker push $1 2> /dev/null > /dev/null
-    out=$?
-  fi
-  [[ $save =~ e ]] && set -e
-  if [ $out -eq 0 ]; then
-    ViashNotice "Container '$1' push succeeded."
-  else
-    ViashError "Container '$1' push errored. You might not be logged in or have the necessary permissions."
-  fi
-  return $out
-}
-
-# ViashDockerPullElseBuild: pull a Docker image, else build it
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# ViashDockerBuild    : a Bash function which builds a docker image, takes image identifier as argument.
-# examples:
-#   ViashDockerPullElseBuild mynewcomponent
-function ViashDockerPullElseBuild {
-  local save=$-; set +e
-  ViashDockerPull $1
-  local out=$?
-  [[ $save =~ e ]] && set -e
-  if [ $out -ne 0 ]; then
-    ViashDockerBuild $@
-  fi
-}
-
-# ViashDockerSetup: create a Docker image, according to specified docker setup strategy
-#
-# $1          : image identifier with format `[registry/]image[:tag]`
-# $2          : docker setup strategy, see DockerSetupStrategy.scala
-# examples:
-#   ViashDockerSetup mynewcomponent alwaysbuild
-function ViashDockerSetup {
-  local image_id="$1"
-  local setup_strategy="$2"
-  if [ "$setup_strategy" == "alwaysbuild" -o "$setup_strategy" == "build" -o "$setup_strategy" == "b" ]; then
-    ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-  elif [ "$setup_strategy" == "alwayspull" -o "$setup_strategy" == "pull" -o "$setup_strategy" == "p" ]; then
-    ViashDockerPull $image_id
-  elif [ "$setup_strategy" == "alwayspullelsebuild" -o "$setup_strategy" == "pullelsebuild" ]; then
-    ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-  elif [ "$setup_strategy" == "alwayspullelsecachedbuild" -o "$setup_strategy" == "pullelsecachedbuild" ]; then
-    ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-  elif [ "$setup_strategy" == "alwayscachedbuild" -o "$setup_strategy" == "cachedbuild" -o "$setup_strategy" == "cb" ]; then
-    ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-  elif [[ "$setup_strategy" =~ ^ifneedbe ]]; then
-    local save=$-; set +e
-    ViashDockerLocalTagCheck $image_id
-    local outCheck=$?
-    [[ $save =~ e ]] && set -e
-    if [ $outCheck -eq 0 ]; then
-      ViashInfo "Image $image_id already exists"
-    elif [ "$setup_strategy" == "ifneedbebuild" ]; then
-      ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-    elif [ "$setup_strategy" == "ifneedbecachedbuild" ]; then
-      ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-    elif [ "$setup_strategy" == "ifneedbepull" ]; then
-      ViashDockerPull $image_id
-    elif [ "$setup_strategy" == "ifneedbepullelsebuild" ]; then
-      ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-    elif [ "$setup_strategy" == "ifneedbepullelsecachedbuild" ]; then
-      ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-    else
-      ViashError "Unrecognised Docker strategy: $setup_strategy"
-      exit 1
-    fi
-  elif [ "$setup_strategy" == "push" -o "$setup_strategy" == "forcepush" -o "$setup_strategy" == "alwayspush" ]; then
-    ViashDockerPush "$image_id"
-  elif [ "$setup_strategy" == "pushifnotpresent" -o "$setup_strategy" == "gentlepush" -o "$setup_strategy" == "maybepush" ]; then
-    local save=$-; set +e
-    ViashDockerRemoteTagCheck $image_id
-    local outCheck=$?
-    [[ $save =~ e ]] && set -e
-    if [ $outCheck -eq 0 ]; then
-      ViashNotice "Container '$image_id' exists, doing nothing."
-    else
-      ViashNotice "Container '$image_id' does not yet exist."
-      ViashDockerPush "$image_id"
-    fi
-  elif [ "$setup_strategy" == "donothing" -o "$setup_strategy" == "meh" ]; then
-    ViashNotice "Skipping setup."
-  else
-    ViashError "Unrecognised Docker strategy: $setup_strategy"
-    exit 1
-  fi
-}
-
-# ViashDockerCheckCommands: Check whether a docker container has the required commands
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# $@                  : commands to verify being present
-# examples:
-#   ViashDockerCheckCommands bash:4.0 bash ps foo
-function ViashDockerCheckCommands {
-  local image_id="$1"
-  shift 1
-  local commands="$@"
-  local save=$-; set +e
-  local missing # mark 'missing' as local in advance, otherwise the exit code of the command will be missing and always be '0'
-  missing=$(docker run --rm --entrypoint=sh "$image_id" -c "for command in $commands; do command -v \$command >/dev/null 2>&1; if [ \$? -ne 0 ]; then echo \$command; exit 1; fi; done")
-  local outCheck=$?
-  [[ $save =~ e ]] && set -e
-  if [ $outCheck -ne 0 ]; then
-  	ViashError "Docker container '$image_id' does not contain command '$missing'."
-  	exit 1
-  fi
-}
-
-# ViashDockerBuild: build a docker image
-# $1                               : image identifier with format `[registry/]image[:tag]`
-# $...                             : additional arguments to pass to docker build
-# $VIASH_META_TEMP_DIR             : temporary directory to store dockerfile & optional resources in
-# $VIASH_META_NAME                 : name of the component
-# $VIASH_META_RESOURCES_DIR        : directory containing the resources
-# $VIASH_VERBOSITY                 : verbosity level
-# exit code $?                     : whether or not the image was built successfully
-function ViashDockerBuild {
-  local image_id="$1"
-  shift 1
-
-  # create temporary directory to store dockerfile & optional resources in
-  local tmpdir=$(mktemp -d "$VIASH_META_TEMP_DIR/dockerbuild-$VIASH_META_NAME-XXXXXX")
-  local dockerfile="$tmpdir/Dockerfile"
-  function clean_up {
-    rm -rf "$tmpdir"
-  }
-  trap clean_up EXIT
-
-  # store dockerfile and resources
-  ViashDockerfile "$VIASH_ENGINE_ID" > "$dockerfile"
-
-  # generate the build command
-  local docker_build_cmd="docker build -t '$image_id' $@ '$VIASH_META_RESOURCES_DIR' -f '$dockerfile'"
-
-  # build the container
-  ViashNotice "Building container '$image_id' with Dockerfile"
-  ViashInfo "$docker_build_cmd"
-  local save=$-; set +e
-  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
-    eval $docker_build_cmd
-  else
-    eval $docker_build_cmd &> "$tmpdir/docker_build.log"
-  fi
-
-  # check exit code
-  local out=$?
-  [[ $save =~ e ]] && set -e
-  if [ $out -ne 0 ]; then
-    ViashError "Error occurred while building container '$image_id'"
-    if [ $VIASH_VERBOSITY -lt $VIASH_LOGCODE_INFO ]; then
-      ViashError "Transcript: --------------------------------"
-      cat "$tmpdir/docker_build.log"
-      ViashError "End of transcript --------------------------"
-    fi
-    exit 1
-  fi
-}
-
-######## End of helper functions for setting up Docker images for viash ########
-
-# ViashDockerFile: print the dockerfile to stdout
-# $1    : engine identifier
-# return : dockerfile required to run this component
-# examples:
-#   ViashDockerFile
-function ViashDockerfile {
-  local engine_id="$1"
-
-  if [[ "$engine_id" == "docker" ]]; then
-    cat << 'VIASHDOCKER'
-FROM python:3.12-slim
-ENTRYPOINT []
-RUN apt-get update && \
-  DEBIAN_FRONTEND=noninteractive apt-get install -y procps gzip bzip2 && \
-  rm -rf /var/lib/apt/lists/*
-
-ENV STAR_VERSION 2.7.11b
-ENV PACKAGES gcc g++ make wget zlib1g-dev unzip xxd
-RUN apt-get update && \
-  apt-get install -y --no-install-recommends ${PACKAGES} && \
-  cd /tmp && \
-  wget --no-check-certificate https://github.com/alexdobin/STAR/archive/refs/tags/${STAR_VERSION}.zip && \
-  unzip ${STAR_VERSION}.zip && \
-  cd STAR-${STAR_VERSION}/source && \
-  make STARstatic CXXFLAGS_SIMD=-std=c++11 && \
-  cp STAR /usr/local/bin && \
-  cd / && \
-  rm -rf /tmp/STAR-${STAR_VERSION} /tmp/${STAR_VERSION}.zip && \
-  apt-get --purge autoremove -y ${PACKAGES} && \
-  apt-get clean
-
-RUN pip install --upgrade pip && \
-  pip install --upgrade --no-cache-dir "pyyaml"
-
-RUN STAR --version | sed 's#\(.*\)#star: "\1"#' > /var/software_versions.txt
-
-LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Robrecht Cannoodt"
-LABEL org.opencontainers.image.description="Companion container for running component star star_align_reads"
-LABEL org.opencontainers.image.created="2024-12-03T10:33:54Z"
-LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-LABEL org.opencontainers.image.version="main"
-
-VIASHDOCKER
-  fi
-}
-
-# ViashDockerBuildArgs: return the arguments to pass to docker build
-# $1    : engine identifier
-# return : arguments to pass to docker build
-function ViashDockerBuildArgs {
-  local engine_id="$1"
-
-  if [[ "$engine_id" == "docker" ]]; then
-    echo ""
-  fi
-}
-
-# ViashAbsolutePath: generate absolute path from relative path
-# borrowed from https://stackoverflow.com/a/21951256
-# $1     : relative filename
-# return : absolute path
-# examples:
-#   ViashAbsolutePath some_file.txt   # returns /path/to/some_file.txt
-#   ViashAbsolutePath /foo/bar/..     # returns /foo
-function ViashAbsolutePath {
-  local thePath
-  local parr
-  local outp
-  local len
-  if [[ ! "$1" =~ ^/ ]]; then
-    thePath="$PWD/$1"
-  else
-    thePath="$1"
-  fi
-  echo "$thePath" | (
-    IFS=/
-    read -a parr
-    declare -a outp
-    for i in "${parr[@]}"; do
-      case "$i" in
-      ''|.) continue ;;
-      ..)
-        len=${#outp[@]}
-        if ((len==0)); then
-          continue
-        else
-          unset outp[$((len-1))]
-        fi
-        ;;
-      *)
-        len=${#outp[@]}
-        outp[$len]="$i"
-      ;;
-      esac
-    done
-    echo /"${outp[*]}"
-  )
-}
-# ViashDockerAutodetectMount: auto configuring docker mounts from parameters
-# $1                             : The parameter value
-# returns                        : New parameter
-# $VIASH_DIRECTORY_MOUNTS        : Added another parameter to be passed to docker
-# $VIASH_DOCKER_AUTOMOUNT_PREFIX : The prefix to be used for the automounts
-# examples:
-#   ViashDockerAutodetectMount /path/to/bar      # returns '/viash_automount/path/to/bar'
-#   ViashDockerAutodetectMountArg /path/to/bar   # returns '--volume="/path/to:/viash_automount/path/to"'
-function ViashDockerAutodetectMount {
-  local abs_path=$(ViashAbsolutePath "$1")
-  local mount_source
-  local base_name
-  if [ -d "$abs_path" ]; then
-    mount_source="$abs_path"
-    base_name=""
-  else
-    mount_source=`dirname "$abs_path"`
-    base_name=`basename "$abs_path"`
-  fi
-  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
-  if [ -z "$base_name" ]; then
-    echo "$mount_target"
-  else
-    echo "$mount_target/$base_name"
-  fi
-}
-function ViashDockerAutodetectMountArg {
-  local abs_path=$(ViashAbsolutePath "$1")
-  local mount_source
-  local base_name
-  if [ -d "$abs_path" ]; then
-    mount_source="$abs_path"
-    base_name=""
-  else
-    mount_source=`dirname "$abs_path"`
-    base_name=`basename "$abs_path"`
-  fi
-  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
-  ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target"
-  echo "--volume=\"$mount_source:$mount_target\""
-}
-function ViashDockerStripAutomount {
-  local abs_path=$(ViashAbsolutePath "$1")
-  echo "${abs_path#$VIASH_DOCKER_AUTOMOUNT_PREFIX}"
-}
-# initialise variables
-VIASH_DIRECTORY_MOUNTS=()
-
-# configure default docker automount prefix if it is unset
-if [ -z "${VIASH_DOCKER_AUTOMOUNT_PREFIX+x}" ]; then
-  VIASH_DOCKER_AUTOMOUNT_PREFIX="/viash_automount"
-fi
-
-# initialise docker variables
-VIASH_DOCKER_RUN_ARGS=(-i --rm)
-
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/star/star_genome_generate/.config.vsh.yaml b/target/executable/star/star_genome_generate/.config.vsh.yaml
index caf1333c..13a918a9 100644
--- a/target/executable/star/star_genome_generate/.config.vsh.yaml
+++ b/target/executable/star/star_genome_generate/.config.vsh.yaml
@@ -221,6 +221,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -332,16 +335,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/star/star_genome_generate"
   executable: "target/executable/star/star_genome_generate/star_genome_generate"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/star/star_genome_generate/star_genome_generate b/target/executable/star/star_genome_generate/star_genome_generate
index 6e1f62a4..fefdf299 100755
--- a/target/executable/star/star_genome_generate/star_genome_generate
+++ b/target/executable/star/star_genome_generate/star_genome_generate
@@ -2,7 +2,7 @@
 
 # star_genome_generate main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,116 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "star_genome_generate main"
-  echo ""
-  echo "Create index for STAR"
-  echo ""
-  echo "Input:"
-  echo "    --genome_fasta_files"
-  echo "        type: file, required parameter, multiple values allowed, file must exist"
-  echo "        Path(s) to the fasta files with the genome sequences, separated by"
-  echo "        spaces. These files should be plain text FASTA files, they *cannot* be"
-  echo "        zipped."
-  echo ""
-  echo "    --sjdb_gtf_file"
-  echo "        type: file, file must exist"
-  echo "        Path to the GTF file with annotations"
-  echo ""
-  echo "    --sjdb_overhang"
-  echo "        type: integer"
-  echo "        example: 100"
-  echo "        Length of the donor/acceptor sequence on each side of the junctions,"
-  echo "        ideally = (mate_length - 1)"
-  echo ""
-  echo "    --sjdb_gtf_chr_prefix"
-  echo "        type: string"
-  echo "        Prefix for chromosome names in a GTF file (e.g. 'chr' for using ENSMEBL"
-  echo "        annotations with UCSC genomes)"
-  echo ""
-  echo "    --sjdb_gtf_feature_exon"
-  echo "        type: string"
-  echo "        example: exon"
-  echo "        Feature type in GTF file to be used as exons for building transcripts"
-  echo ""
-  echo "    --sjdb_gtf_tag_exon_parent_transcript"
-  echo "        type: string"
-  echo "        example: transcript_id"
-  echo "        GTF attribute name for parent transcript ID (default \"transcript_id\""
-  echo "        works for GTF files)"
-  echo ""
-  echo "    --sjdb_gtf_tag_exon_parent_gene"
-  echo "        type: string"
-  echo "        example: gene_id"
-  echo "        GTF attribute name for parent gene ID (default \"gene_id\" works for GTF"
-  echo "        files)"
-  echo ""
-  echo "    --sjdb_gtf_tag_exon_parent_gene_name"
-  echo "        type: string, multiple values allowed"
-  echo "        example: gene_name"
-  echo "        GTF attribute name for parent gene name"
-  echo ""
-  echo "    --sjdb_gtf_tag_exon_parent_gene_type"
-  echo "        type: string, multiple values allowed"
-  echo "        example: gene_type;gene_biotype"
-  echo "        GTF attribute name for parent gene type"
-  echo ""
-  echo "    --limit_genome_generate_ram"
-  echo "        type: long"
-  echo "        example: 31000000000"
-  echo "        Maximum available RAM (bytes) for genome generation"
-  echo ""
-  echo "    --genome_sa_index_nbases"
-  echo "        type: integer"
-  echo "        example: 14"
-  echo "        Length (bases) of the SA pre-indexing string. Typically between 10 and"
-  echo "        15. Longer strings will use much more memory, but allow faster searches."
-  echo "        For small genomes, this parameter must be scaled down to min(14,"
-  echo "        log2(GenomeLength)/2 - 1)."
-  echo ""
-  echo "    --genome_chr_bin_nbits"
-  echo "        type: integer"
-  echo "        example: 18"
-  echo "        Defined as log2(chrBin), where chrBin is the size of the bins for genome"
-  echo "        storage. Each chromosome will occupy an integer number of bins. For a"
-  echo "        genome with large number of contigs, it is recommended to scale this"
-  echo "        parameter as min(18,"
-  echo "        log2[max(GenomeLength/NumberOfReferences,ReadLength)])."
-  echo ""
-  echo "    --genome_sa_sparse_d"
-  echo "        type: integer"
-  echo "        example: 1"
-  echo "        min: 0"
-  echo "        Suffux array sparsity, i.e. distance between indices. Use bigger numbers"
-  echo "        to decrease needed RAM at the cost of mapping speed reduction."
-  echo ""
-  echo "    --genome_suffix_length_max"
-  echo "        type: integer"
-  echo "        example: -1"
-  echo "        Maximum length of the suffixes, has to be longer than read length. Use"
-  echo "        -1 for infinite length."
-  echo ""
-  echo "    --genome_transform_type"
-  echo "        type: string"
-  echo "        example: None"
-  echo "        Type of genome transformation"
-  echo "          None       ... no transformation"
-  echo "          Haploid    ... replace reference alleles with alternative alleles from"
-  echo "        VCF file (e.g. consensus allele)"
-  echo "          Diploid    ... create two haplotypes for each chromosome listed in VCF"
-  echo "        file, for genotypes 1|2, assumes perfect phasing (e.g. personal genome)"
-  echo ""
-  echo "    --genome_transform_vcf"
-  echo "        type: file, file must exist"
-  echo "        path to VCF file for genome transformation"
-  echo ""
-  echo "Output:"
-  echo "    --index"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        default: STAR_index"
-  echo "        STAR index directory."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -577,9 +467,9 @@ RUN STAR --version | sed 's#\(.*\)#star: "\1"#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
 LABEL org.opencontainers.image.description="Companion container for running component star star_genome_generate"
-LABEL org.opencontainers.image.created="2024-12-03T10:33:55Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:36Z"
 LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -694,6 +584,142 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "star_genome_generate main"
+  echo ""
+  echo "Create index for STAR"
+  echo ""
+  echo "Input:"
+  echo "    --genome_fasta_files"
+  echo "        type: file, required parameter, multiple values allowed, file must exist"
+  echo "        Path(s) to the fasta files with the genome sequences, separated by"
+  echo "        spaces. These files should be plain text FASTA files, they *cannot* be"
+  echo "        zipped."
+  echo ""
+  echo "    --sjdb_gtf_file"
+  echo "        type: file, file must exist"
+  echo "        Path to the GTF file with annotations"
+  echo ""
+  echo "    --sjdb_overhang"
+  echo "        type: integer"
+  echo "        example: 100"
+  echo "        Length of the donor/acceptor sequence on each side of the junctions,"
+  echo "        ideally = (mate_length - 1)"
+  echo ""
+  echo "    --sjdb_gtf_chr_prefix"
+  echo "        type: string"
+  echo "        Prefix for chromosome names in a GTF file (e.g. 'chr' for using ENSMEBL"
+  echo "        annotations with UCSC genomes)"
+  echo ""
+  echo "    --sjdb_gtf_feature_exon"
+  echo "        type: string"
+  echo "        example: exon"
+  echo "        Feature type in GTF file to be used as exons for building transcripts"
+  echo ""
+  echo "    --sjdb_gtf_tag_exon_parent_transcript"
+  echo "        type: string"
+  echo "        example: transcript_id"
+  echo "        GTF attribute name for parent transcript ID (default \"transcript_id\""
+  echo "        works for GTF files)"
+  echo ""
+  echo "    --sjdb_gtf_tag_exon_parent_gene"
+  echo "        type: string"
+  echo "        example: gene_id"
+  echo "        GTF attribute name for parent gene ID (default \"gene_id\" works for GTF"
+  echo "        files)"
+  echo ""
+  echo "    --sjdb_gtf_tag_exon_parent_gene_name"
+  echo "        type: string, multiple values allowed"
+  echo "        example: gene_name"
+  echo "        GTF attribute name for parent gene name"
+  echo ""
+  echo "    --sjdb_gtf_tag_exon_parent_gene_type"
+  echo "        type: string, multiple values allowed"
+  echo "        example: gene_type;gene_biotype"
+  echo "        GTF attribute name for parent gene type"
+  echo ""
+  echo "    --limit_genome_generate_ram"
+  echo "        type: long"
+  echo "        example: 31000000000"
+  echo "        Maximum available RAM (bytes) for genome generation"
+  echo ""
+  echo "    --genome_sa_index_nbases"
+  echo "        type: integer"
+  echo "        example: 14"
+  echo "        Length (bases) of the SA pre-indexing string. Typically between 10 and"
+  echo "        15. Longer strings will use much more memory, but allow faster searches."
+  echo "        For small genomes, this parameter must be scaled down to min(14,"
+  echo "        log2(GenomeLength)/2 - 1)."
+  echo ""
+  echo "    --genome_chr_bin_nbits"
+  echo "        type: integer"
+  echo "        example: 18"
+  echo "        Defined as log2(chrBin), where chrBin is the size of the bins for genome"
+  echo "        storage. Each chromosome will occupy an integer number of bins. For a"
+  echo "        genome with large number of contigs, it is recommended to scale this"
+  echo "        parameter as min(18,"
+  echo "        log2[max(GenomeLength/NumberOfReferences,ReadLength)])."
+  echo ""
+  echo "    --genome_sa_sparse_d"
+  echo "        type: integer"
+  echo "        example: 1"
+  echo "        min: 0"
+  echo "        Suffux array sparsity, i.e. distance between indices. Use bigger numbers"
+  echo "        to decrease needed RAM at the cost of mapping speed reduction."
+  echo ""
+  echo "    --genome_suffix_length_max"
+  echo "        type: integer"
+  echo "        example: -1"
+  echo "        Maximum length of the suffixes, has to be longer than read length. Use"
+  echo "        -1 for infinite length."
+  echo ""
+  echo "    --genome_transform_type"
+  echo "        type: string"
+  echo "        example: None"
+  echo "        Type of genome transformation"
+  echo "          None       ... no transformation"
+  echo "          Haploid    ... replace reference alleles with alternative alleles from"
+  echo "        VCF file (e.g. consensus allele)"
+  echo "          Diploid    ... create two haplotypes for each chromosome listed in VCF"
+  echo "        file, for genotypes 1|2, assumes perfect phasing (e.g. personal genome)"
+  echo ""
+  echo "    --genome_transform_vcf"
+  echo "        type: file, file must exist"
+  echo "        path to VCF file for genome transformation"
+  echo ""
+  echo "Output:"
+  echo "    --index"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        default: STAR_index"
+  echo "        STAR index directory."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
@@ -1429,10 +1455,10 @@ STAR \\
     \${par_genome_sa_index_nbases:+--genomeSAindexNbases "\${par_genome_sa_index_nbases}"} \\
     \${par_sjdb_gtf_chr_prefix:+--sjdbGTFchrPrefix "\${par_sjdb_gtf_chr_prefix}"} \\
     \${par_sjdb_gtf_feature_exon:+--sjdbGTFfeatureExon "\${par_sjdb_gtf_feature_exon}"} \\
-    \${par_sjdb_gtf_tag_exon_parent_transcript:+--sjdbGTFtag_exon_parent_transcript "\${par_sjdb_gtf_tag_exon_parent_transcript}"} \\
-    \${par_sjdb_gtf_tag_exon_parent_gene:+--sjdbGTFtag_exon_parent_gene "\${par_sjdb_gtf_tag_exon_parent_gene}"} \\
-    \${par_sjdb_gtf_tag_exon_parent_geneName:+--sjdbGTFtag_exon_parent_geneName "\${par_sjdb_gtf_tag_exon_parent_geneName}"} \\
-    \${par_sjdb_gtf_tag_exon_parent_geneType:+--sjdbGTFtag_exon_parent_geneType "\${sjdbGTFtag_exon_parent_geneType}"} \\
+    \${par_sjdb_gtf_tag_exon_parent_transcript:+--sjdbGTFtagExonParentTranscript "\${par_sjdb_gtf_tag_exon_parent_transcript}"} \\
+    \${par_sjdb_gtf_tag_exon_parent_gene:+--sjdbGTFtagExonParentGene "\${par_sjdb_gtf_tag_exon_parent_gene}"} \\
+    \${sjdb_gtf_tag_exon_parent_gene_name:+--sjdbGTFtagExonParentGeneName "\${sjdb_gtf_tag_exon_parent_gene_name}"} \\
+    \${sjdb_gtf_tag_exon_parent_gene_type:+--sjdbGTFtagExonParentGeneType "\${sjdb_gtf_tag_exon_parent_gene_type}"} \\
     \${par_limit_genome_generate_ram:+--limitGenomeGenerateRAM "\${par_limit_genome_generate_ram}"} \\
     \${par_genome_chr_bin_nbits:+--genomeChrBinNbits "\${par_genome_chr_bin_nbits}"} \\
     \${par_genome_sa_sparse_d:+--genomeSAsparseD "\${par_genome_sa_sparse_d}"} \\
diff --git a/target/executable/trimgalore/.config.vsh.yaml b/target/executable/trimgalore/.config.vsh.yaml
index 8d9beabd..d13aeff1 100644
--- a/target/executable/trimgalore/.config.vsh.yaml
+++ b/target/executable/trimgalore/.config.vsh.yaml
@@ -668,6 +668,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -769,16 +772,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/trimgalore"
   executable: "target/executable/trimgalore/trimgalore"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/trimgalore/trimgalore b/target/executable/trimgalore/trimgalore
index ab00133c..6f72b107 100755
--- a/target/executable/trimgalore/trimgalore
+++ b/target/executable/trimgalore/trimgalore
@@ -2,7 +2,7 @@
 
 # trimgalore main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,6 +172,404 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
+
+# initialise variables
+VIASH_MODE='run'
+VIASH_ENGINE_ID='docker'
+
+######## Helper functions for setting up Docker images for viash ########
+# expects: ViashDockerBuild
+
+# ViashDockerInstallationCheck: check whether Docker is installed correctly
+#
+# examples:
+#   ViashDockerInstallationCheck
+function ViashDockerInstallationCheck {
+  ViashDebug "Checking whether Docker is installed"
+  if [ ! command -v docker &> /dev/null ]; then
+    ViashCritical "Docker doesn't seem to be installed. See 'https://docs.docker.com/get-docker/' for instructions."
+    exit 1
+  fi
+
+  ViashDebug "Checking whether the Docker daemon is running"
+  local save=$-; set +e
+  local docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
+  local out=$?
+  [[ $save =~ e ]] && set -e
+  if [ $out -ne 0 ]; then
+    ViashCritical "Docker daemon does not seem to be running. Try one of the following:"
+    ViashCritical "- Try running 'dockerd' in the command line"
+    ViashCritical "- See https://docs.docker.com/config/daemon/"
+    exit 1
+  fi
+}
+
+# ViashDockerRemoteTagCheck: check whether a Docker image is available 
+# on a remote. Assumes `docker login` has been performed, if relevant.
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   ViashDockerRemoteTagCheck python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerRemoteTagCheck sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerRemoteTagCheck {
+  docker manifest inspect $1 > /dev/null 2> /dev/null
+}
+
+# ViashDockerLocalTagCheck: check whether a Docker image is available locally
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   docker pull python:latest
+#   ViashDockerLocalTagCheck python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerLocalTagCheck sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerLocalTagCheck {
+  [ -n "$(docker images -q $1)" ]
+}
+
+# ViashDockerPull: pull a Docker image
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   ViashDockerPull python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerPull sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerPull {
+  ViashNotice "Checking if Docker image is available at '$1'"
+  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
+    docker pull $1 && return 0 || return 1
+  else
+    local save=$-; set +e
+    docker pull $1 2> /dev/null > /dev/null
+    local out=$?
+    [[ $save =~ e ]] && set -e
+    if [ $out -ne 0 ]; then
+      ViashWarning "Could not pull from '$1'. Docker image doesn't exist or is not accessible."
+    fi
+    return $out
+  fi
+}
+
+# ViashDockerPush: push a Docker image
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   ViashDockerPush python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerPush sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerPush {
+  ViashNotice "Pushing image to '$1'"
+  local save=$-; set +e
+  local out
+  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
+    docker push $1
+    out=$?
+  else
+    docker push $1 2> /dev/null > /dev/null
+    out=$?
+  fi
+  [[ $save =~ e ]] && set -e
+  if [ $out -eq 0 ]; then
+    ViashNotice "Container '$1' push succeeded."
+  else
+    ViashError "Container '$1' push errored. You might not be logged in or have the necessary permissions."
+  fi
+  return $out
+}
+
+# ViashDockerPullElseBuild: pull a Docker image, else build it
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# ViashDockerBuild    : a Bash function which builds a docker image, takes image identifier as argument.
+# examples:
+#   ViashDockerPullElseBuild mynewcomponent
+function ViashDockerPullElseBuild {
+  local save=$-; set +e
+  ViashDockerPull $1
+  local out=$?
+  [[ $save =~ e ]] && set -e
+  if [ $out -ne 0 ]; then
+    ViashDockerBuild $@
+  fi
+}
+
+# ViashDockerSetup: create a Docker image, according to specified docker setup strategy
+#
+# $1          : image identifier with format `[registry/]image[:tag]`
+# $2          : docker setup strategy, see DockerSetupStrategy.scala
+# examples:
+#   ViashDockerSetup mynewcomponent alwaysbuild
+function ViashDockerSetup {
+  local image_id="$1"
+  local setup_strategy="$2"
+  if [ "$setup_strategy" == "alwaysbuild" -o "$setup_strategy" == "build" -o "$setup_strategy" == "b" ]; then
+    ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+  elif [ "$setup_strategy" == "alwayspull" -o "$setup_strategy" == "pull" -o "$setup_strategy" == "p" ]; then
+    ViashDockerPull $image_id
+  elif [ "$setup_strategy" == "alwayspullelsebuild" -o "$setup_strategy" == "pullelsebuild" ]; then
+    ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+  elif [ "$setup_strategy" == "alwayspullelsecachedbuild" -o "$setup_strategy" == "pullelsecachedbuild" ]; then
+    ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+  elif [ "$setup_strategy" == "alwayscachedbuild" -o "$setup_strategy" == "cachedbuild" -o "$setup_strategy" == "cb" ]; then
+    ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+  elif [[ "$setup_strategy" =~ ^ifneedbe ]]; then
+    local save=$-; set +e
+    ViashDockerLocalTagCheck $image_id
+    local outCheck=$?
+    [[ $save =~ e ]] && set -e
+    if [ $outCheck -eq 0 ]; then
+      ViashInfo "Image $image_id already exists"
+    elif [ "$setup_strategy" == "ifneedbebuild" ]; then
+      ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+    elif [ "$setup_strategy" == "ifneedbecachedbuild" ]; then
+      ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+    elif [ "$setup_strategy" == "ifneedbepull" ]; then
+      ViashDockerPull $image_id
+    elif [ "$setup_strategy" == "ifneedbepullelsebuild" ]; then
+      ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+    elif [ "$setup_strategy" == "ifneedbepullelsecachedbuild" ]; then
+      ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+    else
+      ViashError "Unrecognised Docker strategy: $setup_strategy"
+      exit 1
+    fi
+  elif [ "$setup_strategy" == "push" -o "$setup_strategy" == "forcepush" -o "$setup_strategy" == "alwayspush" ]; then
+    ViashDockerPush "$image_id"
+  elif [ "$setup_strategy" == "pushifnotpresent" -o "$setup_strategy" == "gentlepush" -o "$setup_strategy" == "maybepush" ]; then
+    local save=$-; set +e
+    ViashDockerRemoteTagCheck $image_id
+    local outCheck=$?
+    [[ $save =~ e ]] && set -e
+    if [ $outCheck -eq 0 ]; then
+      ViashNotice "Container '$image_id' exists, doing nothing."
+    else
+      ViashNotice "Container '$image_id' does not yet exist."
+      ViashDockerPush "$image_id"
+    fi
+  elif [ "$setup_strategy" == "donothing" -o "$setup_strategy" == "meh" ]; then
+    ViashNotice "Skipping setup."
+  else
+    ViashError "Unrecognised Docker strategy: $setup_strategy"
+    exit 1
+  fi
+}
+
+# ViashDockerCheckCommands: Check whether a docker container has the required commands
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# $@                  : commands to verify being present
+# examples:
+#   ViashDockerCheckCommands bash:4.0 bash ps foo
+function ViashDockerCheckCommands {
+  local image_id="$1"
+  shift 1
+  local commands="$@"
+  local save=$-; set +e
+  local missing # mark 'missing' as local in advance, otherwise the exit code of the command will be missing and always be '0'
+  missing=$(docker run --rm --entrypoint=sh "$image_id" -c "for command in $commands; do command -v \$command >/dev/null 2>&1; if [ \$? -ne 0 ]; then echo \$command; exit 1; fi; done")
+  local outCheck=$?
+  [[ $save =~ e ]] && set -e
+  if [ $outCheck -ne 0 ]; then
+  	ViashError "Docker container '$image_id' does not contain command '$missing'."
+  	exit 1
+  fi
+}
+
+# ViashDockerBuild: build a docker image
+# $1                               : image identifier with format `[registry/]image[:tag]`
+# $...                             : additional arguments to pass to docker build
+# $VIASH_META_TEMP_DIR             : temporary directory to store dockerfile & optional resources in
+# $VIASH_META_NAME                 : name of the component
+# $VIASH_META_RESOURCES_DIR        : directory containing the resources
+# $VIASH_VERBOSITY                 : verbosity level
+# exit code $?                     : whether or not the image was built successfully
+function ViashDockerBuild {
+  local image_id="$1"
+  shift 1
+
+  # create temporary directory to store dockerfile & optional resources in
+  local tmpdir=$(mktemp -d "$VIASH_META_TEMP_DIR/dockerbuild-$VIASH_META_NAME-XXXXXX")
+  local dockerfile="$tmpdir/Dockerfile"
+  function clean_up {
+    rm -rf "$tmpdir"
+  }
+  trap clean_up EXIT
+
+  # store dockerfile and resources
+  ViashDockerfile "$VIASH_ENGINE_ID" > "$dockerfile"
+
+  # generate the build command
+  local docker_build_cmd="docker build -t '$image_id' $@ '$VIASH_META_RESOURCES_DIR' -f '$dockerfile'"
+
+  # build the container
+  ViashNotice "Building container '$image_id' with Dockerfile"
+  ViashInfo "$docker_build_cmd"
+  local save=$-; set +e
+  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
+    eval $docker_build_cmd
+  else
+    eval $docker_build_cmd &> "$tmpdir/docker_build.log"
+  fi
+
+  # check exit code
+  local out=$?
+  [[ $save =~ e ]] && set -e
+  if [ $out -ne 0 ]; then
+    ViashError "Error occurred while building container '$image_id'"
+    if [ $VIASH_VERBOSITY -lt $VIASH_LOGCODE_INFO ]; then
+      ViashError "Transcript: --------------------------------"
+      cat "$tmpdir/docker_build.log"
+      ViashError "End of transcript --------------------------"
+    fi
+    exit 1
+  fi
+}
+
+######## End of helper functions for setting up Docker images for viash ########
+
+# ViashDockerFile: print the dockerfile to stdout
+# $1    : engine identifier
+# return : dockerfile required to run this component
+# examples:
+#   ViashDockerFile
+function ViashDockerfile {
+  local engine_id="$1"
+
+  if [[ "$engine_id" == "docker" ]]; then
+    cat << 'VIASHDOCKER'
+FROM quay.io/biocontainers/trim-galore:0.6.10--hdfd78af_0
+ENTRYPOINT []
+RUN echo "TrimGalore: `trim_galore --version | sed -n 's/.*version\s\+\([0-9]\+\.[0-9]\+\.[0-9]\+\).*/\1/p'`" > /var/software_versions.txt
+
+LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
+LABEL org.opencontainers.image.description="Companion container for running component trimgalore"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:36Z"
+LABEL org.opencontainers.image.source="https://github.com/FelixKrueger/TrimGalore"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+LABEL org.opencontainers.image.version="main"
+
+VIASHDOCKER
+  fi
+}
+
+# ViashDockerBuildArgs: return the arguments to pass to docker build
+# $1    : engine identifier
+# return : arguments to pass to docker build
+function ViashDockerBuildArgs {
+  local engine_id="$1"
+
+  if [[ "$engine_id" == "docker" ]]; then
+    echo ""
+  fi
+}
+
+# ViashAbsolutePath: generate absolute path from relative path
+# borrowed from https://stackoverflow.com/a/21951256
+# $1     : relative filename
+# return : absolute path
+# examples:
+#   ViashAbsolutePath some_file.txt   # returns /path/to/some_file.txt
+#   ViashAbsolutePath /foo/bar/..     # returns /foo
+function ViashAbsolutePath {
+  local thePath
+  local parr
+  local outp
+  local len
+  if [[ ! "$1" =~ ^/ ]]; then
+    thePath="$PWD/$1"
+  else
+    thePath="$1"
+  fi
+  echo "$thePath" | (
+    IFS=/
+    read -a parr
+    declare -a outp
+    for i in "${parr[@]}"; do
+      case "$i" in
+      ''|.) continue ;;
+      ..)
+        len=${#outp[@]}
+        if ((len==0)); then
+          continue
+        else
+          unset outp[$((len-1))]
+        fi
+        ;;
+      *)
+        len=${#outp[@]}
+        outp[$len]="$i"
+      ;;
+      esac
+    done
+    echo /"${outp[*]}"
+  )
+}
+# ViashDockerAutodetectMount: auto configuring docker mounts from parameters
+# $1                             : The parameter value
+# returns                        : New parameter
+# $VIASH_DIRECTORY_MOUNTS        : Added another parameter to be passed to docker
+# $VIASH_DOCKER_AUTOMOUNT_PREFIX : The prefix to be used for the automounts
+# examples:
+#   ViashDockerAutodetectMount /path/to/bar      # returns '/viash_automount/path/to/bar'
+#   ViashDockerAutodetectMountArg /path/to/bar   # returns '--volume="/path/to:/viash_automount/path/to"'
+function ViashDockerAutodetectMount {
+  local abs_path=$(ViashAbsolutePath "$1")
+  local mount_source
+  local base_name
+  if [ -d "$abs_path" ]; then
+    mount_source="$abs_path"
+    base_name=""
+  else
+    mount_source=`dirname "$abs_path"`
+    base_name=`basename "$abs_path"`
+  fi
+  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
+  if [ -z "$base_name" ]; then
+    echo "$mount_target"
+  else
+    echo "$mount_target/$base_name"
+  fi
+}
+function ViashDockerAutodetectMountArg {
+  local abs_path=$(ViashAbsolutePath "$1")
+  local mount_source
+  local base_name
+  if [ -d "$abs_path" ]; then
+    mount_source="$abs_path"
+    base_name=""
+  else
+    mount_source=`dirname "$abs_path"`
+    base_name=`basename "$abs_path"`
+  fi
+  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
+  ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target"
+  echo "--volume=\"$mount_source:$mount_target\""
+}
+function ViashDockerStripAutomount {
+  local abs_path=$(ViashAbsolutePath "$1")
+  echo "${abs_path#$VIASH_DOCKER_AUTOMOUNT_PREFIX}"
+}
+# initialise variables
+VIASH_DIRECTORY_MOUNTS=()
+
+# configure default docker automount prefix if it is unset
+if [ -z "${VIASH_DOCKER_AUTOMOUNT_PREFIX+x}" ]; then
+  VIASH_DOCKER_AUTOMOUNT_PREFIX="/viash_automount"
+fi
+
+# initialise docker variables
+VIASH_DOCKER_RUN_ARGS=(-i --rm)
+
+
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
   echo "trimgalore main"
@@ -600,404 +998,32 @@ function ViashHelp {
   echo "        example: unpaired_read_2.fastq"
   echo "        Output file for unpaired read 2. Only works when 1 file (single-end) or"
   echo "        2 files (paired-end) are specified, but not for longer lists."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
 }
 
-# initialise variables
-VIASH_MODE='run'
-VIASH_ENGINE_ID='docker'
-
-######## Helper functions for setting up Docker images for viash ########
-# expects: ViashDockerBuild
-
-# ViashDockerInstallationCheck: check whether Docker is installed correctly
-#
-# examples:
-#   ViashDockerInstallationCheck
-function ViashDockerInstallationCheck {
-  ViashDebug "Checking whether Docker is installed"
-  if [ ! command -v docker &> /dev/null ]; then
-    ViashCritical "Docker doesn't seem to be installed. See 'https://docs.docker.com/get-docker/' for instructions."
-    exit 1
-  fi
-
-  ViashDebug "Checking whether the Docker daemon is running"
-  local save=$-; set +e
-  local docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
-  local out=$?
-  [[ $save =~ e ]] && set -e
-  if [ $out -ne 0 ]; then
-    ViashCritical "Docker daemon does not seem to be running. Try one of the following:"
-    ViashCritical "- Try running 'dockerd' in the command line"
-    ViashCritical "- See https://docs.docker.com/config/daemon/"
-    exit 1
-  fi
-}
-
-# ViashDockerRemoteTagCheck: check whether a Docker image is available 
-# on a remote. Assumes `docker login` has been performed, if relevant.
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   ViashDockerRemoteTagCheck python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerRemoteTagCheck sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerRemoteTagCheck {
-  docker manifest inspect $1 > /dev/null 2> /dev/null
-}
-
-# ViashDockerLocalTagCheck: check whether a Docker image is available locally
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   docker pull python:latest
-#   ViashDockerLocalTagCheck python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerLocalTagCheck sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerLocalTagCheck {
-  [ -n "$(docker images -q $1)" ]
-}
-
-# ViashDockerPull: pull a Docker image
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   ViashDockerPull python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerPull sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerPull {
-  ViashNotice "Checking if Docker image is available at '$1'"
-  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
-    docker pull $1 && return 0 || return 1
-  else
-    local save=$-; set +e
-    docker pull $1 2> /dev/null > /dev/null
-    local out=$?
-    [[ $save =~ e ]] && set -e
-    if [ $out -ne 0 ]; then
-      ViashWarning "Could not pull from '$1'. Docker image doesn't exist or is not accessible."
-    fi
-    return $out
-  fi
-}
-
-# ViashDockerPush: push a Docker image
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   ViashDockerPush python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerPush sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerPush {
-  ViashNotice "Pushing image to '$1'"
-  local save=$-; set +e
-  local out
-  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
-    docker push $1
-    out=$?
-  else
-    docker push $1 2> /dev/null > /dev/null
-    out=$?
-  fi
-  [[ $save =~ e ]] && set -e
-  if [ $out -eq 0 ]; then
-    ViashNotice "Container '$1' push succeeded."
-  else
-    ViashError "Container '$1' push errored. You might not be logged in or have the necessary permissions."
-  fi
-  return $out
-}
-
-# ViashDockerPullElseBuild: pull a Docker image, else build it
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# ViashDockerBuild    : a Bash function which builds a docker image, takes image identifier as argument.
-# examples:
-#   ViashDockerPullElseBuild mynewcomponent
-function ViashDockerPullElseBuild {
-  local save=$-; set +e
-  ViashDockerPull $1
-  local out=$?
-  [[ $save =~ e ]] && set -e
-  if [ $out -ne 0 ]; then
-    ViashDockerBuild $@
-  fi
-}
-
-# ViashDockerSetup: create a Docker image, according to specified docker setup strategy
-#
-# $1          : image identifier with format `[registry/]image[:tag]`
-# $2          : docker setup strategy, see DockerSetupStrategy.scala
-# examples:
-#   ViashDockerSetup mynewcomponent alwaysbuild
-function ViashDockerSetup {
-  local image_id="$1"
-  local setup_strategy="$2"
-  if [ "$setup_strategy" == "alwaysbuild" -o "$setup_strategy" == "build" -o "$setup_strategy" == "b" ]; then
-    ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-  elif [ "$setup_strategy" == "alwayspull" -o "$setup_strategy" == "pull" -o "$setup_strategy" == "p" ]; then
-    ViashDockerPull $image_id
-  elif [ "$setup_strategy" == "alwayspullelsebuild" -o "$setup_strategy" == "pullelsebuild" ]; then
-    ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-  elif [ "$setup_strategy" == "alwayspullelsecachedbuild" -o "$setup_strategy" == "pullelsecachedbuild" ]; then
-    ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-  elif [ "$setup_strategy" == "alwayscachedbuild" -o "$setup_strategy" == "cachedbuild" -o "$setup_strategy" == "cb" ]; then
-    ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-  elif [[ "$setup_strategy" =~ ^ifneedbe ]]; then
-    local save=$-; set +e
-    ViashDockerLocalTagCheck $image_id
-    local outCheck=$?
-    [[ $save =~ e ]] && set -e
-    if [ $outCheck -eq 0 ]; then
-      ViashInfo "Image $image_id already exists"
-    elif [ "$setup_strategy" == "ifneedbebuild" ]; then
-      ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-    elif [ "$setup_strategy" == "ifneedbecachedbuild" ]; then
-      ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-    elif [ "$setup_strategy" == "ifneedbepull" ]; then
-      ViashDockerPull $image_id
-    elif [ "$setup_strategy" == "ifneedbepullelsebuild" ]; then
-      ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-    elif [ "$setup_strategy" == "ifneedbepullelsecachedbuild" ]; then
-      ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-    else
-      ViashError "Unrecognised Docker strategy: $setup_strategy"
-      exit 1
-    fi
-  elif [ "$setup_strategy" == "push" -o "$setup_strategy" == "forcepush" -o "$setup_strategy" == "alwayspush" ]; then
-    ViashDockerPush "$image_id"
-  elif [ "$setup_strategy" == "pushifnotpresent" -o "$setup_strategy" == "gentlepush" -o "$setup_strategy" == "maybepush" ]; then
-    local save=$-; set +e
-    ViashDockerRemoteTagCheck $image_id
-    local outCheck=$?
-    [[ $save =~ e ]] && set -e
-    if [ $outCheck -eq 0 ]; then
-      ViashNotice "Container '$image_id' exists, doing nothing."
-    else
-      ViashNotice "Container '$image_id' does not yet exist."
-      ViashDockerPush "$image_id"
-    fi
-  elif [ "$setup_strategy" == "donothing" -o "$setup_strategy" == "meh" ]; then
-    ViashNotice "Skipping setup."
-  else
-    ViashError "Unrecognised Docker strategy: $setup_strategy"
-    exit 1
-  fi
-}
-
-# ViashDockerCheckCommands: Check whether a docker container has the required commands
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# $@                  : commands to verify being present
-# examples:
-#   ViashDockerCheckCommands bash:4.0 bash ps foo
-function ViashDockerCheckCommands {
-  local image_id="$1"
-  shift 1
-  local commands="$@"
-  local save=$-; set +e
-  local missing # mark 'missing' as local in advance, otherwise the exit code of the command will be missing and always be '0'
-  missing=$(docker run --rm --entrypoint=sh "$image_id" -c "for command in $commands; do command -v \$command >/dev/null 2>&1; if [ \$? -ne 0 ]; then echo \$command; exit 1; fi; done")
-  local outCheck=$?
-  [[ $save =~ e ]] && set -e
-  if [ $outCheck -ne 0 ]; then
-  	ViashError "Docker container '$image_id' does not contain command '$missing'."
-  	exit 1
-  fi
-}
-
-# ViashDockerBuild: build a docker image
-# $1                               : image identifier with format `[registry/]image[:tag]`
-# $...                             : additional arguments to pass to docker build
-# $VIASH_META_TEMP_DIR             : temporary directory to store dockerfile & optional resources in
-# $VIASH_META_NAME                 : name of the component
-# $VIASH_META_RESOURCES_DIR        : directory containing the resources
-# $VIASH_VERBOSITY                 : verbosity level
-# exit code $?                     : whether or not the image was built successfully
-function ViashDockerBuild {
-  local image_id="$1"
-  shift 1
-
-  # create temporary directory to store dockerfile & optional resources in
-  local tmpdir=$(mktemp -d "$VIASH_META_TEMP_DIR/dockerbuild-$VIASH_META_NAME-XXXXXX")
-  local dockerfile="$tmpdir/Dockerfile"
-  function clean_up {
-    rm -rf "$tmpdir"
-  }
-  trap clean_up EXIT
-
-  # store dockerfile and resources
-  ViashDockerfile "$VIASH_ENGINE_ID" > "$dockerfile"
-
-  # generate the build command
-  local docker_build_cmd="docker build -t '$image_id' $@ '$VIASH_META_RESOURCES_DIR' -f '$dockerfile'"
-
-  # build the container
-  ViashNotice "Building container '$image_id' with Dockerfile"
-  ViashInfo "$docker_build_cmd"
-  local save=$-; set +e
-  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
-    eval $docker_build_cmd
-  else
-    eval $docker_build_cmd &> "$tmpdir/docker_build.log"
-  fi
-
-  # check exit code
-  local out=$?
-  [[ $save =~ e ]] && set -e
-  if [ $out -ne 0 ]; then
-    ViashError "Error occurred while building container '$image_id'"
-    if [ $VIASH_VERBOSITY -lt $VIASH_LOGCODE_INFO ]; then
-      ViashError "Transcript: --------------------------------"
-      cat "$tmpdir/docker_build.log"
-      ViashError "End of transcript --------------------------"
-    fi
-    exit 1
-  fi
-}
-
-######## End of helper functions for setting up Docker images for viash ########
-
-# ViashDockerFile: print the dockerfile to stdout
-# $1    : engine identifier
-# return : dockerfile required to run this component
-# examples:
-#   ViashDockerFile
-function ViashDockerfile {
-  local engine_id="$1"
-
-  if [[ "$engine_id" == "docker" ]]; then
-    cat << 'VIASHDOCKER'
-FROM quay.io/biocontainers/trim-galore:0.6.10--hdfd78af_0
-ENTRYPOINT []
-RUN echo "TrimGalore: `trim_galore --version | sed -n 's/.*version\s\+\([0-9]\+\.[0-9]\+\.[0-9]\+\).*/\1/p'`" > /var/software_versions.txt
-
-LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
-LABEL org.opencontainers.image.description="Companion container for running component trimgalore"
-LABEL org.opencontainers.image.created="2024-12-03T10:33:56Z"
-LABEL org.opencontainers.image.source="https://github.com/FelixKrueger/TrimGalore"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-LABEL org.opencontainers.image.version="main"
-
-VIASHDOCKER
-  fi
-}
-
-# ViashDockerBuildArgs: return the arguments to pass to docker build
-# $1    : engine identifier
-# return : arguments to pass to docker build
-function ViashDockerBuildArgs {
-  local engine_id="$1"
-
-  if [[ "$engine_id" == "docker" ]]; then
-    echo ""
-  fi
-}
-
-# ViashAbsolutePath: generate absolute path from relative path
-# borrowed from https://stackoverflow.com/a/21951256
-# $1     : relative filename
-# return : absolute path
-# examples:
-#   ViashAbsolutePath some_file.txt   # returns /path/to/some_file.txt
-#   ViashAbsolutePath /foo/bar/..     # returns /foo
-function ViashAbsolutePath {
-  local thePath
-  local parr
-  local outp
-  local len
-  if [[ ! "$1" =~ ^/ ]]; then
-    thePath="$PWD/$1"
-  else
-    thePath="$1"
-  fi
-  echo "$thePath" | (
-    IFS=/
-    read -a parr
-    declare -a outp
-    for i in "${parr[@]}"; do
-      case "$i" in
-      ''|.) continue ;;
-      ..)
-        len=${#outp[@]}
-        if ((len==0)); then
-          continue
-        else
-          unset outp[$((len-1))]
-        fi
-        ;;
-      *)
-        len=${#outp[@]}
-        outp[$len]="$i"
-      ;;
-      esac
-    done
-    echo /"${outp[*]}"
-  )
-}
-# ViashDockerAutodetectMount: auto configuring docker mounts from parameters
-# $1                             : The parameter value
-# returns                        : New parameter
-# $VIASH_DIRECTORY_MOUNTS        : Added another parameter to be passed to docker
-# $VIASH_DOCKER_AUTOMOUNT_PREFIX : The prefix to be used for the automounts
-# examples:
-#   ViashDockerAutodetectMount /path/to/bar      # returns '/viash_automount/path/to/bar'
-#   ViashDockerAutodetectMountArg /path/to/bar   # returns '--volume="/path/to:/viash_automount/path/to"'
-function ViashDockerAutodetectMount {
-  local abs_path=$(ViashAbsolutePath "$1")
-  local mount_source
-  local base_name
-  if [ -d "$abs_path" ]; then
-    mount_source="$abs_path"
-    base_name=""
-  else
-    mount_source=`dirname "$abs_path"`
-    base_name=`basename "$abs_path"`
-  fi
-  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
-  if [ -z "$base_name" ]; then
-    echo "$mount_target"
-  else
-    echo "$mount_target/$base_name"
-  fi
-}
-function ViashDockerAutodetectMountArg {
-  local abs_path=$(ViashAbsolutePath "$1")
-  local mount_source
-  local base_name
-  if [ -d "$abs_path" ]; then
-    mount_source="$abs_path"
-    base_name=""
-  else
-    mount_source=`dirname "$abs_path"`
-    base_name=`basename "$abs_path"`
-  fi
-  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
-  ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target"
-  echo "--volume=\"$mount_source:$mount_target\""
-}
-function ViashDockerStripAutomount {
-  local abs_path=$(ViashAbsolutePath "$1")
-  echo "${abs_path#$VIASH_DOCKER_AUTOMOUNT_PREFIX}"
-}
-# initialise variables
-VIASH_DIRECTORY_MOUNTS=()
-
-# configure default docker automount prefix if it is unset
-if [ -z "${VIASH_DOCKER_AUTOMOUNT_PREFIX+x}" ]; then
-  VIASH_DOCKER_AUTOMOUNT_PREFIX="/viash_automount"
-fi
-
-# initialise docker variables
-VIASH_DOCKER_RUN_ARGS=(-i --rm)
-
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml b/target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml
index cd74403c..2cf5622e 100644
--- a/target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml
+++ b/target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml
@@ -509,6 +509,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -610,16 +613,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/umi_tools/umi_tools_dedup"
   executable: "target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup b/target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup
index 676e6b77..e65dd352 100755
--- a/target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup
+++ b/target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup
@@ -2,7 +2,7 @@
 
 # umi_tools_dedup main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -172,6 +172,404 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
+
+# initialise variables
+VIASH_MODE='run'
+VIASH_ENGINE_ID='docker'
+
+######## Helper functions for setting up Docker images for viash ########
+# expects: ViashDockerBuild
+
+# ViashDockerInstallationCheck: check whether Docker is installed correctly
+#
+# examples:
+#   ViashDockerInstallationCheck
+function ViashDockerInstallationCheck {
+  ViashDebug "Checking whether Docker is installed"
+  if [ ! command -v docker &> /dev/null ]; then
+    ViashCritical "Docker doesn't seem to be installed. See 'https://docs.docker.com/get-docker/' for instructions."
+    exit 1
+  fi
+
+  ViashDebug "Checking whether the Docker daemon is running"
+  local save=$-; set +e
+  local docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
+  local out=$?
+  [[ $save =~ e ]] && set -e
+  if [ $out -ne 0 ]; then
+    ViashCritical "Docker daemon does not seem to be running. Try one of the following:"
+    ViashCritical "- Try running 'dockerd' in the command line"
+    ViashCritical "- See https://docs.docker.com/config/daemon/"
+    exit 1
+  fi
+}
+
+# ViashDockerRemoteTagCheck: check whether a Docker image is available 
+# on a remote. Assumes `docker login` has been performed, if relevant.
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   ViashDockerRemoteTagCheck python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerRemoteTagCheck sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerRemoteTagCheck {
+  docker manifest inspect $1 > /dev/null 2> /dev/null
+}
+
+# ViashDockerLocalTagCheck: check whether a Docker image is available locally
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   docker pull python:latest
+#   ViashDockerLocalTagCheck python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerLocalTagCheck sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerLocalTagCheck {
+  [ -n "$(docker images -q $1)" ]
+}
+
+# ViashDockerPull: pull a Docker image
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   ViashDockerPull python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerPull sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerPull {
+  ViashNotice "Checking if Docker image is available at '$1'"
+  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
+    docker pull $1 && return 0 || return 1
+  else
+    local save=$-; set +e
+    docker pull $1 2> /dev/null > /dev/null
+    local out=$?
+    [[ $save =~ e ]] && set -e
+    if [ $out -ne 0 ]; then
+      ViashWarning "Could not pull from '$1'. Docker image doesn't exist or is not accessible."
+    fi
+    return $out
+  fi
+}
+
+# ViashDockerPush: push a Docker image
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# exit code $?        : whether or not the image was found
+# examples:
+#   ViashDockerPush python:latest
+#   echo $?                                     # returns '0'
+#   ViashDockerPush sdaizudceahifu
+#   echo $?                                     # returns '1'
+function ViashDockerPush {
+  ViashNotice "Pushing image to '$1'"
+  local save=$-; set +e
+  local out
+  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
+    docker push $1
+    out=$?
+  else
+    docker push $1 2> /dev/null > /dev/null
+    out=$?
+  fi
+  [[ $save =~ e ]] && set -e
+  if [ $out -eq 0 ]; then
+    ViashNotice "Container '$1' push succeeded."
+  else
+    ViashError "Container '$1' push errored. You might not be logged in or have the necessary permissions."
+  fi
+  return $out
+}
+
+# ViashDockerPullElseBuild: pull a Docker image, else build it
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# ViashDockerBuild    : a Bash function which builds a docker image, takes image identifier as argument.
+# examples:
+#   ViashDockerPullElseBuild mynewcomponent
+function ViashDockerPullElseBuild {
+  local save=$-; set +e
+  ViashDockerPull $1
+  local out=$?
+  [[ $save =~ e ]] && set -e
+  if [ $out -ne 0 ]; then
+    ViashDockerBuild $@
+  fi
+}
+
+# ViashDockerSetup: create a Docker image, according to specified docker setup strategy
+#
+# $1          : image identifier with format `[registry/]image[:tag]`
+# $2          : docker setup strategy, see DockerSetupStrategy.scala
+# examples:
+#   ViashDockerSetup mynewcomponent alwaysbuild
+function ViashDockerSetup {
+  local image_id="$1"
+  local setup_strategy="$2"
+  if [ "$setup_strategy" == "alwaysbuild" -o "$setup_strategy" == "build" -o "$setup_strategy" == "b" ]; then
+    ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+  elif [ "$setup_strategy" == "alwayspull" -o "$setup_strategy" == "pull" -o "$setup_strategy" == "p" ]; then
+    ViashDockerPull $image_id
+  elif [ "$setup_strategy" == "alwayspullelsebuild" -o "$setup_strategy" == "pullelsebuild" ]; then
+    ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+  elif [ "$setup_strategy" == "alwayspullelsecachedbuild" -o "$setup_strategy" == "pullelsecachedbuild" ]; then
+    ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+  elif [ "$setup_strategy" == "alwayscachedbuild" -o "$setup_strategy" == "cachedbuild" -o "$setup_strategy" == "cb" ]; then
+    ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+  elif [[ "$setup_strategy" =~ ^ifneedbe ]]; then
+    local save=$-; set +e
+    ViashDockerLocalTagCheck $image_id
+    local outCheck=$?
+    [[ $save =~ e ]] && set -e
+    if [ $outCheck -eq 0 ]; then
+      ViashInfo "Image $image_id already exists"
+    elif [ "$setup_strategy" == "ifneedbebuild" ]; then
+      ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+    elif [ "$setup_strategy" == "ifneedbecachedbuild" ]; then
+      ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+    elif [ "$setup_strategy" == "ifneedbepull" ]; then
+      ViashDockerPull $image_id
+    elif [ "$setup_strategy" == "ifneedbepullelsebuild" ]; then
+      ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
+    elif [ "$setup_strategy" == "ifneedbepullelsecachedbuild" ]; then
+      ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
+    else
+      ViashError "Unrecognised Docker strategy: $setup_strategy"
+      exit 1
+    fi
+  elif [ "$setup_strategy" == "push" -o "$setup_strategy" == "forcepush" -o "$setup_strategy" == "alwayspush" ]; then
+    ViashDockerPush "$image_id"
+  elif [ "$setup_strategy" == "pushifnotpresent" -o "$setup_strategy" == "gentlepush" -o "$setup_strategy" == "maybepush" ]; then
+    local save=$-; set +e
+    ViashDockerRemoteTagCheck $image_id
+    local outCheck=$?
+    [[ $save =~ e ]] && set -e
+    if [ $outCheck -eq 0 ]; then
+      ViashNotice "Container '$image_id' exists, doing nothing."
+    else
+      ViashNotice "Container '$image_id' does not yet exist."
+      ViashDockerPush "$image_id"
+    fi
+  elif [ "$setup_strategy" == "donothing" -o "$setup_strategy" == "meh" ]; then
+    ViashNotice "Skipping setup."
+  else
+    ViashError "Unrecognised Docker strategy: $setup_strategy"
+    exit 1
+  fi
+}
+
+# ViashDockerCheckCommands: Check whether a docker container has the required commands
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# $@                  : commands to verify being present
+# examples:
+#   ViashDockerCheckCommands bash:4.0 bash ps foo
+function ViashDockerCheckCommands {
+  local image_id="$1"
+  shift 1
+  local commands="$@"
+  local save=$-; set +e
+  local missing # mark 'missing' as local in advance, otherwise the exit code of the command will be missing and always be '0'
+  missing=$(docker run --rm --entrypoint=sh "$image_id" -c "for command in $commands; do command -v \$command >/dev/null 2>&1; if [ \$? -ne 0 ]; then echo \$command; exit 1; fi; done")
+  local outCheck=$?
+  [[ $save =~ e ]] && set -e
+  if [ $outCheck -ne 0 ]; then
+  	ViashError "Docker container '$image_id' does not contain command '$missing'."
+  	exit 1
+  fi
+}
+
+# ViashDockerBuild: build a docker image
+# $1                               : image identifier with format `[registry/]image[:tag]`
+# $...                             : additional arguments to pass to docker build
+# $VIASH_META_TEMP_DIR             : temporary directory to store dockerfile & optional resources in
+# $VIASH_META_NAME                 : name of the component
+# $VIASH_META_RESOURCES_DIR        : directory containing the resources
+# $VIASH_VERBOSITY                 : verbosity level
+# exit code $?                     : whether or not the image was built successfully
+function ViashDockerBuild {
+  local image_id="$1"
+  shift 1
+
+  # create temporary directory to store dockerfile & optional resources in
+  local tmpdir=$(mktemp -d "$VIASH_META_TEMP_DIR/dockerbuild-$VIASH_META_NAME-XXXXXX")
+  local dockerfile="$tmpdir/Dockerfile"
+  function clean_up {
+    rm -rf "$tmpdir"
+  }
+  trap clean_up EXIT
+
+  # store dockerfile and resources
+  ViashDockerfile "$VIASH_ENGINE_ID" > "$dockerfile"
+
+  # generate the build command
+  local docker_build_cmd="docker build -t '$image_id' $@ '$VIASH_META_RESOURCES_DIR' -f '$dockerfile'"
+
+  # build the container
+  ViashNotice "Building container '$image_id' with Dockerfile"
+  ViashInfo "$docker_build_cmd"
+  local save=$-; set +e
+  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
+    eval $docker_build_cmd
+  else
+    eval $docker_build_cmd &> "$tmpdir/docker_build.log"
+  fi
+
+  # check exit code
+  local out=$?
+  [[ $save =~ e ]] && set -e
+  if [ $out -ne 0 ]; then
+    ViashError "Error occurred while building container '$image_id'"
+    if [ $VIASH_VERBOSITY -lt $VIASH_LOGCODE_INFO ]; then
+      ViashError "Transcript: --------------------------------"
+      cat "$tmpdir/docker_build.log"
+      ViashError "End of transcript --------------------------"
+    fi
+    exit 1
+  fi
+}
+
+######## End of helper functions for setting up Docker images for viash ########
+
+# ViashDockerFile: print the dockerfile to stdout
+# $1    : engine identifier
+# return : dockerfile required to run this component
+# examples:
+#   ViashDockerFile
+function ViashDockerfile {
+  local engine_id="$1"
+
+  if [[ "$engine_id" == "docker" ]]; then
+    cat << 'VIASHDOCKER'
+FROM quay.io/biocontainers/umi_tools:1.1.5--py39hf95cd2a_1
+ENTRYPOINT []
+RUN umi_tools -v | sed 's/ version//g' > /var/software_versions.txt
+
+LABEL org.opencontainers.image.authors="Emma Rousseau"
+LABEL org.opencontainers.image.description="Companion container for running component umi_tools umi_tools_dedup"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:40Z"
+LABEL org.opencontainers.image.source="https://github.com/CGATOxford/UMI-tools"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+LABEL org.opencontainers.image.version="main"
+
+VIASHDOCKER
+  fi
+}
+
+# ViashDockerBuildArgs: return the arguments to pass to docker build
+# $1    : engine identifier
+# return : arguments to pass to docker build
+function ViashDockerBuildArgs {
+  local engine_id="$1"
+
+  if [[ "$engine_id" == "docker" ]]; then
+    echo ""
+  fi
+}
+
+# ViashAbsolutePath: generate absolute path from relative path
+# borrowed from https://stackoverflow.com/a/21951256
+# $1     : relative filename
+# return : absolute path
+# examples:
+#   ViashAbsolutePath some_file.txt   # returns /path/to/some_file.txt
+#   ViashAbsolutePath /foo/bar/..     # returns /foo
+function ViashAbsolutePath {
+  local thePath
+  local parr
+  local outp
+  local len
+  if [[ ! "$1" =~ ^/ ]]; then
+    thePath="$PWD/$1"
+  else
+    thePath="$1"
+  fi
+  echo "$thePath" | (
+    IFS=/
+    read -a parr
+    declare -a outp
+    for i in "${parr[@]}"; do
+      case "$i" in
+      ''|.) continue ;;
+      ..)
+        len=${#outp[@]}
+        if ((len==0)); then
+          continue
+        else
+          unset outp[$((len-1))]
+        fi
+        ;;
+      *)
+        len=${#outp[@]}
+        outp[$len]="$i"
+      ;;
+      esac
+    done
+    echo /"${outp[*]}"
+  )
+}
+# ViashDockerAutodetectMount: auto configuring docker mounts from parameters
+# $1                             : The parameter value
+# returns                        : New parameter
+# $VIASH_DIRECTORY_MOUNTS        : Added another parameter to be passed to docker
+# $VIASH_DOCKER_AUTOMOUNT_PREFIX : The prefix to be used for the automounts
+# examples:
+#   ViashDockerAutodetectMount /path/to/bar      # returns '/viash_automount/path/to/bar'
+#   ViashDockerAutodetectMountArg /path/to/bar   # returns '--volume="/path/to:/viash_automount/path/to"'
+function ViashDockerAutodetectMount {
+  local abs_path=$(ViashAbsolutePath "$1")
+  local mount_source
+  local base_name
+  if [ -d "$abs_path" ]; then
+    mount_source="$abs_path"
+    base_name=""
+  else
+    mount_source=`dirname "$abs_path"`
+    base_name=`basename "$abs_path"`
+  fi
+  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
+  if [ -z "$base_name" ]; then
+    echo "$mount_target"
+  else
+    echo "$mount_target/$base_name"
+  fi
+}
+function ViashDockerAutodetectMountArg {
+  local abs_path=$(ViashAbsolutePath "$1")
+  local mount_source
+  local base_name
+  if [ -d "$abs_path" ]; then
+    mount_source="$abs_path"
+    base_name=""
+  else
+    mount_source=`dirname "$abs_path"`
+    base_name=`basename "$abs_path"`
+  fi
+  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
+  ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target"
+  echo "--volume=\"$mount_source:$mount_target\""
+}
+function ViashDockerStripAutomount {
+  local abs_path=$(ViashAbsolutePath "$1")
+  echo "${abs_path#$VIASH_DOCKER_AUTOMOUNT_PREFIX}"
+}
+# initialise variables
+VIASH_DIRECTORY_MOUNTS=()
+
+# configure default docker automount prefix if it is unset
+if [ -z "${VIASH_DOCKER_AUTOMOUNT_PREFIX+x}" ]; then
+  VIASH_DOCKER_AUTOMOUNT_PREFIX="/viash_automount"
+fi
+
+# initialise docker variables
+VIASH_DOCKER_RUN_ARGS=(-i --rm)
+
+
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
   echo "umi_tools_dedup main"
@@ -489,404 +887,32 @@ function ViashHelp {
   echo "    --timeit_header"
   echo "        type: string"
   echo "        Add header for timing information."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
 }
 
-# initialise variables
-VIASH_MODE='run'
-VIASH_ENGINE_ID='docker'
-
-######## Helper functions for setting up Docker images for viash ########
-# expects: ViashDockerBuild
-
-# ViashDockerInstallationCheck: check whether Docker is installed correctly
-#
-# examples:
-#   ViashDockerInstallationCheck
-function ViashDockerInstallationCheck {
-  ViashDebug "Checking whether Docker is installed"
-  if [ ! command -v docker &> /dev/null ]; then
-    ViashCritical "Docker doesn't seem to be installed. See 'https://docs.docker.com/get-docker/' for instructions."
-    exit 1
-  fi
-
-  ViashDebug "Checking whether the Docker daemon is running"
-  local save=$-; set +e
-  local docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
-  local out=$?
-  [[ $save =~ e ]] && set -e
-  if [ $out -ne 0 ]; then
-    ViashCritical "Docker daemon does not seem to be running. Try one of the following:"
-    ViashCritical "- Try running 'dockerd' in the command line"
-    ViashCritical "- See https://docs.docker.com/config/daemon/"
-    exit 1
-  fi
-}
-
-# ViashDockerRemoteTagCheck: check whether a Docker image is available 
-# on a remote. Assumes `docker login` has been performed, if relevant.
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   ViashDockerRemoteTagCheck python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerRemoteTagCheck sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerRemoteTagCheck {
-  docker manifest inspect $1 > /dev/null 2> /dev/null
-}
-
-# ViashDockerLocalTagCheck: check whether a Docker image is available locally
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   docker pull python:latest
-#   ViashDockerLocalTagCheck python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerLocalTagCheck sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerLocalTagCheck {
-  [ -n "$(docker images -q $1)" ]
-}
-
-# ViashDockerPull: pull a Docker image
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   ViashDockerPull python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerPull sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerPull {
-  ViashNotice "Checking if Docker image is available at '$1'"
-  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
-    docker pull $1 && return 0 || return 1
-  else
-    local save=$-; set +e
-    docker pull $1 2> /dev/null > /dev/null
-    local out=$?
-    [[ $save =~ e ]] && set -e
-    if [ $out -ne 0 ]; then
-      ViashWarning "Could not pull from '$1'. Docker image doesn't exist or is not accessible."
-    fi
-    return $out
-  fi
-}
-
-# ViashDockerPush: push a Docker image
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# exit code $?        : whether or not the image was found
-# examples:
-#   ViashDockerPush python:latest
-#   echo $?                                     # returns '0'
-#   ViashDockerPush sdaizudceahifu
-#   echo $?                                     # returns '1'
-function ViashDockerPush {
-  ViashNotice "Pushing image to '$1'"
-  local save=$-; set +e
-  local out
-  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
-    docker push $1
-    out=$?
-  else
-    docker push $1 2> /dev/null > /dev/null
-    out=$?
-  fi
-  [[ $save =~ e ]] && set -e
-  if [ $out -eq 0 ]; then
-    ViashNotice "Container '$1' push succeeded."
-  else
-    ViashError "Container '$1' push errored. You might not be logged in or have the necessary permissions."
-  fi
-  return $out
-}
-
-# ViashDockerPullElseBuild: pull a Docker image, else build it
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# ViashDockerBuild    : a Bash function which builds a docker image, takes image identifier as argument.
-# examples:
-#   ViashDockerPullElseBuild mynewcomponent
-function ViashDockerPullElseBuild {
-  local save=$-; set +e
-  ViashDockerPull $1
-  local out=$?
-  [[ $save =~ e ]] && set -e
-  if [ $out -ne 0 ]; then
-    ViashDockerBuild $@
-  fi
-}
-
-# ViashDockerSetup: create a Docker image, according to specified docker setup strategy
-#
-# $1          : image identifier with format `[registry/]image[:tag]`
-# $2          : docker setup strategy, see DockerSetupStrategy.scala
-# examples:
-#   ViashDockerSetup mynewcomponent alwaysbuild
-function ViashDockerSetup {
-  local image_id="$1"
-  local setup_strategy="$2"
-  if [ "$setup_strategy" == "alwaysbuild" -o "$setup_strategy" == "build" -o "$setup_strategy" == "b" ]; then
-    ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-  elif [ "$setup_strategy" == "alwayspull" -o "$setup_strategy" == "pull" -o "$setup_strategy" == "p" ]; then
-    ViashDockerPull $image_id
-  elif [ "$setup_strategy" == "alwayspullelsebuild" -o "$setup_strategy" == "pullelsebuild" ]; then
-    ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-  elif [ "$setup_strategy" == "alwayspullelsecachedbuild" -o "$setup_strategy" == "pullelsecachedbuild" ]; then
-    ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-  elif [ "$setup_strategy" == "alwayscachedbuild" -o "$setup_strategy" == "cachedbuild" -o "$setup_strategy" == "cb" ]; then
-    ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-  elif [[ "$setup_strategy" =~ ^ifneedbe ]]; then
-    local save=$-; set +e
-    ViashDockerLocalTagCheck $image_id
-    local outCheck=$?
-    [[ $save =~ e ]] && set -e
-    if [ $outCheck -eq 0 ]; then
-      ViashInfo "Image $image_id already exists"
-    elif [ "$setup_strategy" == "ifneedbebuild" ]; then
-      ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-    elif [ "$setup_strategy" == "ifneedbecachedbuild" ]; then
-      ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-    elif [ "$setup_strategy" == "ifneedbepull" ]; then
-      ViashDockerPull $image_id
-    elif [ "$setup_strategy" == "ifneedbepullelsebuild" ]; then
-      ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
-    elif [ "$setup_strategy" == "ifneedbepullelsecachedbuild" ]; then
-      ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
-    else
-      ViashError "Unrecognised Docker strategy: $setup_strategy"
-      exit 1
-    fi
-  elif [ "$setup_strategy" == "push" -o "$setup_strategy" == "forcepush" -o "$setup_strategy" == "alwayspush" ]; then
-    ViashDockerPush "$image_id"
-  elif [ "$setup_strategy" == "pushifnotpresent" -o "$setup_strategy" == "gentlepush" -o "$setup_strategy" == "maybepush" ]; then
-    local save=$-; set +e
-    ViashDockerRemoteTagCheck $image_id
-    local outCheck=$?
-    [[ $save =~ e ]] && set -e
-    if [ $outCheck -eq 0 ]; then
-      ViashNotice "Container '$image_id' exists, doing nothing."
-    else
-      ViashNotice "Container '$image_id' does not yet exist."
-      ViashDockerPush "$image_id"
-    fi
-  elif [ "$setup_strategy" == "donothing" -o "$setup_strategy" == "meh" ]; then
-    ViashNotice "Skipping setup."
-  else
-    ViashError "Unrecognised Docker strategy: $setup_strategy"
-    exit 1
-  fi
-}
-
-# ViashDockerCheckCommands: Check whether a docker container has the required commands
-#
-# $1                  : image identifier with format `[registry/]image[:tag]`
-# $@                  : commands to verify being present
-# examples:
-#   ViashDockerCheckCommands bash:4.0 bash ps foo
-function ViashDockerCheckCommands {
-  local image_id="$1"
-  shift 1
-  local commands="$@"
-  local save=$-; set +e
-  local missing # mark 'missing' as local in advance, otherwise the exit code of the command will be missing and always be '0'
-  missing=$(docker run --rm --entrypoint=sh "$image_id" -c "for command in $commands; do command -v \$command >/dev/null 2>&1; if [ \$? -ne 0 ]; then echo \$command; exit 1; fi; done")
-  local outCheck=$?
-  [[ $save =~ e ]] && set -e
-  if [ $outCheck -ne 0 ]; then
-  	ViashError "Docker container '$image_id' does not contain command '$missing'."
-  	exit 1
-  fi
-}
-
-# ViashDockerBuild: build a docker image
-# $1                               : image identifier with format `[registry/]image[:tag]`
-# $...                             : additional arguments to pass to docker build
-# $VIASH_META_TEMP_DIR             : temporary directory to store dockerfile & optional resources in
-# $VIASH_META_NAME                 : name of the component
-# $VIASH_META_RESOURCES_DIR        : directory containing the resources
-# $VIASH_VERBOSITY                 : verbosity level
-# exit code $?                     : whether or not the image was built successfully
-function ViashDockerBuild {
-  local image_id="$1"
-  shift 1
-
-  # create temporary directory to store dockerfile & optional resources in
-  local tmpdir=$(mktemp -d "$VIASH_META_TEMP_DIR/dockerbuild-$VIASH_META_NAME-XXXXXX")
-  local dockerfile="$tmpdir/Dockerfile"
-  function clean_up {
-    rm -rf "$tmpdir"
-  }
-  trap clean_up EXIT
-
-  # store dockerfile and resources
-  ViashDockerfile "$VIASH_ENGINE_ID" > "$dockerfile"
-
-  # generate the build command
-  local docker_build_cmd="docker build -t '$image_id' $@ '$VIASH_META_RESOURCES_DIR' -f '$dockerfile'"
-
-  # build the container
-  ViashNotice "Building container '$image_id' with Dockerfile"
-  ViashInfo "$docker_build_cmd"
-  local save=$-; set +e
-  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
-    eval $docker_build_cmd
-  else
-    eval $docker_build_cmd &> "$tmpdir/docker_build.log"
-  fi
-
-  # check exit code
-  local out=$?
-  [[ $save =~ e ]] && set -e
-  if [ $out -ne 0 ]; then
-    ViashError "Error occurred while building container '$image_id'"
-    if [ $VIASH_VERBOSITY -lt $VIASH_LOGCODE_INFO ]; then
-      ViashError "Transcript: --------------------------------"
-      cat "$tmpdir/docker_build.log"
-      ViashError "End of transcript --------------------------"
-    fi
-    exit 1
-  fi
-}
-
-######## End of helper functions for setting up Docker images for viash ########
-
-# ViashDockerFile: print the dockerfile to stdout
-# $1    : engine identifier
-# return : dockerfile required to run this component
-# examples:
-#   ViashDockerFile
-function ViashDockerfile {
-  local engine_id="$1"
-
-  if [[ "$engine_id" == "docker" ]]; then
-    cat << 'VIASHDOCKER'
-FROM quay.io/biocontainers/umi_tools:1.1.5--py39hf95cd2a_1
-ENTRYPOINT []
-RUN umi_tools -v | sed 's/ version//g' > /var/software_versions.txt
-
-LABEL org.opencontainers.image.authors="Emma Rousseau"
-LABEL org.opencontainers.image.description="Companion container for running component umi_tools umi_tools_dedup"
-LABEL org.opencontainers.image.created="2024-12-03T10:33:57Z"
-LABEL org.opencontainers.image.source="https://github.com/CGATOxford/UMI-tools"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-LABEL org.opencontainers.image.version="main"
-
-VIASHDOCKER
-  fi
-}
-
-# ViashDockerBuildArgs: return the arguments to pass to docker build
-# $1    : engine identifier
-# return : arguments to pass to docker build
-function ViashDockerBuildArgs {
-  local engine_id="$1"
-
-  if [[ "$engine_id" == "docker" ]]; then
-    echo ""
-  fi
-}
-
-# ViashAbsolutePath: generate absolute path from relative path
-# borrowed from https://stackoverflow.com/a/21951256
-# $1     : relative filename
-# return : absolute path
-# examples:
-#   ViashAbsolutePath some_file.txt   # returns /path/to/some_file.txt
-#   ViashAbsolutePath /foo/bar/..     # returns /foo
-function ViashAbsolutePath {
-  local thePath
-  local parr
-  local outp
-  local len
-  if [[ ! "$1" =~ ^/ ]]; then
-    thePath="$PWD/$1"
-  else
-    thePath="$1"
-  fi
-  echo "$thePath" | (
-    IFS=/
-    read -a parr
-    declare -a outp
-    for i in "${parr[@]}"; do
-      case "$i" in
-      ''|.) continue ;;
-      ..)
-        len=${#outp[@]}
-        if ((len==0)); then
-          continue
-        else
-          unset outp[$((len-1))]
-        fi
-        ;;
-      *)
-        len=${#outp[@]}
-        outp[$len]="$i"
-      ;;
-      esac
-    done
-    echo /"${outp[*]}"
-  )
-}
-# ViashDockerAutodetectMount: auto configuring docker mounts from parameters
-# $1                             : The parameter value
-# returns                        : New parameter
-# $VIASH_DIRECTORY_MOUNTS        : Added another parameter to be passed to docker
-# $VIASH_DOCKER_AUTOMOUNT_PREFIX : The prefix to be used for the automounts
-# examples:
-#   ViashDockerAutodetectMount /path/to/bar      # returns '/viash_automount/path/to/bar'
-#   ViashDockerAutodetectMountArg /path/to/bar   # returns '--volume="/path/to:/viash_automount/path/to"'
-function ViashDockerAutodetectMount {
-  local abs_path=$(ViashAbsolutePath "$1")
-  local mount_source
-  local base_name
-  if [ -d "$abs_path" ]; then
-    mount_source="$abs_path"
-    base_name=""
-  else
-    mount_source=`dirname "$abs_path"`
-    base_name=`basename "$abs_path"`
-  fi
-  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
-  if [ -z "$base_name" ]; then
-    echo "$mount_target"
-  else
-    echo "$mount_target/$base_name"
-  fi
-}
-function ViashDockerAutodetectMountArg {
-  local abs_path=$(ViashAbsolutePath "$1")
-  local mount_source
-  local base_name
-  if [ -d "$abs_path" ]; then
-    mount_source="$abs_path"
-    base_name=""
-  else
-    mount_source=`dirname "$abs_path"`
-    base_name=`basename "$abs_path"`
-  fi
-  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
-  ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target"
-  echo "--volume=\"$mount_source:$mount_target\""
-}
-function ViashDockerStripAutomount {
-  local abs_path=$(ViashAbsolutePath "$1")
-  echo "${abs_path#$VIASH_DOCKER_AUTOMOUNT_PREFIX}"
-}
-# initialise variables
-VIASH_DIRECTORY_MOUNTS=()
-
-# configure default docker automount prefix if it is unset
-if [ -z "${VIASH_DOCKER_AUTOMOUNT_PREFIX+x}" ]; then
-  VIASH_DOCKER_AUTOMOUNT_PREFIX="/viash_automount"
-fi
-
-# initialise docker variables
-VIASH_DOCKER_RUN_ARGS=(-i --rm)
-
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml b/target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml
index 6fc5a531..b173621c 100644
--- a/target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml
+++ b/target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml
@@ -331,6 +331,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -433,16 +436,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/umi_tools/umi_tools_extract"
   executable: "target/executable/umi_tools/umi_tools_extract/umi_tools_extract"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/umi_tools/umi_tools_extract/umi_tools_extract b/target/executable/umi_tools/umi_tools_extract/umi_tools_extract
index cde49724..84b648a6 100755
--- a/target/executable/umi_tools/umi_tools_extract/umi_tools_extract
+++ b/target/executable/umi_tools/umi_tools_extract/umi_tools_extract
@@ -2,7 +2,7 @@
 
 # umi_tools_extract main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -169,188 +169,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "umi_tools_extract main"
-  echo ""
-  echo "Flexible removal of UMI sequences from fastq reads."
-  echo "UMIs are removed and appended to the read name. Any other barcode, for example a"
-  echo "library barcode,"
-  echo "is left on the read. Can also filter reads by quality or against a whitelist."
-  echo ""
-  echo "Input:"
-  echo "    --input"
-  echo "        type: file, required parameter, file must exist"
-  echo "        example: sample.fastq"
-  echo "        File containing the input data."
-  echo ""
-  echo "    --read2_in"
-  echo "        type: file, file must exist"
-  echo "        example: sample_R2.fastq"
-  echo "        File containing the input data for the R2 reads (if paired). If"
-  echo "        provided, a <list of other required arguments> need to be provided."
-  echo ""
-  echo "    -p, --bc_pattern"
-  echo "        type: string"
-  echo "        The UMI barcode pattern to use e.g. 'NNNNNN' indicates that the first 6"
-  echo "        nucleotides"
-  echo "        of the read are from the UMI."
-  echo ""
-  echo "    --bc_pattern2"
-  echo "        type: string"
-  echo "        The UMI barcode pattern to use for read 2."
-  echo ""
-  echo "Output:"
-  echo "    --output"
-  echo "        type: file, required parameter, output, file must exist"
-  echo "        Output file for read 1."
-  echo ""
-  echo "    --read2_out"
-  echo "        type: file, output, file must exist"
-  echo "        Output file for read 2."
-  echo ""
-  echo "    --filtered_out"
-  echo "        type: file, file must exist"
-  echo "        Write out reads not matching regex pattern or cell barcode whitelist to"
-  echo "        this file."
-  echo ""
-  echo "    --filtered_out2"
-  echo "        type: file, file must exist"
-  echo "        Write out read pairs not matching regex pattern or cell barcode"
-  echo "        whitelist to this file."
-  echo ""
-  echo "Extract Options:"
-  echo "    --extract_method"
-  echo "        type: string"
-  echo "        example: string"
-  echo "        choices: [ string, regex ]"
-  echo "        UMI pattern to use. Default: \`string\`."
-  echo ""
-  echo "    --error_correct_cell"
-  echo "        type: boolean_true"
-  echo "        Error correct cell barcodes to the whitelist."
-  echo ""
-  echo "    --whitelist"
-  echo "        type: file, file must exist"
-  echo "        Whitelist of accepted cell barcodes tab-separated format, where column 1"
-  echo "        is the whitelisted"
-  echo "        cell barcodes and column 2 is the list (comma-separated) of other cell"
-  echo "        barcodes which should"
-  echo "        be corrected to the barcode in column 1. If the --error_correct_cell"
-  echo "        option is not used, this"
-  echo "        column will be ignored."
-  echo ""
-  echo "    --blacklist"
-  echo "        type: file, file must exist"
-  echo "        BlackWhitelist of cell barcodes to discard."
-  echo ""
-  echo "    --subset_reads"
-  echo "        type: integer"
-  echo "        Only parse the first N reads."
-  echo ""
-  echo "    --quality_filter_threshold"
-  echo "        type: integer"
-  echo "        Remove reads where any UMI base quality score falls below this"
-  echo "        threshold."
-  echo ""
-  echo "    --quality_filter_mask"
-  echo "        type: string"
-  echo "        If a UMI base has a quality below this threshold, replace the base with"
-  echo "        'N'."
-  echo ""
-  echo "    --quality_encoding"
-  echo "        type: string"
-  echo "        choices: [ phred33, phred64, solexa ]"
-  echo "        Quality score encoding. Choose from:"
-  echo "          * phred33 [33-77]"
-  echo "          * phred64 [64-106]"
-  echo "          * solexa [59-106]"
-  echo ""
-  echo "    --reconcile_pairs"
-  echo "        type: boolean_true"
-  echo "        Allow read 2 infile to contain reads not in read 1 infile. This enables"
-  echo "        support for upstream protocols"
-  echo "        where read one contains cell barcodes, and the read pairs have been"
-  echo "        filtered and corrected without regard"
-  echo "        to the read2."
-  echo ""
-  echo "    --3prime, --three_prime"
-  echo "        type: boolean_true"
-  echo "        By default the barcode is assumed to be on the 5' end of the read, but"
-  echo "        use this option to sepecify that it is"
-  echo "        on the 3' end instead. This option only works with"
-  echo "        --extract_method=string since 3' encoding can be specified"
-  echo "        explicitly with a regex, e.g \`.*(?P<umi_1>.{5})\$\`."
-  echo ""
-  echo "    --ignore_read_pair_suffixes"
-  echo "        type: boolean_true"
-  echo "        Ignore \"/1\" and \"/2\" read name suffixes. Note that this options is"
-  echo "        required if the suffixes are not whitespace"
-  echo "        separated from the rest of the read name."
-  echo "        arguments:"
-  echo ""
-  echo "    --umi_separator"
-  echo "        type: string"
-  echo "        example: _"
-  echo "        The character that separates the UMI in the read name. Most likely a"
-  echo "        colon if you skipped the extraction with"
-  echo "        UMI-tools and used other software. Default: \`_\`"
-  echo ""
-  echo "    --grouping_method"
-  echo "        type: string"
-  echo "        example: directional"
-  echo "        choices: [ unique, percentile, cluster, adjacency, directional ]"
-  echo "        Method to use to determine read groups by subsuming those with similar"
-  echo "        UMIs. All methods start by identifying"
-  echo "        the reads with the same mapping position, but treat similar yet"
-  echo "        nonidentical UMIs differently. Default: \`directional\`"
-  echo ""
-  echo "Common Options:"
-  echo "    --log"
-  echo "        type: file, output, file must exist"
-  echo "        File with logging information."
-  echo ""
-  echo "    --log2stderr"
-  echo "        type: boolean_true"
-  echo "        Send logging information to stderr."
-  echo ""
-  echo "    --verbose"
-  echo "        type: integer"
-  echo "        Log level. The higher, the more output."
-  echo ""
-  echo "    --error"
-  echo "        type: file, output, file must exist"
-  echo "        File with error information."
-  echo ""
-  echo "    --temp_dir"
-  echo "        type: string"
-  echo "        Directory for temporary files. If not set, the bash environmental"
-  echo "        variable TMPDIR is used."
-  echo ""
-  echo "    --compresslevel"
-  echo "        type: integer"
-  echo "        example: 6"
-  echo "        Level of Gzip compression to use. Default=6 matches GNU gzip rather than"
-  echo "        python gzip default (which is 9)."
-  echo "        Default \`6\`."
-  echo ""
-  echo "    --timeit"
-  echo "        type: file, output, file must exist"
-  echo "        Store timing information in file."
-  echo ""
-  echo "    --timeit_name"
-  echo "        type: string"
-  echo "        default: all"
-  echo "        Name in timing file for this class of jobs."
-  echo ""
-  echo "    --timeit_header"
-  echo "        type: boolean_true"
-  echo "        Add header for timing information."
-  echo ""
-  echo "    --random_seed"
-  echo "        type: integer"
-  echo "        Random seed to initialize number generator with."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -630,9 +448,9 @@ ENTRYPOINT []
 RUN umi_tools -v | sed 's/ version//g' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.description="Companion container for running component umi_tools umi_tools_extract"
-LABEL org.opencontainers.image.created="2024-12-03T10:33:57Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:40Z"
 LABEL org.opencontainers.image.source="https://github.com/CGATOxford/UMI-tools"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -747,6 +565,214 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "umi_tools_extract main"
+  echo ""
+  echo "Flexible removal of UMI sequences from fastq reads."
+  echo "UMIs are removed and appended to the read name. Any other barcode, for example a"
+  echo "library barcode,"
+  echo "is left on the read. Can also filter reads by quality or against a whitelist."
+  echo ""
+  echo "Input:"
+  echo "    --input"
+  echo "        type: file, required parameter, file must exist"
+  echo "        example: sample.fastq"
+  echo "        File containing the input data."
+  echo ""
+  echo "    --read2_in"
+  echo "        type: file, file must exist"
+  echo "        example: sample_R2.fastq"
+  echo "        File containing the input data for the R2 reads (if paired). If"
+  echo "        provided, a <list of other required arguments> need to be provided."
+  echo ""
+  echo "    -p, --bc_pattern"
+  echo "        type: string"
+  echo "        The UMI barcode pattern to use e.g. 'NNNNNN' indicates that the first 6"
+  echo "        nucleotides"
+  echo "        of the read are from the UMI."
+  echo ""
+  echo "    --bc_pattern2"
+  echo "        type: string"
+  echo "        The UMI barcode pattern to use for read 2."
+  echo ""
+  echo "Output:"
+  echo "    --output"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        Output file for read 1."
+  echo ""
+  echo "    --read2_out"
+  echo "        type: file, output, file must exist"
+  echo "        Output file for read 2."
+  echo ""
+  echo "    --filtered_out"
+  echo "        type: file, file must exist"
+  echo "        Write out reads not matching regex pattern or cell barcode whitelist to"
+  echo "        this file."
+  echo ""
+  echo "    --filtered_out2"
+  echo "        type: file, file must exist"
+  echo "        Write out read pairs not matching regex pattern or cell barcode"
+  echo "        whitelist to this file."
+  echo ""
+  echo "Extract Options:"
+  echo "    --extract_method"
+  echo "        type: string"
+  echo "        example: string"
+  echo "        choices: [ string, regex ]"
+  echo "        UMI pattern to use. Default: \`string\`."
+  echo ""
+  echo "    --error_correct_cell"
+  echo "        type: boolean_true"
+  echo "        Error correct cell barcodes to the whitelist."
+  echo ""
+  echo "    --whitelist"
+  echo "        type: file, file must exist"
+  echo "        Whitelist of accepted cell barcodes tab-separated format, where column 1"
+  echo "        is the whitelisted"
+  echo "        cell barcodes and column 2 is the list (comma-separated) of other cell"
+  echo "        barcodes which should"
+  echo "        be corrected to the barcode in column 1. If the --error_correct_cell"
+  echo "        option is not used, this"
+  echo "        column will be ignored."
+  echo ""
+  echo "    --blacklist"
+  echo "        type: file, file must exist"
+  echo "        BlackWhitelist of cell barcodes to discard."
+  echo ""
+  echo "    --subset_reads"
+  echo "        type: integer"
+  echo "        Only parse the first N reads."
+  echo ""
+  echo "    --quality_filter_threshold"
+  echo "        type: integer"
+  echo "        Remove reads where any UMI base quality score falls below this"
+  echo "        threshold."
+  echo ""
+  echo "    --quality_filter_mask"
+  echo "        type: string"
+  echo "        If a UMI base has a quality below this threshold, replace the base with"
+  echo "        'N'."
+  echo ""
+  echo "    --quality_encoding"
+  echo "        type: string"
+  echo "        choices: [ phred33, phred64, solexa ]"
+  echo "        Quality score encoding. Choose from:"
+  echo "          * phred33 [33-77]"
+  echo "          * phred64 [64-106]"
+  echo "          * solexa [59-106]"
+  echo ""
+  echo "    --reconcile_pairs"
+  echo "        type: boolean_true"
+  echo "        Allow read 2 infile to contain reads not in read 1 infile. This enables"
+  echo "        support for upstream protocols"
+  echo "        where read one contains cell barcodes, and the read pairs have been"
+  echo "        filtered and corrected without regard"
+  echo "        to the read2."
+  echo ""
+  echo "    --3prime, --three_prime"
+  echo "        type: boolean_true"
+  echo "        By default the barcode is assumed to be on the 5' end of the read, but"
+  echo "        use this option to sepecify that it is"
+  echo "        on the 3' end instead. This option only works with"
+  echo "        --extract_method=string since 3' encoding can be specified"
+  echo "        explicitly with a regex, e.g \`.*(?P<umi_1>.{5})\$\`."
+  echo ""
+  echo "    --ignore_read_pair_suffixes"
+  echo "        type: boolean_true"
+  echo "        Ignore \"/1\" and \"/2\" read name suffixes. Note that this options is"
+  echo "        required if the suffixes are not whitespace"
+  echo "        separated from the rest of the read name."
+  echo "        arguments:"
+  echo ""
+  echo "    --umi_separator"
+  echo "        type: string"
+  echo "        example: _"
+  echo "        The character that separates the UMI in the read name. Most likely a"
+  echo "        colon if you skipped the extraction with"
+  echo "        UMI-tools and used other software. Default: \`_\`"
+  echo ""
+  echo "    --grouping_method"
+  echo "        type: string"
+  echo "        example: directional"
+  echo "        choices: [ unique, percentile, cluster, adjacency, directional ]"
+  echo "        Method to use to determine read groups by subsuming those with similar"
+  echo "        UMIs. All methods start by identifying"
+  echo "        the reads with the same mapping position, but treat similar yet"
+  echo "        nonidentical UMIs differently. Default: \`directional\`"
+  echo ""
+  echo "Common Options:"
+  echo "    --log"
+  echo "        type: file, output, file must exist"
+  echo "        File with logging information."
+  echo ""
+  echo "    --log2stderr"
+  echo "        type: boolean_true"
+  echo "        Send logging information to stderr."
+  echo ""
+  echo "    --verbose"
+  echo "        type: integer"
+  echo "        Log level. The higher, the more output."
+  echo ""
+  echo "    --error"
+  echo "        type: file, output, file must exist"
+  echo "        File with error information."
+  echo ""
+  echo "    --temp_dir"
+  echo "        type: string"
+  echo "        Directory for temporary files. If not set, the bash environmental"
+  echo "        variable TMPDIR is used."
+  echo ""
+  echo "    --compresslevel"
+  echo "        type: integer"
+  echo "        example: 6"
+  echo "        Level of Gzip compression to use. Default=6 matches GNU gzip rather than"
+  echo "        python gzip default (which is 9)."
+  echo "        Default \`6\`."
+  echo ""
+  echo "    --timeit"
+  echo "        type: file, output, file must exist"
+  echo "        Store timing information in file."
+  echo ""
+  echo "    --timeit_name"
+  echo "        type: string"
+  echo "        default: all"
+  echo "        Name in timing file for this class of jobs."
+  echo ""
+  echo "    --timeit_header"
+  echo "        type: boolean_true"
+  echo "        Add header for timing information."
+  echo ""
+  echo "    --random_seed"
+  echo "        type: integer"
+  echo "        Random seed to initialize number generator with."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/executable/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml b/target/executable/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml
index f3fa98b5..11726d20 100644
--- a/target/executable/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml
+++ b/target/executable/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml
@@ -153,6 +153,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -255,16 +258,16 @@ build_info:
   engine: "docker|native"
   output: "target/executable/umi_tools/umi_tools_prepareforrsem"
   executable: "target/executable/umi_tools/umi_tools_prepareforrsem/umi_tools_prepareforrsem"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/executable/umi_tools/umi_tools_prepareforrsem/umi_tools_prepareforrsem b/target/executable/umi_tools/umi_tools_prepareforrsem/umi_tools_prepareforrsem
index fabc416d..b89d7f03 100755
--- a/target/executable/umi_tools/umi_tools_prepareforrsem/umi_tools_prepareforrsem
+++ b/target/executable/umi_tools/umi_tools_prepareforrsem/umi_tools_prepareforrsem
@@ -2,7 +2,7 @@
 
 # umi_tools_prepareforrsem main
 # 
-# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -169,77 +169,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 
-# ViashHelp: Display helpful explanation about this executable
-function ViashHelp {
-  echo "umi_tools_prepareforrsem main"
-  echo ""
-  echo "Make the output from umi-tools dedup or group compatible with RSEM"
-  echo ""
-  echo "Input:"
-  echo "    -I, --stdin, --input"
-  echo "        type: file, required parameter, file must exist"
-  echo "        example: \$id.transcriptome.bam"
-  echo ""
-  echo "Output:"
-  echo "    -S, --stdout, --output"
-  echo "        type: file, output, file must exist"
-  echo "        example: \$id.transcriptome_sorted.bam"
-  echo ""
-  echo "    -L, --log"
-  echo "        type: file, output, file must exist"
-  echo "        File with logging information [default = stdout]."
-  echo ""
-  echo "    -E, --error"
-  echo "        type: file, output, file must exist"
-  echo "        File with error information [default = stderr]."
-  echo ""
-  echo "    --log2stderr"
-  echo "        type: boolean_true"
-  echo "        Send logging information to stderr [default = False]."
-  echo ""
-  echo "    --temp_dir"
-  echo "        type: string"
-  echo "        Directory for temporary files. If not set, the bash environmental"
-  echo "        variable"
-  echo "        TMPDIR is used."
-  echo ""
-  echo "    --compresslevel"
-  echo "        type: integer"
-  echo "        Level of Gzip compression to use. Default (6) matchesGNU gzip rather"
-  echo "        than python"
-  echo "        gzip default (which is 9)."
-  echo ""
-  echo "Options:"
-  echo "    --tags"
-  echo "        type: string"
-  echo "        example: UG,BX"
-  echo "        Comma-seperated list of tags to transfer from read1 to read2 (Default:"
-  echo "        'UG,BX')"
-  echo ""
-  echo "    --sam"
-  echo "        type: boolean_true"
-  echo "        Input and output SAM rather than BAM."
-  echo ""
-  echo "    --timeit"
-  echo "        type: string"
-  echo "        Store timeing information in file [none]."
-  echo ""
-  echo "    --timeit_name"
-  echo "        type: string"
-  echo "        Name in timing file for this class of jobs [all]."
-  echo ""
-  echo "    --timeit_header"
-  echo "        type: boolean_true"
-  echo "        Add header for timing information [none]."
-  echo ""
-  echo "    -v, --verbose"
-  echo "        type: integer"
-  echo "        Loglevel [1]. The higher, the more output."
-  echo ""
-  echo "    --random_seed"
-  echo "        type: integer"
-  echo "        Random seed to initialize number generator with [none]."
-}
 
 # initialise variables
 VIASH_MODE='run'
@@ -519,9 +448,9 @@ ENTRYPOINT []
 RUN umi_tools -v | sed 's/ version//g' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.description="Companion container for running component umi_tools umi_tools_prepareforrsem"
-LABEL org.opencontainers.image.created="2024-12-03T10:33:58Z"
+LABEL org.opencontainers.image.created="2025-03-06T09:19:40Z"
 LABEL org.opencontainers.image.source="https://github.com/CGATOxford/UMI-tools"
-LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
+LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -636,6 +565,103 @@ fi
 # initialise docker variables
 VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "umi_tools_prepareforrsem main"
+  echo ""
+  echo "Make the output from umi-tools dedup or group compatible with RSEM"
+  echo ""
+  echo "Input:"
+  echo "    -I, --stdin, --input"
+  echo "        type: file, required parameter, file must exist"
+  echo "        example: \$id.transcriptome.bam"
+  echo ""
+  echo "Output:"
+  echo "    -S, --stdout, --output"
+  echo "        type: file, output, file must exist"
+  echo "        example: \$id.transcriptome_sorted.bam"
+  echo ""
+  echo "    -L, --log"
+  echo "        type: file, output, file must exist"
+  echo "        File with logging information [default = stdout]."
+  echo ""
+  echo "    -E, --error"
+  echo "        type: file, output, file must exist"
+  echo "        File with error information [default = stderr]."
+  echo ""
+  echo "    --log2stderr"
+  echo "        type: boolean_true"
+  echo "        Send logging information to stderr [default = False]."
+  echo ""
+  echo "    --temp_dir"
+  echo "        type: string"
+  echo "        Directory for temporary files. If not set, the bash environmental"
+  echo "        variable"
+  echo "        TMPDIR is used."
+  echo ""
+  echo "    --compresslevel"
+  echo "        type: integer"
+  echo "        Level of Gzip compression to use. Default (6) matchesGNU gzip rather"
+  echo "        than python"
+  echo "        gzip default (which is 9)."
+  echo ""
+  echo "Options:"
+  echo "    --tags"
+  echo "        type: string"
+  echo "        example: UG,BX"
+  echo "        Comma-seperated list of tags to transfer from read1 to read2 (Default:"
+  echo "        'UG,BX')"
+  echo ""
+  echo "    --sam"
+  echo "        type: boolean_true"
+  echo "        Input and output SAM rather than BAM."
+  echo ""
+  echo "    --timeit"
+  echo "        type: string"
+  echo "        Store timeing information in file [none]."
+  echo ""
+  echo "    --timeit_name"
+  echo "        type: string"
+  echo "        Name in timing file for this class of jobs [all]."
+  echo ""
+  echo "    --timeit_header"
+  echo "        type: boolean_true"
+  echo "        Add header for timing information [none]."
+  echo ""
+  echo "    -v, --verbose"
+  echo "        type: integer"
+  echo "        Loglevel [1]. The higher, the more output."
+  echo ""
+  echo "    --random_seed"
+  echo "        type: integer"
+  echo "        Random seed to initialize number generator with [none]."
+  echo ""
+  echo "Viash built in Computational Requirements:"
+  echo "    ---cpus=INT"
+  echo "        Number of CPUs to use"
+  echo "    ---memory=STRING"
+  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
+  echo ""
+  echo "Viash built in Docker:"
+  echo "    ---setup=STRATEGY"
+  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
+  echo "        Default: ifneedbepullelsecachedbuild"
+  echo "    ---dockerfile"
+  echo "        Print the dockerfile to stdout."
+  echo "    ---docker_run_args=ARG"
+  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
+  echo "    ---docker_image_id"
+  echo "        Print the docker image id to stdout."
+  echo "    ---debug"
+  echo "        Enter the docker container for debugging purposes."
+  echo ""
+  echo "Viash built in Engines:"
+  echo "    ---engine=ENGINE_ID"
+  echo "        Specify the engine to use. Options are: docker, native."
+  echo "        Default: docker"
+}
+
 # initialise array
 VIASH_POSITIONAL_ARGS=''
 
diff --git a/target/nextflow/agat/agat_convert_bed2gff/.config.vsh.yaml b/target/nextflow/agat/agat_convert_bed2gff/.config.vsh.yaml
index cfcb7718..2fe93e30 100644
--- a/target/nextflow/agat/agat_convert_bed2gff/.config.vsh.yaml
+++ b/target/nextflow/agat/agat_convert_bed2gff/.config.vsh.yaml
@@ -133,6 +133,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -234,16 +237,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/agat/agat_convert_bed2gff"
   executable: "target/nextflow/agat/agat_convert_bed2gff/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/agat/agat_convert_bed2gff/main.nf b/target/nextflow/agat/agat_convert_bed2gff/main.nf
index 9d203b76..cee1ff9c 100644
--- a/target/nextflow/agat/agat_convert_bed2gff/main.nf
+++ b/target/nextflow/agat/agat_convert_bed2gff/main.nf
@@ -1,6 +1,6 @@
 // agat_convert_bed2gff main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -2969,6 +3200,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3091,16 +3326,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/agat/agat_convert_bed2gff",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml b/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml
index a7bd8320..64344c46 100644
--- a/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml
+++ b/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml
@@ -123,6 +123,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -224,16 +227,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/agat/agat_convert_embl2gff"
   executable: "target/nextflow/agat/agat_convert_embl2gff/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/agat/agat_convert_embl2gff/main.nf b/target/nextflow/agat/agat_convert_embl2gff/main.nf
index 2da07938..63eaeaa9 100644
--- a/target/nextflow/agat/agat_convert_embl2gff/main.nf
+++ b/target/nextflow/agat/agat_convert_embl2gff/main.nf
@@ -1,6 +1,6 @@
 // agat_convert_embl2gff main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -2962,6 +3193,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3084,16 +3319,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/agat/agat_convert_embl2gff",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/agat/agat_convert_genscan2gff/.config.vsh.yaml b/target/nextflow/agat/agat_convert_genscan2gff/.config.vsh.yaml
index 04291ad4..f1e26f96 100644
--- a/target/nextflow/agat/agat_convert_genscan2gff/.config.vsh.yaml
+++ b/target/nextflow/agat/agat_convert_genscan2gff/.config.vsh.yaml
@@ -127,6 +127,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -229,16 +232,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/agat/agat_convert_genscan2gff"
   executable: "target/nextflow/agat/agat_convert_genscan2gff/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/agat/agat_convert_genscan2gff/main.nf b/target/nextflow/agat/agat_convert_genscan2gff/main.nf
index 14e03d8e..80f0bc0f 100644
--- a/target/nextflow/agat/agat_convert_genscan2gff/main.nf
+++ b/target/nextflow/agat/agat_convert_genscan2gff/main.nf
@@ -1,6 +1,6 @@
 // agat_convert_genscan2gff main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -2963,6 +3194,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3086,16 +3321,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/agat/agat_convert_genscan2gff",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/agat/agat_convert_mfannot2gff/.config.vsh.yaml b/target/nextflow/agat/agat_convert_mfannot2gff/.config.vsh.yaml
index 975300c9..f83cf2d2 100644
--- a/target/nextflow/agat/agat_convert_mfannot2gff/.config.vsh.yaml
+++ b/target/nextflow/agat/agat_convert_mfannot2gff/.config.vsh.yaml
@@ -83,6 +83,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -90,7 +93,7 @@ keywords:
 - "gene annotations"
 - "GFF"
 - "Mfannot"
-license: "GPL-3."
+license: "GPL-3.0"
 references:
   doi:
   - "10.5281/zenodo.3552717"
@@ -185,16 +188,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/agat/agat_convert_mfannot2gff"
   executable: "target/nextflow/agat/agat_convert_mfannot2gff/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/agat/agat_convert_mfannot2gff/main.nf b/target/nextflow/agat/agat_convert_mfannot2gff/main.nf
index a6c8fbaa..e736efb4 100644
--- a/target/nextflow/agat/agat_convert_mfannot2gff/main.nf
+++ b/target/nextflow/agat/agat_convert_mfannot2gff/main.nf
@@ -1,6 +1,6 @@
 // agat_convert_mfannot2gff main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -2923,6 +3154,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -2933,7 +3168,7 @@ meta = [
     "GFF",
     "Mfannot"
   ],
-  "license" : "GPL-3.",
+  "license" : "GPL-3.0",
   "references" : {
     "doi" : [
       "10.5281/zenodo.3552717"
@@ -3046,16 +3281,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/agat/agat_convert_mfannot2gff",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml b/target/nextflow/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml
index a949071a..80902618 100644
--- a/target/nextflow/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml
+++ b/target/nextflow/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml
@@ -126,6 +126,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -227,16 +230,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/agat/agat_convert_sp_gff2gtf"
   executable: "target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf b/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf
index 521ca40f..bd39ac2a 100644
--- a/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf
+++ b/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf
@@ -1,6 +1,6 @@
 // agat_convert_sp_gff2gtf main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -2945,6 +3176,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3067,16 +3302,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/agat/agat_convert_sp_gff2gtf",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml b/target/nextflow/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml
index 7c0bfbb3..007f8b57 100644
--- a/target/nextflow/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml
+++ b/target/nextflow/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml
@@ -86,6 +86,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -187,16 +190,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/agat/agat_convert_sp_gff2tsv"
   executable: "target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf b/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf
index 6aea07dd..1f08d955 100644
--- a/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf
+++ b/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf
@@ -1,6 +1,6 @@
 // agat_convert_sp_gff2tsv main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -2923,6 +3154,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3045,16 +3280,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/agat/agat_convert_sp_gff2tsv",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml b/target/nextflow/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml
index 48929ad1..77473703 100644
--- a/target/nextflow/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml
+++ b/target/nextflow/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml
@@ -93,6 +93,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -194,16 +197,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/agat/agat_convert_sp_gxf2gxf"
   executable: "target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf b/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf
index 1ca00eef..d8ab2023 100644
--- a/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf
+++ b/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf
@@ -1,6 +1,6 @@
 // agat_convert_sp_gxf2gxf main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -2923,6 +3154,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3045,16 +3280,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/agat/agat_convert_sp_gxf2gxf",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/agat/agat_sp_add_introns/.config.vsh.yaml b/target/nextflow/agat/agat_sp_add_introns/.config.vsh.yaml
index 826a1b06..acd15f72 100644
--- a/target/nextflow/agat/agat_sp_add_introns/.config.vsh.yaml
+++ b/target/nextflow/agat/agat_sp_add_introns/.config.vsh.yaml
@@ -84,6 +84,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -185,16 +188,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/agat/agat_sp_add_introns"
   executable: "target/nextflow/agat/agat_sp_add_introns/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/agat/agat_sp_add_introns/main.nf b/target/nextflow/agat/agat_sp_add_introns/main.nf
index e19d0c93..a24ce412 100644
--- a/target/nextflow/agat/agat_sp_add_introns/main.nf
+++ b/target/nextflow/agat/agat_sp_add_introns/main.nf
@@ -1,6 +1,6 @@
 // agat_sp_add_introns main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -2926,6 +3157,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3048,16 +3283,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/agat/agat_sp_add_introns",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/agat/agat_sp_filter_feature_from_kill_list/.config.vsh.yaml b/target/nextflow/agat/agat_sp_filter_feature_from_kill_list/.config.vsh.yaml
index 497003e9..ac047278 100644
--- a/target/nextflow/agat/agat_sp_filter_feature_from_kill_list/.config.vsh.yaml
+++ b/target/nextflow/agat/agat_sp_filter_feature_from_kill_list/.config.vsh.yaml
@@ -133,6 +133,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -235,16 +238,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/agat/agat_sp_filter_feature_from_kill_list"
   executable: "target/nextflow/agat/agat_sp_filter_feature_from_kill_list/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/agat/agat_sp_filter_feature_from_kill_list/main.nf b/target/nextflow/agat/agat_sp_filter_feature_from_kill_list/main.nf
index dbaf11fb..118e3b70 100644
--- a/target/nextflow/agat/agat_sp_filter_feature_from_kill_list/main.nf
+++ b/target/nextflow/agat/agat_sp_filter_feature_from_kill_list/main.nf
@@ -1,6 +1,6 @@
 // agat_sp_filter_feature_from_kill_list main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -2972,6 +3203,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3095,16 +3330,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/agat/agat_sp_filter_feature_from_kill_list",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/agat/agat_sp_merge_annotations/.config.vsh.yaml b/target/nextflow/agat/agat_sp_merge_annotations/.config.vsh.yaml
index b9c1b1ee..d88240d5 100644
--- a/target/nextflow/agat/agat_sp_merge_annotations/.config.vsh.yaml
+++ b/target/nextflow/agat/agat_sp_merge_annotations/.config.vsh.yaml
@@ -81,6 +81,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -183,16 +186,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/agat/agat_sp_merge_annotations"
   executable: "target/nextflow/agat/agat_sp_merge_annotations/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/agat/agat_sp_merge_annotations/main.nf b/target/nextflow/agat/agat_sp_merge_annotations/main.nf
index 65e7dd1a..7f10e2e9 100644
--- a/target/nextflow/agat/agat_sp_merge_annotations/main.nf
+++ b/target/nextflow/agat/agat_sp_merge_annotations/main.nf
@@ -1,6 +1,6 @@
 // agat_sp_merge_annotations main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -2922,6 +3153,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3045,16 +3280,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/agat/agat_sp_merge_annotations",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/agat/agat_sp_statistics/.config.vsh.yaml b/target/nextflow/agat/agat_sp_statistics/.config.vsh.yaml
index c21f1646..907c01d6 100644
--- a/target/nextflow/agat/agat_sp_statistics/.config.vsh.yaml
+++ b/target/nextflow/agat/agat_sp_statistics/.config.vsh.yaml
@@ -128,6 +128,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -230,16 +233,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/agat/agat_sp_statistics"
   executable: "target/nextflow/agat/agat_sp_statistics/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/agat/agat_sp_statistics/main.nf b/target/nextflow/agat/agat_sp_statistics/main.nf
index 3d7cf01c..7ab53b26 100644
--- a/target/nextflow/agat/agat_sp_statistics/main.nf
+++ b/target/nextflow/agat/agat_sp_statistics/main.nf
@@ -1,6 +1,6 @@
 // agat_sp_statistics main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -2972,6 +3203,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3095,16 +3330,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/agat/agat_sp_statistics",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/agat/agat_sq_stat_basic/.config.vsh.yaml b/target/nextflow/agat/agat_sq_stat_basic/.config.vsh.yaml
index b9953201..ddb97ba0 100644
--- a/target/nextflow/agat/agat_sq_stat_basic/.config.vsh.yaml
+++ b/target/nextflow/agat/agat_sq_stat_basic/.config.vsh.yaml
@@ -124,6 +124,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -226,16 +229,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/agat/agat_sq_stat_basic"
   executable: "target/nextflow/agat/agat_sq_stat_basic/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/agat/agat_sq_stat_basic/main.nf b/target/nextflow/agat/agat_sq_stat_basic/main.nf
index 291b12db..54192b06 100644
--- a/target/nextflow/agat/agat_sq_stat_basic/main.nf
+++ b/target/nextflow/agat/agat_sq_stat_basic/main.nf
@@ -1,6 +1,6 @@
 // agat_sq_stat_basic main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -2958,6 +3189,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3081,16 +3316,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/agat/agat_sq_stat_basic",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/arriba/.config.vsh.yaml b/target/nextflow/arriba/.config.vsh.yaml
index adcc572c..908a7ca3 100644
--- a/target/nextflow/arriba/.config.vsh.yaml
+++ b/target/nextflow/arriba/.config.vsh.yaml
@@ -603,6 +603,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   cpus: 1
   commands:
@@ -705,16 +708,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/arriba"
   executable: "target/nextflow/arriba/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/arriba/main.nf b/target/nextflow/arriba/main.nf
index 29fd7d44..c6c0825b 100644
--- a/target/nextflow/arriba/main.nf
+++ b/target/nextflow/arriba/main.nf
@@ -1,6 +1,6 @@
 // arriba main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3469,6 +3700,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "cpus" : 1,
     "commands" : [
@@ -3591,16 +3826,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/arriba",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/bases2fastq/.config.vsh.yaml b/target/nextflow/bases2fastq/.config.vsh.yaml
index 803a290f..77adc60d 100644
--- a/target/nextflow/bases2fastq/.config.vsh.yaml
+++ b/target/nextflow/bases2fastq/.config.vsh.yaml
@@ -285,6 +285,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -393,16 +396,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/bases2fastq"
   executable: "target/nextflow/bases2fastq/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/bases2fastq/main.nf b/target/nextflow/bases2fastq/main.nf
index 984a44d2..3e96a16a 100644
--- a/target/nextflow/bases2fastq/main.nf
+++ b/target/nextflow/bases2fastq/main.nf
@@ -1,6 +1,6 @@
 // bases2fastq main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3149,6 +3380,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3283,16 +3518,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/bases2fastq",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/bbmap/bbmap_bbsplit/.config.vsh.yaml b/target/nextflow/bbmap/bbmap_bbsplit/.config.vsh.yaml
index d1152815..34bc672f 100644
--- a/target/nextflow/bbmap/bbmap_bbsplit/.config.vsh.yaml
+++ b/target/nextflow/bbmap/bbmap_bbsplit/.config.vsh.yaml
@@ -267,6 +267,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -367,16 +370,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/bbmap/bbmap_bbsplit"
   executable: "target/nextflow/bbmap/bbmap_bbsplit/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/bbmap/bbmap_bbsplit/main.nf b/target/nextflow/bbmap/bbmap_bbsplit/main.nf
index be42fc55..5535732a 100644
--- a/target/nextflow/bbmap/bbmap_bbsplit/main.nf
+++ b/target/nextflow/bbmap/bbmap_bbsplit/main.nf
@@ -1,6 +1,6 @@
 // bbmap_bbsplit main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -173,7 +173,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -192,15 +192,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -213,6 +206,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1666,6 +1669,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1723,8 +1882,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1737,7 +1894,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1749,33 +1906,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1806,13 +1947,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1829,7 +1967,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1860,13 +1998,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1874,18 +2008,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2559,7 +2692,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2716,12 +2850,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2734,19 +2892,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2755,23 +2988,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3101,6 +3332,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3219,16 +3454,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/bbmap/bbmap_bbsplit",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/bcftools/bcftools_annotate/.config.vsh.yaml b/target/nextflow/bcftools/bcftools_annotate/.config.vsh.yaml
index 0bbc3442..04d7c3bb 100644
--- a/target/nextflow/bcftools/bcftools_annotate/.config.vsh.yaml
+++ b/target/nextflow/bcftools/bcftools_annotate/.config.vsh.yaml
@@ -355,6 +355,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -468,16 +471,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/bcftools/bcftools_annotate"
   executable: "target/nextflow/bcftools/bcftools_annotate/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/bcftools/bcftools_annotate/main.nf b/target/nextflow/bcftools/bcftools_annotate/main.nf
index ff2d7bb7..6d1af5de 100644
--- a/target/nextflow/bcftools/bcftools_annotate/main.nf
+++ b/target/nextflow/bcftools/bcftools_annotate/main.nf
@@ -1,6 +1,6 @@
 // bcftools_annotate main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3194,6 +3425,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3334,16 +3569,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/bcftools/bcftools_annotate",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/bcftools/bcftools_concat/.config.vsh.yaml b/target/nextflow/bcftools/bcftools_concat/.config.vsh.yaml
index 55ad2d28..54bb83e5 100644
--- a/target/nextflow/bcftools/bcftools_concat/.config.vsh.yaml
+++ b/target/nextflow/bcftools/bcftools_concat/.config.vsh.yaml
@@ -221,6 +221,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -334,16 +337,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/bcftools/bcftools_concat"
   executable: "target/nextflow/bcftools/bcftools_concat/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/bcftools/bcftools_concat/main.nf b/target/nextflow/bcftools/bcftools_concat/main.nf
index b08c31f4..aadfd27a 100644
--- a/target/nextflow/bcftools/bcftools_concat/main.nf
+++ b/target/nextflow/bcftools/bcftools_concat/main.nf
@@ -1,6 +1,6 @@
 // bcftools_concat main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3066,6 +3297,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3206,16 +3441,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/bcftools/bcftools_concat",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/bcftools/bcftools_norm/.config.vsh.yaml b/target/nextflow/bcftools/bcftools_norm/.config.vsh.yaml
index 1cc23827..95813eb0 100644
--- a/target/nextflow/bcftools/bcftools_norm/.config.vsh.yaml
+++ b/target/nextflow/bcftools/bcftools_norm/.config.vsh.yaml
@@ -302,6 +302,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -415,16 +418,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/bcftools/bcftools_norm"
   executable: "target/nextflow/bcftools/bcftools_norm/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/bcftools/bcftools_norm/main.nf b/target/nextflow/bcftools/bcftools_norm/main.nf
index b96b07bb..08de353d 100644
--- a/target/nextflow/bcftools/bcftools_norm/main.nf
+++ b/target/nextflow/bcftools/bcftools_norm/main.nf
@@ -1,6 +1,6 @@
 // bcftools_norm main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3159,6 +3390,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3299,16 +3534,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/bcftools/bcftools_norm",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/bcftools/bcftools_sort/.config.vsh.yaml b/target/nextflow/bcftools/bcftools_sort/.config.vsh.yaml
index 2ee5be5f..5a27a99a 100644
--- a/target/nextflow/bcftools/bcftools_sort/.config.vsh.yaml
+++ b/target/nextflow/bcftools/bcftools_sort/.config.vsh.yaml
@@ -76,6 +76,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -184,16 +187,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/bcftools/bcftools_sort"
   executable: "target/nextflow/bcftools/bcftools_sort/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/bcftools/bcftools_sort/main.nf b/target/nextflow/bcftools/bcftools_sort/main.nf
index 7973d6d2..7bd3a01b 100644
--- a/target/nextflow/bcftools/bcftools_sort/main.nf
+++ b/target/nextflow/bcftools/bcftools_sort/main.nf
@@ -1,6 +1,6 @@
 // bcftools_sort main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -2916,6 +3147,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3047,16 +3282,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/bcftools/bcftools_sort",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/bcftools/bcftools_stats/.config.vsh.yaml b/target/nextflow/bcftools/bcftools_stats/.config.vsh.yaml
index 79c51a92..d3c84388 100644
--- a/target/nextflow/bcftools/bcftools_stats/.config.vsh.yaml
+++ b/target/nextflow/bcftools/bcftools_stats/.config.vsh.yaml
@@ -344,6 +344,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -457,16 +460,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/bcftools/bcftools_stats"
   executable: "target/nextflow/bcftools/bcftools_stats/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/bcftools/bcftools_stats/main.nf b/target/nextflow/bcftools/bcftools_stats/main.nf
index cd95e4a9..b08d2156 100644
--- a/target/nextflow/bcftools/bcftools_stats/main.nf
+++ b/target/nextflow/bcftools/bcftools_stats/main.nf
@@ -1,6 +1,6 @@
 // bcftools_stats main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3196,6 +3427,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3336,16 +3571,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/bcftools/bcftools_stats",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/bcl_convert/.config.vsh.yaml b/target/nextflow/bcl_convert/.config.vsh.yaml
index 8e3bc337..b0b7488e 100644
--- a/target/nextflow/bcl_convert/.config.vsh.yaml
+++ b/target/nextflow/bcl_convert/.config.vsh.yaml
@@ -290,6 +290,16 @@ argument_groups:
     direction: "output"
     multiple: false
     multiple_sep: ";"
+  - type: "boolean"
+    name: "--force"
+    description: "Allow destination directory to already exist and overwrite files.\n"
+    info: null
+    example:
+    - true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
 resources:
 - type: "bash_script"
   path: "script.sh"
@@ -303,6 +313,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -417,16 +430,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/bcl_convert"
   executable: "target/nextflow/bcl_convert/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/bcl_convert/main.nf b/target/nextflow/bcl_convert/main.nf
index fa2cffc0..3ef6bcf2 100644
--- a/target/nextflow/bcl_convert/main.nf
+++ b/target/nextflow/bcl_convert/main.nf
@@ -1,6 +1,6 @@
 // bcl_convert main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -177,7 +177,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -196,15 +196,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -217,6 +210,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1670,6 +1673,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1727,8 +1886,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1741,7 +1898,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1753,33 +1910,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1810,13 +1951,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1833,7 +1971,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1864,13 +2002,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1878,18 +2012,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2563,7 +2696,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2720,12 +2854,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2738,19 +2896,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2759,23 +2992,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3172,6 +3403,18 @@ meta = [
           "direction" : "output",
           "multiple" : false,
           "multiple_sep" : ";"
+        },
+        {
+          "type" : "boolean",
+          "name" : "--force",
+          "description" : "Allow destination directory to already exist and overwrite files.\n",
+          "example" : [
+            true
+          ],
+          "required" : false,
+          "direction" : "input",
+          "multiple" : false,
+          "multiple_sep" : ";"
         }
       ]
     }
@@ -3192,6 +3435,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3328,16 +3575,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/bcl_convert",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
@@ -3395,6 +3642,7 @@ $( if [ ! -z ${VIASH_PAR_BCL_SAMPLEPROJECT_SUBDIRECTORIES+x} ]; then echo "${VIA
 $( if [ ! -z ${VIASH_PAR_FASTQ_GZIP_COMPRESSION_LEVEL+x} ]; then echo "${VIASH_PAR_FASTQ_GZIP_COMPRESSION_LEVEL}" | sed "s#'#'\\"'\\"'#g;s#.*#par_fastq_gzip_compression_level='&'#" ; else echo "# par_fastq_gzip_compression_level="; fi )
 $( if [ ! -z ${VIASH_PAR_REPORTS+x} ]; then echo "${VIASH_PAR_REPORTS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_reports='&'#" ; else echo "# par_reports="; fi )
 $( if [ ! -z ${VIASH_PAR_LOGS+x} ]; then echo "${VIASH_PAR_LOGS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_logs='&'#" ; else echo "# par_logs="; fi )
+$( if [ ! -z ${VIASH_PAR_FORCE+x} ]; then echo "${VIASH_PAR_FORCE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_force='&'#" ; else echo "# par_force="; fi )
 $( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "${VIASH_META_NAME}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_name='&'#" ; else echo "# meta_name="; fi )
 $( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "${VIASH_META_FUNCTIONALITY_NAME}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_functionality_name='&'#" ; else echo "# meta_functionality_name="; fi )
 $( if [ ! -z ${VIASH_META_RESOURCES_DIR+x} ]; then echo "${VIASH_META_RESOURCES_DIR}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_resources_dir='&'#" ; else echo "# meta_resources_dir="; fi )
@@ -3419,9 +3667,13 @@ $( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}"
 
 set -eo pipefail
 
+[[ "\\$par_force" == "false" ]] && unset par_force
+
+
 \\$(which bcl-convert) \\\\
  --bcl-input-directory "\\$par_bcl_input_directory" \\\\
  --output-directory "\\$par_output_directory" \\\\
+  \\${par_force:+--force} \\\\
   \\${par_sample_sheet:+ --sample-sheet "\\$par_sample_sheet"} \\\\
   \\${par_run_info:+ --run-info "\\$par_run_info"} \\\\
   \\${par_bcl_only_lane:+ --bcl-only-lane "\\$par_bcl_only_lane"} \\\\
diff --git a/target/nextflow/bcl_convert/nextflow_schema.json b/target/nextflow/bcl_convert/nextflow_schema.json
index 2eec36de..9a5f8f8d 100644
--- a/target/nextflow/bcl_convert/nextflow_schema.json
+++ b/target/nextflow/bcl_convert/nextflow_schema.json
@@ -286,6 +286,16 @@
             }
     
 
+        ,
+                "force": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean`, example: `true`. Allow destination directory to already exist and overwrite files",
+                "help_text": "Type: `boolean`, example: `true`. Allow destination directory to already exist and overwrite files.\n"
+            
+            }
+    
+
 }
 },
     
diff --git a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml
index 276857a2..cd694ef5 100644
--- a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml
+++ b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml
@@ -159,6 +159,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -273,16 +276,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/bd_rhapsody/bd_rhapsody_make_reference"
   executable: "target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf
index c9451404..6fc23448 100644
--- a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf
+++ b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf
@@ -1,6 +1,6 @@
 // bd_rhapsody_make_reference main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -177,7 +177,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -196,15 +196,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -217,6 +210,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1670,6 +1673,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1727,8 +1886,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1741,7 +1898,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1753,33 +1910,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1810,13 +1951,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1833,7 +1971,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1864,13 +2002,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1878,18 +2012,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2563,7 +2696,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2720,12 +2854,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2738,19 +2896,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2759,23 +2992,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3004,6 +3235,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3145,16 +3380,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/bd_rhapsody/bd_rhapsody_make_reference",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml b/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml
index 7ef82413..49f74a12 100644
--- a/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml
+++ b/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml
@@ -989,6 +989,9 @@ test_resources:
   path: "helpers"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -1114,16 +1117,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis"
   executable: "target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/main.nf b/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/main.nf
index a76bbfa9..6fb0f07c 100644
--- a/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/main.nf
+++ b/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/main.nf
@@ -1,6 +1,6 @@
 // bd_rhapsody_sequence_analysis main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -177,7 +177,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -196,15 +196,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -217,6 +210,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1670,6 +1673,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1727,8 +1886,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1741,7 +1898,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1753,33 +1910,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1810,13 +1951,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1833,7 +1971,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1864,13 +2002,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1878,18 +2012,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2563,7 +2696,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2720,12 +2854,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2738,19 +2896,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2759,23 +2992,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -4036,6 +4267,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -4192,16 +4427,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/bedtools/bedtools_bamtobed/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_bamtobed/.config.vsh.yaml
index c2444185..32b4e9fd 100644
--- a/target/nextflow/bedtools/bedtools_bamtobed/.config.vsh.yaml
+++ b/target/nextflow/bedtools/bedtools_bamtobed/.config.vsh.yaml
@@ -124,6 +124,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -234,16 +237,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/bedtools/bedtools_bamtobed"
   executable: "target/nextflow/bedtools/bedtools_bamtobed/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/bedtools/bedtools_bamtobed/main.nf b/target/nextflow/bedtools/bedtools_bamtobed/main.nf
index f4957ec7..d22683bd 100644
--- a/target/nextflow/bedtools/bedtools_bamtobed/main.nf
+++ b/target/nextflow/bedtools/bedtools_bamtobed/main.nf
@@ -1,6 +1,6 @@
 // bedtools_bamtobed main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -2967,6 +3198,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3100,16 +3335,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/bedtools/bedtools_bamtobed",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml
index 495971a9..22a8671a 100644
--- a/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml
+++ b/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml
@@ -78,6 +78,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -186,16 +189,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/bedtools/bedtools_bamtofastq"
   executable: "target/nextflow/bedtools/bedtools_bamtofastq/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/bedtools/bedtools_bamtofastq/main.nf b/target/nextflow/bedtools/bedtools_bamtofastq/main.nf
index e2a2821e..96fb2bd3 100644
--- a/target/nextflow/bedtools/bedtools_bamtofastq/main.nf
+++ b/target/nextflow/bedtools/bedtools_bamtofastq/main.nf
@@ -1,6 +1,6 @@
 // bedtools_bamtofastq main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -2918,6 +3149,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3049,16 +3284,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/bedtools/bedtools_bamtofastq",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/bedtools/bedtools_bed12tobed6/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_bed12tobed6/.config.vsh.yaml
index 1d509846..119a044b 100644
--- a/target/nextflow/bedtools/bedtools_bed12tobed6/.config.vsh.yaml
+++ b/target/nextflow/bedtools/bedtools_bed12tobed6/.config.vsh.yaml
@@ -67,6 +67,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -175,16 +178,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/bedtools/bedtools_bed12tobed6"
   executable: "target/nextflow/bedtools/bedtools_bed12tobed6/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/bedtools/bedtools_bed12tobed6/main.nf b/target/nextflow/bedtools/bedtools_bed12tobed6/main.nf
index 16019625..6b41feac 100644
--- a/target/nextflow/bedtools/bedtools_bed12tobed6/main.nf
+++ b/target/nextflow/bedtools/bedtools_bed12tobed6/main.nf
@@ -1,6 +1,6 @@
 // bedtools_bed12tobed6 main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -2903,6 +3134,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3034,16 +3269,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/bedtools/bedtools_bed12tobed6",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml
index a518d2a1..9f7449af 100644
--- a/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml
+++ b/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml
@@ -98,6 +98,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -213,16 +216,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/bedtools/bedtools_bedtobam"
   executable: "target/nextflow/bedtools/bedtools_bedtobam/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/bedtools/bedtools_bedtobam/main.nf b/target/nextflow/bedtools/bedtools_bedtobam/main.nf
index 17adadae..81d6f526 100644
--- a/target/nextflow/bedtools/bedtools_bedtobam/main.nf
+++ b/target/nextflow/bedtools/bedtools_bedtobam/main.nf
@@ -1,6 +1,6 @@
 // bedtools_bedtobam main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -2940,6 +3171,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3082,16 +3317,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/bedtools/bedtools_bedtobam",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/bedtools/bedtools_genomecov/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_genomecov/.config.vsh.yaml
index 49a48c44..a88cc9fa 100644
--- a/target/nextflow/bedtools/bedtools_genomecov/.config.vsh.yaml
+++ b/target/nextflow/bedtools/bedtools_genomecov/.config.vsh.yaml
@@ -226,6 +226,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -336,16 +339,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/bedtools/bedtools_genomecov"
   executable: "target/nextflow/bedtools/bedtools_genomecov/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/bedtools/bedtools_genomecov/main.nf b/target/nextflow/bedtools/bedtools_genomecov/main.nf
index ff93428f..18aabc64 100644
--- a/target/nextflow/bedtools/bedtools_genomecov/main.nf
+++ b/target/nextflow/bedtools/bedtools_genomecov/main.nf
@@ -1,6 +1,6 @@
 // bedtools_genomecov main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3073,6 +3304,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3206,16 +3441,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/bedtools/bedtools_genomecov",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml
index dea43eb2..def30f30 100644
--- a/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml
+++ b/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml
@@ -123,6 +123,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -231,16 +234,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/bedtools/bedtools_getfasta"
   executable: "target/nextflow/bedtools/bedtools_getfasta/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/bedtools/bedtools_getfasta/main.nf b/target/nextflow/bedtools/bedtools_getfasta/main.nf
index d7826b8f..d42c74c9 100644
--- a/target/nextflow/bedtools/bedtools_getfasta/main.nf
+++ b/target/nextflow/bedtools/bedtools_getfasta/main.nf
@@ -1,6 +1,6 @@
 // bedtools_getfasta main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -2954,6 +3185,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3085,16 +3320,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/bedtools/bedtools_getfasta",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/bedtools/bedtools_groupby/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_groupby/.config.vsh.yaml
index 1cdd65d6..06b293d8 100644
--- a/target/nextflow/bedtools/bedtools_groupby/.config.vsh.yaml
+++ b/target/nextflow/bedtools/bedtools_groupby/.config.vsh.yaml
@@ -165,6 +165,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -272,16 +275,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/bedtools/bedtools_groupby"
   executable: "target/nextflow/bedtools/bedtools_groupby/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/bedtools/bedtools_groupby/main.nf b/target/nextflow/bedtools/bedtools_groupby/main.nf
index e473e220..40091865 100644
--- a/target/nextflow/bedtools/bedtools_groupby/main.nf
+++ b/target/nextflow/bedtools/bedtools_groupby/main.nf
@@ -1,6 +1,6 @@
 // bedtools_groupby main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -2999,6 +3230,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3129,16 +3364,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/bedtools/bedtools_groupby",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml
index add5f521..e5086a3e 100644
--- a/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml
+++ b/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml
@@ -301,6 +301,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -409,16 +412,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/bedtools/bedtools_intersect"
   executable: "target/nextflow/bedtools/bedtools_intersect/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/bedtools/bedtools_intersect/main.nf b/target/nextflow/bedtools/bedtools_intersect/main.nf
index 06311b92..c390b898 100644
--- a/target/nextflow/bedtools/bedtools_intersect/main.nf
+++ b/target/nextflow/bedtools/bedtools_intersect/main.nf
@@ -1,6 +1,6 @@
 // bedtools_intersect main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3150,6 +3381,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3281,16 +3516,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/bedtools/bedtools_intersect",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/bedtools/bedtools_links/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_links/.config.vsh.yaml
index 489b4461..0efcf7ad 100644
--- a/target/nextflow/bedtools/bedtools_links/.config.vsh.yaml
+++ b/target/nextflow/bedtools/bedtools_links/.config.vsh.yaml
@@ -100,6 +100,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -209,16 +212,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/bedtools/bedtools_links"
   executable: "target/nextflow/bedtools/bedtools_links/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/bedtools/bedtools_links/main.nf b/target/nextflow/bedtools/bedtools_links/main.nf
index 7dfc9e68..225d3f62 100644
--- a/target/nextflow/bedtools/bedtools_links/main.nf
+++ b/target/nextflow/bedtools/bedtools_links/main.nf
@@ -1,6 +1,6 @@
 // bedtools_links main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -2940,6 +3171,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3072,16 +3307,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/bedtools/bedtools_links",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/bedtools/bedtools_merge/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_merge/.config.vsh.yaml
index fd43b1c2..07ca993b 100644
--- a/target/nextflow/bedtools/bedtools_merge/.config.vsh.yaml
+++ b/target/nextflow/bedtools/bedtools_merge/.config.vsh.yaml
@@ -174,6 +174,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -278,16 +281,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/bedtools/bedtools_merge"
   executable: "target/nextflow/bedtools/bedtools_merge/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/bedtools/bedtools_merge/main.nf b/target/nextflow/bedtools/bedtools_merge/main.nf
index fc77ba2f..bbe032c6 100644
--- a/target/nextflow/bedtools/bedtools_merge/main.nf
+++ b/target/nextflow/bedtools/bedtools_merge/main.nf
@@ -1,6 +1,6 @@
 // bedtools_merge main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3007,6 +3238,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3133,16 +3368,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/bedtools/bedtools_merge",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml
index 66a2fdac..ef220eca 100644
--- a/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml
+++ b/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml
@@ -114,6 +114,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -221,16 +224,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/bedtools/bedtools_sort"
   executable: "target/nextflow/bedtools/bedtools_sort/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/bedtools/bedtools_sort/main.nf b/target/nextflow/bedtools/bedtools_sort/main.nf
index ed86b7a5..b15881c5 100644
--- a/target/nextflow/bedtools/bedtools_sort/main.nf
+++ b/target/nextflow/bedtools/bedtools_sort/main.nf
@@ -1,6 +1,6 @@
 // bedtools_sort main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -2961,6 +3192,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3091,16 +3326,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/bedtools/bedtools_sort",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml b/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml
index a874174e..1ad42c11 100644
--- a/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml
+++ b/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml
@@ -58,6 +58,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -157,16 +160,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/busco/busco_download_datasets"
   executable: "target/nextflow/busco/busco_download_datasets/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/busco/busco_download_datasets/main.nf b/target/nextflow/busco/busco_download_datasets/main.nf
index 4c261314..cb5a23e3 100644
--- a/target/nextflow/busco/busco_download_datasets/main.nf
+++ b/target/nextflow/busco/busco_download_datasets/main.nf
@@ -1,6 +1,6 @@
 // busco_download_datasets main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -2890,6 +3121,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3010,16 +3245,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/busco/busco_download_datasets",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml b/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml
index c511dc27..0e805d82 100644
--- a/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml
+++ b/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml
@@ -45,6 +45,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -144,16 +147,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/busco/busco_list_datasets"
   executable: "target/nextflow/busco/busco_list_datasets/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/busco/busco_list_datasets/main.nf b/target/nextflow/busco/busco_list_datasets/main.nf
index 6694dfc6..b19a9852 100644
--- a/target/nextflow/busco/busco_list_datasets/main.nf
+++ b/target/nextflow/busco/busco_list_datasets/main.nf
@@ -1,6 +1,6 @@
 // busco_list_datasets main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -2876,6 +3107,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -2996,16 +3231,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/busco/busco_list_datasets",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/busco/busco_run/.config.vsh.yaml b/target/nextflow/busco/busco_run/.config.vsh.yaml
index 52c6719b..fbac0abd 100644
--- a/target/nextflow/busco/busco_run/.config.vsh.yaml
+++ b/target/nextflow/busco/busco_run/.config.vsh.yaml
@@ -322,6 +322,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -422,16 +425,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/busco/busco_run"
   executable: "target/nextflow/busco/busco_run/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/busco/busco_run/main.nf b/target/nextflow/busco/busco_run/main.nf
index df9b3f54..d773ed76 100644
--- a/target/nextflow/busco/busco_run/main.nf
+++ b/target/nextflow/busco/busco_run/main.nf
@@ -1,6 +1,6 @@
 // busco_run main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3187,6 +3418,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3308,16 +3543,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/busco/busco_run",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/cellranger/cellranger_mkref/.config.vsh.yaml b/target/nextflow/cellranger/cellranger_mkref/.config.vsh.yaml
index 582288b4..2486aa64 100644
--- a/target/nextflow/cellranger/cellranger_mkref/.config.vsh.yaml
+++ b/target/nextflow/cellranger/cellranger_mkref/.config.vsh.yaml
@@ -75,6 +75,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -194,16 +197,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/cellranger/cellranger_mkref"
   executable: "target/nextflow/cellranger/cellranger_mkref/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/cellranger/cellranger_mkref/main.nf b/target/nextflow/cellranger/cellranger_mkref/main.nf
index 50c96604..dfaefea8 100644
--- a/target/nextflow/cellranger/cellranger_mkref/main.nf
+++ b/target/nextflow/cellranger/cellranger_mkref/main.nf
@@ -1,6 +1,6 @@
 // cellranger_mkref main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -2910,6 +3141,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3058,16 +3293,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/cellranger/cellranger_mkref",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/cutadapt/.config.vsh.yaml b/target/nextflow/cutadapt/.config.vsh.yaml
index 7cbe26aa..e27f3d8a 100644
--- a/target/nextflow/cutadapt/.config.vsh.yaml
+++ b/target/nextflow/cutadapt/.config.vsh.yaml
@@ -633,6 +633,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -739,16 +742,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/cutadapt"
   executable: "target/nextflow/cutadapt/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/cutadapt/main.nf b/target/nextflow/cutadapt/main.nf
index a7f02e16..a8309d4e 100644
--- a/target/nextflow/cutadapt/main.nf
+++ b/target/nextflow/cutadapt/main.nf
@@ -1,6 +1,6 @@
 // cutadapt main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3488,6 +3719,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3618,16 +3853,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/cutadapt",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/falco/.config.vsh.yaml b/target/nextflow/falco/.config.vsh.yaml
index 1040200b..9f76591a 100644
--- a/target/nextflow/falco/.config.vsh.yaml
+++ b/target/nextflow/falco/.config.vsh.yaml
@@ -203,6 +203,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -316,16 +319,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/falco"
   executable: "target/nextflow/falco/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/falco/main.nf b/target/nextflow/falco/main.nf
index 25db12d1..7e1b7edf 100644
--- a/target/nextflow/falco/main.nf
+++ b/target/nextflow/falco/main.nf
@@ -1,6 +1,6 @@
 // falco main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3031,6 +3262,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3169,16 +3404,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/falco",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/fastp/.config.vsh.yaml b/target/nextflow/fastp/.config.vsh.yaml
index 14c8381b..be1bef7b 100644
--- a/target/nextflow/fastp/.config.vsh.yaml
+++ b/target/nextflow/fastp/.config.vsh.yaml
@@ -982,6 +982,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -1082,16 +1085,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/fastp"
   executable: "target/nextflow/fastp/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/fastp/main.nf b/target/nextflow/fastp/main.nf
index b3df0432..945e6b4f 100644
--- a/target/nextflow/fastp/main.nf
+++ b/target/nextflow/fastp/main.nf
@@ -1,6 +1,6 @@
 // fastp main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3901,6 +4132,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -4022,16 +4257,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/fastp",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/fastqc/.config.vsh.yaml b/target/nextflow/fastqc/.config.vsh.yaml
index fdd44163..3bffecbd 100644
--- a/target/nextflow/fastqc/.config.vsh.yaml
+++ b/target/nextflow/fastqc/.config.vsh.yaml
@@ -239,6 +239,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -339,16 +342,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/fastqc"
   executable: "target/nextflow/fastqc/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/fastqc/main.nf b/target/nextflow/fastqc/main.nf
index 221b751c..9305e651 100644
--- a/target/nextflow/fastqc/main.nf
+++ b/target/nextflow/fastqc/main.nf
@@ -1,6 +1,6 @@
 // fastqc main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3062,6 +3293,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3181,16 +3416,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/fastqc",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/featurecounts/.config.vsh.yaml b/target/nextflow/featurecounts/.config.vsh.yaml
index f59e1f1a..51d03b41 100644
--- a/target/nextflow/featurecounts/.config.vsh.yaml
+++ b/target/nextflow/featurecounts/.config.vsh.yaml
@@ -543,6 +543,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -644,16 +647,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/featurecounts"
   executable: "target/nextflow/featurecounts/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/featurecounts/main.nf b/target/nextflow/featurecounts/main.nf
index d9852f3d..107b2863 100644
--- a/target/nextflow/featurecounts/main.nf
+++ b/target/nextflow/featurecounts/main.nf
@@ -1,6 +1,6 @@
 // featurecounts main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3427,6 +3658,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3548,16 +3783,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/featurecounts",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/fq_subsample/.config.vsh.yaml b/target/nextflow/fq_subsample/.config.vsh.yaml
index d56f5cb9..33a112c8 100644
--- a/target/nextflow/fq_subsample/.config.vsh.yaml
+++ b/target/nextflow/fq_subsample/.config.vsh.yaml
@@ -88,6 +88,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -189,16 +192,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/fq_subsample"
   executable: "target/nextflow/fq_subsample/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/fq_subsample/main.nf b/target/nextflow/fq_subsample/main.nf
index ae3f2e3d..ffcf6e1c 100644
--- a/target/nextflow/fq_subsample/main.nf
+++ b/target/nextflow/fq_subsample/main.nf
@@ -1,6 +1,6 @@
 // fq_subsample main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -173,7 +173,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -192,15 +192,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -213,6 +206,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1666,6 +1669,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1723,8 +1882,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1737,7 +1894,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1749,33 +1906,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1806,13 +1947,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1829,7 +1967,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1860,13 +1998,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1874,18 +2008,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2559,7 +2692,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2716,12 +2850,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2734,19 +2892,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2755,23 +2988,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -2914,6 +3145,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3031,16 +3266,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/fq_subsample",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/gffread/.config.vsh.yaml b/target/nextflow/gffread/.config.vsh.yaml
index 54dad4ba..c3dbdb94 100644
--- a/target/nextflow/gffread/.config.vsh.yaml
+++ b/target/nextflow/gffread/.config.vsh.yaml
@@ -582,6 +582,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -684,16 +687,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/gffread"
   executable: "target/nextflow/gffread/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/gffread/main.nf b/target/nextflow/gffread/main.nf
index 0b9416be..c06d5283 100644
--- a/target/nextflow/gffread/main.nf
+++ b/target/nextflow/gffread/main.nf
@@ -1,6 +1,6 @@
 // gffread main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3482,6 +3713,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3605,16 +3840,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/gffread",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml b/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml
index adb39ffd..2803bc9d 100644
--- a/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml
+++ b/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml
@@ -113,6 +113,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -217,16 +220,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/kallisto/kallisto_index"
   executable: "target/nextflow/kallisto/kallisto_index/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/kallisto/kallisto_index/main.nf b/target/nextflow/kallisto/kallisto_index/main.nf
index c324d4a8..00835142 100644
--- a/target/nextflow/kallisto/kallisto_index/main.nf
+++ b/target/nextflow/kallisto/kallisto_index/main.nf
@@ -1,6 +1,6 @@
 // kallisto_index main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -173,7 +173,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -192,15 +192,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -213,6 +206,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1666,6 +1669,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1723,8 +1882,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1737,7 +1894,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1749,33 +1906,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1806,13 +1947,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1829,7 +1967,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1860,13 +1998,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1874,18 +2008,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2559,7 +2692,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2716,12 +2850,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2734,19 +2892,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2755,23 +2988,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -2948,6 +3179,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3070,16 +3305,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/kallisto/kallisto_index",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml b/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml
index 75ae5e74..e3c16c0a 100644
--- a/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml
+++ b/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml
@@ -137,6 +137,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -245,16 +248,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/kallisto/kallisto_quant"
   executable: "target/nextflow/kallisto/kallisto_quant/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/kallisto/kallisto_quant/main.nf b/target/nextflow/kallisto/kallisto_quant/main.nf
index d8f9d467..6bd49ee8 100644
--- a/target/nextflow/kallisto/kallisto_quant/main.nf
+++ b/target/nextflow/kallisto/kallisto_quant/main.nf
@@ -1,6 +1,6 @@
 // kallisto_quant main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -173,7 +173,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -192,15 +192,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -213,6 +206,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1666,6 +1669,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1723,8 +1882,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1737,7 +1894,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1749,33 +1906,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1806,13 +1947,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1829,7 +1967,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1860,13 +1998,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1874,18 +2008,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2559,7 +2692,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2716,12 +2850,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2734,19 +2892,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2755,23 +2988,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -2975,6 +3206,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3104,16 +3339,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/kallisto/kallisto_quant",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml b/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml
index b87e1f30..c350bec1 100644
--- a/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml
+++ b/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml
@@ -403,6 +403,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -506,16 +509,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/lofreq/lofreq_call"
   executable: "target/nextflow/lofreq/lofreq_call/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/lofreq/lofreq_call/main.nf b/target/nextflow/lofreq/lofreq_call/main.nf
index ec74457f..a116bbe5 100644
--- a/target/nextflow/lofreq/lofreq_call/main.nf
+++ b/target/nextflow/lofreq/lofreq_call/main.nf
@@ -1,6 +1,6 @@
 // lofreq_call main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3290,6 +3521,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3413,16 +3648,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/lofreq/lofreq_call",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml b/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml
index c7b51039..56a45ca7 100644
--- a/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml
+++ b/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml
@@ -109,6 +109,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -214,16 +217,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/lofreq/lofreq_indelqual"
   executable: "target/nextflow/lofreq/lofreq_indelqual/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/lofreq/lofreq_indelqual/main.nf b/target/nextflow/lofreq/lofreq_indelqual/main.nf
index 9a41f985..13d0ab4c 100644
--- a/target/nextflow/lofreq/lofreq_indelqual/main.nf
+++ b/target/nextflow/lofreq/lofreq_indelqual/main.nf
@@ -1,6 +1,6 @@
 // lofreq_indelqual main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -2951,6 +3182,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3076,16 +3311,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/lofreq/lofreq_indelqual",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/multiqc/.config.vsh.yaml b/target/nextflow/multiqc/.config.vsh.yaml
index 3475e44c..9e93ba81 100644
--- a/target/nextflow/multiqc/.config.vsh.yaml
+++ b/target/nextflow/multiqc/.config.vsh.yaml
@@ -357,6 +357,9 @@ info:
     doi: "10.1093/bioinformatics/btw354"
   licence: "GPL v3 or later"
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -455,16 +458,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/multiqc"
   executable: "target/nextflow/multiqc/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/multiqc/main.nf b/target/nextflow/multiqc/main.nf
index 71ef4c3a..097b488e 100644
--- a/target/nextflow/multiqc/main.nf
+++ b/target/nextflow/multiqc/main.nf
@@ -1,6 +1,6 @@
 // multiqc main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3246,6 +3477,10 @@ meta = [
     "licence" : "GPL v3 or later"
   },
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3365,16 +3600,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/multiqc",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/nanoplot/.config.vsh.yaml b/target/nextflow/nanoplot/.config.vsh.yaml
index 6cdbe1f9..544d5411 100644
--- a/target/nextflow/nanoplot/.config.vsh.yaml
+++ b/target/nextflow/nanoplot/.config.vsh.yaml
@@ -390,6 +390,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -491,16 +494,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/nanoplot"
   executable: "target/nextflow/nanoplot/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/nanoplot/main.nf b/target/nextflow/nanoplot/main.nf
index 844558f1..cb13563e 100644
--- a/target/nextflow/nanoplot/main.nf
+++ b/target/nextflow/nanoplot/main.nf
@@ -1,6 +1,6 @@
 // nanoplot main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -173,7 +173,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -192,15 +192,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -213,6 +206,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1666,6 +1669,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1723,8 +1882,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1737,7 +1894,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1749,33 +1906,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1806,13 +1947,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1829,7 +1967,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1860,13 +1998,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1874,18 +2008,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2559,7 +2692,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2716,12 +2850,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2734,19 +2892,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2755,23 +2988,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3274,6 +3505,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3396,16 +3631,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/nanoplot",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/pear/.config.vsh.yaml b/target/nextflow/pear/.config.vsh.yaml
index 0eaa52da..bd4c95b9 100644
--- a/target/nextflow/pear/.config.vsh.yaml
+++ b/target/nextflow/pear/.config.vsh.yaml
@@ -295,6 +295,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -397,16 +400,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/pear"
   executable: "target/nextflow/pear/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/pear/main.nf b/target/nextflow/pear/main.nf
index 9a7f180f..9f299948 100644
--- a/target/nextflow/pear/main.nf
+++ b/target/nextflow/pear/main.nf
@@ -1,6 +1,6 @@
 // pear main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3136,6 +3367,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3258,16 +3493,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/pear",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml b/target/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml
index b4b05536..a659a086 100644
--- a/target/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml
+++ b/target/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml
@@ -161,6 +161,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -263,16 +266,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/qualimap/qualimap_rnaseq"
   executable: "target/nextflow/qualimap/qualimap_rnaseq/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/qualimap/qualimap_rnaseq/main.nf b/target/nextflow/qualimap/qualimap_rnaseq/main.nf
index 5acb4baa..50c27e8d 100644
--- a/target/nextflow/qualimap/qualimap_rnaseq/main.nf
+++ b/target/nextflow/qualimap/qualimap_rnaseq/main.nf
@@ -1,6 +1,6 @@
 // qualimap_rnaseq main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3005,6 +3236,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3128,16 +3363,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/qualimap/qualimap_rnaseq",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml b/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml
index 4e942c80..4119280c 100644
--- a/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml
+++ b/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml
@@ -724,6 +724,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -851,16 +854,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/rsem/rsem_calculate_expression"
   executable: "target/nextflow/rsem/rsem_calculate_expression/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/rsem/rsem_calculate_expression/main.nf b/target/nextflow/rsem/rsem_calculate_expression/main.nf
index 56e7d179..142c3e1a 100644
--- a/target/nextflow/rsem/rsem_calculate_expression/main.nf
+++ b/target/nextflow/rsem/rsem_calculate_expression/main.nf
@@ -1,6 +1,6 @@
 // rsem_calculate_expression main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -173,7 +173,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -192,15 +192,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -213,6 +206,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1666,6 +1669,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1723,8 +1882,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1737,7 +1894,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1749,33 +1906,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1806,13 +1947,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1829,7 +1967,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1860,13 +1998,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1874,18 +2008,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2559,7 +2692,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2716,12 +2850,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2734,19 +2892,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2755,23 +2988,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3514,6 +3745,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3660,16 +3895,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/rsem/rsem_calculate_expression",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml b/target/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml
index 94266b8a..0bf22bf8 100644
--- a/target/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml
+++ b/target/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml
@@ -268,6 +268,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -415,16 +418,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/rsem/rsem_prepare_reference"
   executable: "target/nextflow/rsem/rsem_prepare_reference/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/rsem/rsem_prepare_reference/main.nf b/target/nextflow/rsem/rsem_prepare_reference/main.nf
index e4f08ad0..d41661af 100644
--- a/target/nextflow/rsem/rsem_prepare_reference/main.nf
+++ b/target/nextflow/rsem/rsem_prepare_reference/main.nf
@@ -1,6 +1,6 @@
 // rsem_prepare_reference main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3085,6 +3316,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3244,16 +3479,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/rsem/rsem_prepare_reference",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml
index a1eb2e26..bbeee969 100644
--- a/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml
+++ b/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml
@@ -68,6 +68,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -174,16 +177,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/rseqc/rseqc_bamstat"
   executable: "target/nextflow/rseqc/rseqc_bamstat/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/rseqc/rseqc_bamstat/main.nf b/target/nextflow/rseqc/rseqc_bamstat/main.nf
index 043175f4..744ce51a 100644
--- a/target/nextflow/rseqc/rseqc_bamstat/main.nf
+++ b/target/nextflow/rseqc/rseqc_bamstat/main.nf
@@ -1,6 +1,6 @@
 // rseqc_bamstat main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -2905,6 +3136,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3035,16 +3270,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/rseqc/rseqc_bamstat",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml
index dd249054..74c12028 100644
--- a/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml
+++ b/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml
@@ -96,6 +96,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -200,16 +203,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/rseqc/rseqc_inferexperiment"
   executable: "target/nextflow/rseqc/rseqc_inferexperiment/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/rseqc/rseqc_inferexperiment/main.nf b/target/nextflow/rseqc/rseqc_inferexperiment/main.nf
index 8c96bf65..1592c7c7 100644
--- a/target/nextflow/rseqc/rseqc_inferexperiment/main.nf
+++ b/target/nextflow/rseqc/rseqc_inferexperiment/main.nf
@@ -1,6 +1,6 @@
 // rseqc_inferexperiment main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -2942,6 +3173,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3068,16 +3303,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/rseqc/rseqc_inferexperiment",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/rseqc/rseqc_inner_distance/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_inner_distance/.config.vsh.yaml
index 43639d09..ca1e49c5 100644
--- a/target/nextflow/rseqc/rseqc_inner_distance/.config.vsh.yaml
+++ b/target/nextflow/rseqc/rseqc_inner_distance/.config.vsh.yaml
@@ -185,6 +185,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -293,16 +296,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/rseqc/rseqc_inner_distance"
   executable: "target/nextflow/rseqc/rseqc_inner_distance/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/rseqc/rseqc_inner_distance/main.nf b/target/nextflow/rseqc/rseqc_inner_distance/main.nf
index 0a0e0ec0..c75f5ca6 100644
--- a/target/nextflow/rseqc/rseqc_inner_distance/main.nf
+++ b/target/nextflow/rseqc/rseqc_inner_distance/main.nf
@@ -1,6 +1,6 @@
 // rseqc_inner_distance main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3035,6 +3266,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3168,16 +3403,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/rseqc/rseqc_inner_distance",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/salmon/salmon_index/.config.vsh.yaml b/target/nextflow/salmon/salmon_index/.config.vsh.yaml
index 29e1d6a5..c806825b 100644
--- a/target/nextflow/salmon/salmon_index/.config.vsh.yaml
+++ b/target/nextflow/salmon/salmon_index/.config.vsh.yaml
@@ -176,6 +176,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -276,16 +279,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/salmon/salmon_index"
   executable: "target/nextflow/salmon/salmon_index/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/salmon/salmon_index/main.nf b/target/nextflow/salmon/salmon_index/main.nf
index 33a48b3a..539f673c 100644
--- a/target/nextflow/salmon/salmon_index/main.nf
+++ b/target/nextflow/salmon/salmon_index/main.nf
@@ -1,6 +1,6 @@
 // salmon_index main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3007,6 +3238,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3128,16 +3363,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/salmon/salmon_index",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/salmon/salmon_quant/.config.vsh.yaml b/target/nextflow/salmon/salmon_quant/.config.vsh.yaml
index cdcde821..90e00ae0 100644
--- a/target/nextflow/salmon/salmon_quant/.config.vsh.yaml
+++ b/target/nextflow/salmon/salmon_quant/.config.vsh.yaml
@@ -1072,6 +1072,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -1172,16 +1175,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/salmon/salmon_quant"
   executable: "target/nextflow/salmon/salmon_quant/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/salmon/salmon_quant/main.nf b/target/nextflow/salmon/salmon_quant/main.nf
index c86bbd59..1e5235fa 100644
--- a/target/nextflow/salmon/salmon_quant/main.nf
+++ b/target/nextflow/salmon/salmon_quant/main.nf
@@ -1,6 +1,6 @@
 // salmon_quant main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3842,6 +4073,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3963,16 +4198,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/salmon/salmon_quant",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/samtools/samtools_collate/.config.vsh.yaml b/target/nextflow/samtools/samtools_collate/.config.vsh.yaml
index dd352fbd..31cb199a 100644
--- a/target/nextflow/samtools/samtools_collate/.config.vsh.yaml
+++ b/target/nextflow/samtools/samtools_collate/.config.vsh.yaml
@@ -158,6 +158,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -263,16 +266,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/samtools/samtools_collate"
   executable: "target/nextflow/samtools/samtools_collate/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/samtools/samtools_collate/main.nf b/target/nextflow/samtools/samtools_collate/main.nf
index cd738bce..8435fd2a 100644
--- a/target/nextflow/samtools/samtools_collate/main.nf
+++ b/target/nextflow/samtools/samtools_collate/main.nf
@@ -1,6 +1,6 @@
 // samtools_collate main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3014,6 +3245,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3139,16 +3374,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_collate",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml b/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml
index 028cf6e8..8cbf015a 100644
--- a/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml
+++ b/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml
@@ -139,6 +139,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -242,16 +245,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/samtools/samtools_faidx"
   executable: "target/nextflow/samtools/samtools_faidx/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/samtools/samtools_faidx/main.nf b/target/nextflow/samtools/samtools_faidx/main.nf
index 2cb06f78..c18b22fd 100644
--- a/target/nextflow/samtools/samtools_faidx/main.nf
+++ b/target/nextflow/samtools/samtools_faidx/main.nf
@@ -1,6 +1,6 @@
 // samtools_faidx main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -2988,6 +3219,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3111,16 +3346,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_faidx",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml b/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml
index 4cbd67fd..4c3d80bb 100644
--- a/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml
+++ b/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml
@@ -328,6 +328,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -432,16 +435,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/samtools/samtools_fasta"
   executable: "target/nextflow/samtools/samtools_fasta/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/samtools/samtools_fasta/main.nf b/target/nextflow/samtools/samtools_fasta/main.nf
index ff2f5523..1ab5de62 100644
--- a/target/nextflow/samtools/samtools_fasta/main.nf
+++ b/target/nextflow/samtools/samtools_fasta/main.nf
@@ -1,6 +1,6 @@
 // samtools_fasta main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3179,6 +3410,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3303,16 +3538,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_fasta",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml b/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml
index 8dd1bf85..8cab0f46 100644
--- a/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml
+++ b/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml
@@ -328,6 +328,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -432,16 +435,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/samtools/samtools_fastq"
   executable: "target/nextflow/samtools/samtools_fastq/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/samtools/samtools_fastq/main.nf b/target/nextflow/samtools/samtools_fastq/main.nf
index 03d73ad1..b61561a3 100644
--- a/target/nextflow/samtools/samtools_fastq/main.nf
+++ b/target/nextflow/samtools/samtools_fastq/main.nf
@@ -1,6 +1,6 @@
 // samtools_fastq main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3179,6 +3410,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3303,16 +3538,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_fastq",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml b/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml
index 16adec46..d1cb5a55 100644
--- a/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml
+++ b/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml
@@ -66,6 +66,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -172,16 +175,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/samtools/samtools_flagstat"
   executable: "target/nextflow/samtools/samtools_flagstat/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/samtools/samtools_flagstat/main.nf b/target/nextflow/samtools/samtools_flagstat/main.nf
index 31df84f1..b54a8b9c 100644
--- a/target/nextflow/samtools/samtools_flagstat/main.nf
+++ b/target/nextflow/samtools/samtools_flagstat/main.nf
@@ -1,6 +1,6 @@
 // samtools_flagstat main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -2901,6 +3132,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3027,16 +3262,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_flagstat",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml b/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml
index ef273e92..b1857a39 100644
--- a/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml
+++ b/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml
@@ -75,6 +75,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -182,16 +185,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/samtools/samtools_idxstats"
   executable: "target/nextflow/samtools/samtools_idxstats/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/samtools/samtools_idxstats/main.nf b/target/nextflow/samtools/samtools_idxstats/main.nf
index 2729e99b..e52af7f6 100644
--- a/target/nextflow/samtools/samtools_idxstats/main.nf
+++ b/target/nextflow/samtools/samtools_idxstats/main.nf
@@ -1,6 +1,6 @@
 // samtools_idxstats main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -2912,6 +3143,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3039,16 +3274,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_idxstats",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/samtools/samtools_index/.config.vsh.yaml b/target/nextflow/samtools/samtools_index/.config.vsh.yaml
index a4ffaa2e..ed45e4d9 100644
--- a/target/nextflow/samtools/samtools_index/.config.vsh.yaml
+++ b/target/nextflow/samtools/samtools_index/.config.vsh.yaml
@@ -84,6 +84,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -188,16 +191,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/samtools/samtools_index"
   executable: "target/nextflow/samtools/samtools_index/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/samtools/samtools_index/main.nf b/target/nextflow/samtools/samtools_index/main.nf
index 85b710da..dd4a92b0 100644
--- a/target/nextflow/samtools/samtools_index/main.nf
+++ b/target/nextflow/samtools/samtools_index/main.nf
@@ -1,6 +1,6 @@
 // samtools_index main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -2928,6 +3159,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3052,16 +3287,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_index",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/samtools/samtools_sort/.config.vsh.yaml b/target/nextflow/samtools/samtools_sort/.config.vsh.yaml
index d341c2f9..fc9783da 100644
--- a/target/nextflow/samtools/samtools_sort/.config.vsh.yaml
+++ b/target/nextflow/samtools/samtools_sort/.config.vsh.yaml
@@ -227,6 +227,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -331,16 +334,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/samtools/samtools_sort"
   executable: "target/nextflow/samtools/samtools_sort/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/samtools/samtools_sort/main.nf b/target/nextflow/samtools/samtools_sort/main.nf
index 81aa788c..e269b9f2 100644
--- a/target/nextflow/samtools/samtools_sort/main.nf
+++ b/target/nextflow/samtools/samtools_sort/main.nf
@@ -1,6 +1,6 @@
 // samtools_sort main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3100,6 +3331,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3224,16 +3459,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_sort",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/samtools/samtools_stats/.config.vsh.yaml b/target/nextflow/samtools/samtools_stats/.config.vsh.yaml
index 208326ce..4db9eafc 100644
--- a/target/nextflow/samtools/samtools_stats/.config.vsh.yaml
+++ b/target/nextflow/samtools/samtools_stats/.config.vsh.yaml
@@ -295,6 +295,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -400,16 +403,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/samtools/samtools_stats"
   executable: "target/nextflow/samtools/samtools_stats/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/samtools/samtools_stats/main.nf b/target/nextflow/samtools/samtools_stats/main.nf
index 958eac0c..00f50e56 100644
--- a/target/nextflow/samtools/samtools_stats/main.nf
+++ b/target/nextflow/samtools/samtools_stats/main.nf
@@ -1,6 +1,6 @@
 // samtools_stats main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3169,6 +3400,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3294,16 +3529,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_stats",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/samtools/samtools_view/.config.vsh.yaml b/target/nextflow/samtools/samtools_view/.config.vsh.yaml
index 50f9b5d3..f281231b 100644
--- a/target/nextflow/samtools/samtools_view/.config.vsh.yaml
+++ b/target/nextflow/samtools/samtools_view/.config.vsh.yaml
@@ -559,6 +559,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -664,16 +667,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/samtools/samtools_view"
   executable: "target/nextflow/samtools/samtools_view/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/samtools/samtools_view/main.nf b/target/nextflow/samtools/samtools_view/main.nf
index 40a8728d..68ff5f34 100644
--- a/target/nextflow/samtools/samtools_view/main.nf
+++ b/target/nextflow/samtools/samtools_view/main.nf
@@ -1,6 +1,6 @@
 // samtools_view main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3350,6 +3581,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3475,16 +3710,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_view",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml b/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml
index 45d3777c..a76aed02 100644
--- a/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml
+++ b/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml
@@ -80,6 +80,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -172,16 +175,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/seqtk/seqtk_sample"
   executable: "target/nextflow/seqtk/seqtk_sample/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/seqtk/seqtk_sample/main.nf b/target/nextflow/seqtk/seqtk_sample/main.nf
index 2c87f2dc..483799d6 100644
--- a/target/nextflow/seqtk/seqtk_sample/main.nf
+++ b/target/nextflow/seqtk/seqtk_sample/main.nf
@@ -1,6 +1,6 @@
 // seqtk_sample main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -2922,6 +3153,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3029,16 +3264,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/seqtk/seqtk_sample",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml b/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml
index 8807886a..19cdb54f 100644
--- a/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml
+++ b/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml
@@ -99,6 +99,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -195,16 +198,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/seqtk/seqtk_subseq"
   executable: "target/nextflow/seqtk/seqtk_subseq/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/seqtk/seqtk_subseq/main.nf b/target/nextflow/seqtk/seqtk_subseq/main.nf
index d5da1598..b366919c 100644
--- a/target/nextflow/seqtk/seqtk_subseq/main.nf
+++ b/target/nextflow/seqtk/seqtk_subseq/main.nf
@@ -1,6 +1,6 @@
 // seqtk_subseq main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -2944,6 +3175,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3059,16 +3294,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/seqtk/seqtk_subseq",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/sgdemux/.config.vsh.yaml b/target/nextflow/sgdemux/.config.vsh.yaml
index 4161714b..0e48c531 100644
--- a/target/nextflow/sgdemux/.config.vsh.yaml
+++ b/target/nextflow/sgdemux/.config.vsh.yaml
@@ -328,6 +328,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -428,16 +431,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/sgdemux"
   executable: "target/nextflow/sgdemux/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/sgdemux/main.nf b/target/nextflow/sgdemux/main.nf
index 2defb908..cb95dced 100644
--- a/target/nextflow/sgdemux/main.nf
+++ b/target/nextflow/sgdemux/main.nf
@@ -1,6 +1,6 @@
 // sgdemux main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3181,6 +3412,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3302,16 +3537,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/sgdemux",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/snpeff/.config.vsh.yaml b/target/nextflow/snpeff/.config.vsh.yaml
index b597724e..fe4fcb79 100644
--- a/target/nextflow/snpeff/.config.vsh.yaml
+++ b/target/nextflow/snpeff/.config.vsh.yaml
@@ -523,6 +523,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -627,16 +630,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/snpeff"
   executable: "target/nextflow/snpeff/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/snpeff/main.nf b/target/nextflow/snpeff/main.nf
index 3bfe5c5b..be55883e 100644
--- a/target/nextflow/snpeff/main.nf
+++ b/target/nextflow/snpeff/main.nf
@@ -1,6 +1,6 @@
 // snpeff main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -173,7 +173,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -192,15 +192,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -213,6 +206,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1666,6 +1669,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1723,8 +1882,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1737,7 +1894,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1749,33 +1906,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1806,13 +1947,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1829,7 +1967,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1860,13 +1998,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1874,18 +2008,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2559,7 +2692,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2716,12 +2850,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2734,19 +2892,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2755,23 +2988,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3430,6 +3661,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3554,16 +3789,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/snpeff",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/sortmerna/.config.vsh.yaml b/target/nextflow/sortmerna/.config.vsh.yaml
index fff395c0..68783c77 100644
--- a/target/nextflow/sortmerna/.config.vsh.yaml
+++ b/target/nextflow/sortmerna/.config.vsh.yaml
@@ -487,6 +487,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -593,16 +596,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/sortmerna"
   executable: "target/nextflow/sortmerna/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/sortmerna/main.nf b/target/nextflow/sortmerna/main.nf
index ba848a9f..1de70e61 100644
--- a/target/nextflow/sortmerna/main.nf
+++ b/target/nextflow/sortmerna/main.nf
@@ -1,6 +1,6 @@
 // sortmerna main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -173,7 +173,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -192,15 +192,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -213,6 +206,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1666,6 +1669,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1723,8 +1882,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1737,7 +1894,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1749,33 +1906,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1806,13 +1947,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1829,7 +1967,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1860,13 +1998,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1874,18 +2008,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2559,7 +2692,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2716,12 +2850,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2734,19 +2892,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2755,23 +2988,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3333,6 +3564,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3459,16 +3694,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/sortmerna",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/star/star_align_reads/.config.vsh.yaml b/target/nextflow/star/star_align_reads/.config.vsh.yaml
index 86213b48..f05a813f 100644
--- a/target/nextflow/star/star_align_reads/.config.vsh.yaml
+++ b/target/nextflow/star/star_align_reads/.config.vsh.yaml
@@ -2540,6 +2540,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -2662,16 +2665,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/star/star_align_reads"
   executable: "target/nextflow/star/star_align_reads/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/star/star_align_reads/main.nf b/target/nextflow/star/star_align_reads/main.nf
index 97daee43..845d9faa 100644
--- a/target/nextflow/star/star_align_reads/main.nf
+++ b/target/nextflow/star/star_align_reads/main.nf
@@ -1,6 +1,6 @@
 // star_align_reads main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -177,7 +177,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -196,15 +196,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -217,6 +210,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1670,6 +1673,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1727,8 +1886,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1741,7 +1898,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1753,33 +1910,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1810,13 +1951,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1833,7 +1971,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1864,13 +2002,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1878,18 +2012,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2563,7 +2696,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2720,12 +2854,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2738,19 +2896,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2759,23 +2992,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -5794,6 +6025,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -5942,16 +6177,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/star/star_align_reads",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/star/star_genome_generate/.config.vsh.yaml b/target/nextflow/star/star_genome_generate/.config.vsh.yaml
index 2a127406..a3d3a324 100644
--- a/target/nextflow/star/star_genome_generate/.config.vsh.yaml
+++ b/target/nextflow/star/star_genome_generate/.config.vsh.yaml
@@ -221,6 +221,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -332,16 +335,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/star/star_genome_generate"
   executable: "target/nextflow/star/star_genome_generate/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/star/star_genome_generate/main.nf b/target/nextflow/star/star_genome_generate/main.nf
index 17e745a0..a84bf6cd 100644
--- a/target/nextflow/star/star_genome_generate/main.nf
+++ b/target/nextflow/star/star_genome_generate/main.nf
@@ -1,6 +1,6 @@
 // star_genome_generate main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3063,6 +3294,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3194,16 +3429,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/star/star_genome_generate",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
@@ -3292,10 +3527,10 @@ STAR \\\\
     \\${par_genome_sa_index_nbases:+--genomeSAindexNbases "\\${par_genome_sa_index_nbases}"} \\\\
     \\${par_sjdb_gtf_chr_prefix:+--sjdbGTFchrPrefix "\\${par_sjdb_gtf_chr_prefix}"} \\\\
     \\${par_sjdb_gtf_feature_exon:+--sjdbGTFfeatureExon "\\${par_sjdb_gtf_feature_exon}"} \\\\
-    \\${par_sjdb_gtf_tag_exon_parent_transcript:+--sjdbGTFtag_exon_parent_transcript "\\${par_sjdb_gtf_tag_exon_parent_transcript}"} \\\\
-    \\${par_sjdb_gtf_tag_exon_parent_gene:+--sjdbGTFtag_exon_parent_gene "\\${par_sjdb_gtf_tag_exon_parent_gene}"} \\\\
-    \\${par_sjdb_gtf_tag_exon_parent_geneName:+--sjdbGTFtag_exon_parent_geneName "\\${par_sjdb_gtf_tag_exon_parent_geneName}"} \\\\
-    \\${par_sjdb_gtf_tag_exon_parent_geneType:+--sjdbGTFtag_exon_parent_geneType "\\${sjdbGTFtag_exon_parent_geneType}"} \\\\
+    \\${par_sjdb_gtf_tag_exon_parent_transcript:+--sjdbGTFtagExonParentTranscript "\\${par_sjdb_gtf_tag_exon_parent_transcript}"} \\\\
+    \\${par_sjdb_gtf_tag_exon_parent_gene:+--sjdbGTFtagExonParentGene "\\${par_sjdb_gtf_tag_exon_parent_gene}"} \\\\
+    \\${sjdb_gtf_tag_exon_parent_gene_name:+--sjdbGTFtagExonParentGeneName "\\${sjdb_gtf_tag_exon_parent_gene_name}"} \\\\
+    \\${sjdb_gtf_tag_exon_parent_gene_type:+--sjdbGTFtagExonParentGeneType "\\${sjdb_gtf_tag_exon_parent_gene_type}"} \\\\
     \\${par_limit_genome_generate_ram:+--limitGenomeGenerateRAM "\\${par_limit_genome_generate_ram}"} \\\\
     \\${par_genome_chr_bin_nbits:+--genomeChrBinNbits "\\${par_genome_chr_bin_nbits}"} \\\\
     \\${par_genome_sa_sparse_d:+--genomeSAsparseD "\\${par_genome_sa_sparse_d}"} \\\\
diff --git a/target/nextflow/trimgalore/.config.vsh.yaml b/target/nextflow/trimgalore/.config.vsh.yaml
index a46f4921..296794ad 100644
--- a/target/nextflow/trimgalore/.config.vsh.yaml
+++ b/target/nextflow/trimgalore/.config.vsh.yaml
@@ -668,6 +668,9 @@ test_resources:
   is_executable: true
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -769,16 +772,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/trimgalore"
   executable: "target/nextflow/trimgalore/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/trimgalore/main.nf b/target/nextflow/trimgalore/main.nf
index c46ce511..dacfdc3b 100644
--- a/target/nextflow/trimgalore/main.nf
+++ b/target/nextflow/trimgalore/main.nf
@@ -1,6 +1,6 @@
 // trimgalore main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3438,6 +3669,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3559,16 +3794,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/trimgalore",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/umi_tools/umi_tools_dedup/.config.vsh.yaml b/target/nextflow/umi_tools/umi_tools_dedup/.config.vsh.yaml
index 6296dff4..d268cb7d 100644
--- a/target/nextflow/umi_tools/umi_tools_dedup/.config.vsh.yaml
+++ b/target/nextflow/umi_tools/umi_tools_dedup/.config.vsh.yaml
@@ -509,6 +509,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -610,16 +613,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/umi_tools/umi_tools_dedup"
   executable: "target/nextflow/umi_tools/umi_tools_dedup/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/umi_tools/umi_tools_dedup/main.nf b/target/nextflow/umi_tools/umi_tools_dedup/main.nf
index 910e67d1..4e0c2739 100644
--- a/target/nextflow/umi_tools/umi_tools_dedup/main.nf
+++ b/target/nextflow/umi_tools/umi_tools_dedup/main.nf
@@ -1,6 +1,6 @@
 // umi_tools_dedup main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -176,7 +176,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -195,15 +195,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -216,6 +209,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1669,6 +1672,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1726,8 +1885,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1740,7 +1897,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1752,33 +1909,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1809,13 +1950,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1832,7 +1970,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1863,13 +2001,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1877,18 +2011,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2562,7 +2695,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2719,12 +2853,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2737,19 +2895,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2758,23 +2991,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3364,6 +3595,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3486,16 +3721,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/umi_tools/umi_tools_dedup",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml b/target/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml
index dea32d25..0fac1e2f 100644
--- a/target/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml
+++ b/target/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml
@@ -331,6 +331,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -433,16 +436,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/umi_tools/umi_tools_extract"
   executable: "target/nextflow/umi_tools/umi_tools_extract/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/umi_tools/umi_tools_extract/main.nf b/target/nextflow/umi_tools/umi_tools_extract/main.nf
index af503a79..3b4950bf 100644
--- a/target/nextflow/umi_tools/umi_tools_extract/main.nf
+++ b/target/nextflow/umi_tools/umi_tools_extract/main.nf
@@ -1,6 +1,6 @@
 // umi_tools_extract main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -173,7 +173,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -192,15 +192,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -213,6 +206,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1666,6 +1669,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1723,8 +1882,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1737,7 +1894,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1749,33 +1906,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1806,13 +1947,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1829,7 +1967,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1860,13 +1998,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1874,18 +2008,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2559,7 +2692,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2716,12 +2850,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2734,19 +2892,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2755,23 +2988,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -3175,6 +3406,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3298,16 +3533,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/umi_tools/umi_tools_extract",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
diff --git a/target/nextflow/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml b/target/nextflow/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml
index 30bbe4a2..0c3f2392 100644
--- a/target/nextflow/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml
+++ b/target/nextflow/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml
@@ -153,6 +153,9 @@ test_resources:
   path: "test_data"
 info: null
 status: "enabled"
+scope:
+  image: "public"
+  target: "public"
 requirements:
   commands:
   - "ps"
@@ -255,16 +258,16 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/umi_tools/umi_tools_prepareforrsem"
   executable: "target/nextflow/umi_tools/umi_tools_prepareforrsem/main.nf"
-  viash_version: "0.9.0"
-  git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
-  git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-27-g952ff08"
+  viash_version: "0.9.2"
+  git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
+  git_remote: "https://github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-30-g5f6516e"
 package_config:
   name: "biobox"
   version: "main"
   description: "A collection of bioinformatics tools for working with sequence data.\n"
   info: null
-  viash_version: "0.9.0"
+  viash_version: "0.9.2"
   source: "src"
   target: "target"
   config_mods:
diff --git a/target/nextflow/umi_tools/umi_tools_prepareforrsem/main.nf b/target/nextflow/umi_tools/umi_tools_prepareforrsem/main.nf
index df5b652b..6fbffff0 100644
--- a/target/nextflow/umi_tools/umi_tools_prepareforrsem/main.nf
+++ b/target/nextflow/umi_tools/umi_tools_prepareforrsem/main.nf
@@ -1,6 +1,6 @@
 // umi_tools_prepareforrsem main
 // 
-// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -173,7 +173,7 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
 Map _processInputValues(Map inputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
     config.allArguments.each { arg ->
-      if (arg.required) {
+      if (arg.required && arg.direction == "input") {
         assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
           "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
       }
@@ -192,15 +192,8 @@ Map _processInputValues(Map inputs, Map config, String id, String key) {
 }
 
 // helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
-Map _processOutputValues(Map outputs, Map config, String id, String key) {
+Map _checkValidOutputArgument(Map outputs, Map config, String id, String key) {
   if (!workflow.stubRun) {
-    config.allArguments.each { arg ->
-      if (arg.direction == "output" && arg.required) {
-        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
-          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
-      }
-    }
-
     outputs = outputs.collectEntries { name, value ->
       def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
       assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
@@ -213,6 +206,16 @@ Map _processOutputValues(Map outputs, Map config, String id, String key) {
   return outputs
 }
 
+void _checkAllRequiredOuputsPresent(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+  }
+}
 // helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
 class IDChecker {
   final def items = [] as Set
@@ -1666,6 +1669,162 @@ def joinStates(Closure apply_) {
   }
   return joinStatesWf
 }
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishFiles.nf'
+def publishFiles(Map args) {
+  def key_ = args.get("key")
+
+  assert key_ != null : "publishFiles: key must be specified"
+  
+  workflow publishFilesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          [id_, inputFiles_, outputFilenames_]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesWf
+}
+
+process publishFilesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+  echo "Copying output files to destination folder"
+  ${copyCommands.join("\n  ")}
+  """
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishFilesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishFilesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishFilesByConfig: key must be specified"
+  
+  workflow publishFilesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output OR multiple channels were emitted
+                // and the output was just not added to using the channel
+                // that is now being parsed
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$\\{id\\}', id_)
+                  .replaceAll('\\$key', key_)
+                  .replaceAll('\\$\\{key\\}', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+
+          [id_, inputPaths, outputFilenames]
+        }
+        | publishFilesProc
+    emit: input_ch
+  }
+  return publishFilesSimpleWf
+}
+
+
+
+
 // helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
 def collectFiles(obj) {
   if (obj instanceof java.io.File || obj instanceof Path)  {
@@ -1723,8 +1882,6 @@ def publishStates(Map args) {
 
           // the input files and the target output filenames
           def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
-          def inputFiles_ = inputoutputFilenames_[0]
-          def outputFilenames_ = inputoutputFilenames_[1]
 
           def yamlFilename = yamlTemplate_
             .replaceAll('\\$id', id_)
@@ -1737,7 +1894,7 @@ def publishStates(Map args) {
           // convert state to yaml blob
           def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
 
-          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -1749,33 +1906,17 @@ process publishStatesProc {
   publishDir path: "${getPublishDir()}/", mode: "copy"
   tag "$id"
   input:
-    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+    tuple val(id), val(yamlBlob), val(yamlFile)
   output:
-    tuple val(id), path{[yamlFile] + outputFiles}
+    tuple val(id), path{[yamlFile]}
   script:
-  def copyCommands = [
-    inputFiles instanceof List ? inputFiles : [inputFiles],
-    outputFiles instanceof List ? outputFiles : [outputFiles]
-  ]
-    .transpose()
-    .collectMany{infile, outfile ->
-      if (infile.toString() != outfile.toString()) {
-        [
-          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
-          "cp -r '${infile.toString()}' '${outfile.toString()}'"
-        ]
-      } else {
-        // no need to copy if infile is the same as outfile
-        []
-      }
-    }
   """
-mkdir -p "\$(dirname '${yamlFile}')"
-echo "Storing state as yaml"
-echo '${yamlBlob}' > '${yamlFile}'
-echo "Copying output files to destination folder"
-${copyCommands.join("\n  ")}
-"""
+  mkdir -p "\$(dirname '${yamlFile}')"
+  echo "Storing state as yaml"
+  cat > '${yamlFile}' << HERE
+${yamlBlob}
+HERE
+  """
 }
 
 
@@ -1806,13 +1947,10 @@ def publishStatesByConfig(Map args) {
             .replaceAll('\\$\\{key\\}', key_)
           def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
 
-          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          // the processed state is a list of [key, value] tuples, where
           //   - key is a String
           //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
-          //   - inputPath is a List[Path]
-          //   - outputFilename is a List[String]
           //   - (key, value) are the tuples that will be saved to the state.yaml file
-          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
           def processedState =
             config.allArguments
               .findAll { it.direction == "output" }
@@ -1829,7 +1967,7 @@ def publishStatesByConfig(Map args) {
                 // in the state as-is, but is not something that needs 
                 // to be copied from the source path to the dest path
                 if (par.type != "file") {
-                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                  return [[key: plainName_, value: value]]
                 }
                 // if the orig state does not contain this filename,
                 // it's an optional argument for which the user specified
@@ -1860,13 +1998,9 @@ def publishStatesByConfig(Map args) {
                     if (yamlDir != null) {
                       value_ = yamlDir.relativize(value_)
                     }
-                    def inputPath = val instanceof File ? val.toPath() : val
-                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                    return value_
                   }
-                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
-                    [key, outputPerFile.collect{dic -> dic[key]}]
-                  }
-                  return [[key: plainName_] + transposedOutputs]
+                  return [["key": plainName_, "value": outputPerFile]]
                 } else {
                   def value_ = java.nio.file.Paths.get(filename)
                   // if id contains a slash
@@ -1874,18 +2008,17 @@ def publishStatesByConfig(Map args) {
                     value_ = yamlDir.relativize(value_)
                   }
                   def inputPath = value instanceof File ? value.toPath() : value
-                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                  return [["key": plainName_, value: value_]]
                 }
               }
+              
           
           def updatedState_ = processedState.collectEntries{[it.key, it.value]}
-          def inputPaths = processedState.collectMany{it.inputPath}
-          def outputFilenames = processedState.collectMany{it.outputFilename}
           
           // convert state to yaml blob
           def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
 
-          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+          [id_, yamlBlob_, yamlFilename]
         }
         | publishStatesProc
     emit: input_ch
@@ -2559,7 +2692,8 @@ def _debug(workflowArgs, debugKey) {
 def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
   def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
   def key_ = workflowArgs["key"]
-  
+  def multipleArgs = meta.config.allArguments.findAll{ it.multiple }.collect{it.plainName}
+
   workflow workflowInstance {
     take: input_
 
@@ -2716,12 +2850,36 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
-    def chInitialOutput = chArgsWithDefaults
+    def chInitialOutputMulti = chArgsWithDefaults
       | _debug(workflowArgs, "processed")
       // run workflow
       | innerWorkflowFactory(workflowArgs)
-      // check output tuple
-      | map { id_, output_ ->
+    def chInitialOutputList = chInitialOutputMulti instanceof List ? chInitialOutputMulti : [chInitialOutputMulti]
+    assert chInitialOutputList.size() > 0: "should have emitted at least one output channel"
+    // Add a channel ID to the events, which designates the channel the event was emitted from as a running number
+    // This number is used to sort the events later when the events are gathered from across the channels.
+    def chInitialOutputListWithIndexedEvents = chInitialOutputList.withIndex().collect{channel, channelIndex ->
+      def newChannel = channel
+        | map {tuple ->
+          assert tuple instanceof List : 
+          "Error in module '${key_}': element in output channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        
+          def newEvent = [channelIndex] + tuple
+          return newEvent
+        }
+      return newChannel
+    }
+    // Put the events into 1 channel, cover case where there is only one channel is emitted
+    def chInitialOutput = chInitialOutputList.size() > 1 ? \
+      chInitialOutputListWithIndexedEvents[0].mix(*chInitialOutputListWithIndexedEvents.tail()) : \
+      chInitialOutputListWithIndexedEvents[0]
+    def chInitialOutputProcessed = chInitialOutput
+      | map { tuple  ->
+        def channelId = tuple[0]
+        def id_ = tuple[1]
+        def output_ = tuple[2]
 
         // see if output map contains metadata
         def meta_ =
@@ -2734,19 +2892,94 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
         output_ = output_.findAll{k, v -> k != "_meta"}
 
         // check value types
-        output_ = _processOutputValues(output_, meta.config, id_, key_)
+        output_ = _checkValidOutputArgument(output_, meta.config, id_, key_)
 
-        // simplify output if need be
-        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
-          output_ = output_.values()[0]
-        }
-
-        [join_id, id_, output_]
+        [join_id, channelId, id_, output_]
       }
       // | view{"chInitialOutput: ${it.take(3)}"}
 
+    // join the output [prev_id, channel_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chPublishWithPreviousState = safeJoin(chInitialOutputProcessed, chRunFiltered, key_)
+      // input tuple format: [join_id, channel_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, channel_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(2).take(3))
+        tup.take(3) + [new_state] + tup.drop(5)
+      }
+    if (workflowArgs.auto.publish == "state") {
+      def chPublishFiles = chPublishWithPreviousState
+        // input tuple format: [join_id, channel_id, id, new_state, ...]
+        // output tuple format: [join_id, channel_id, id, new_state]
+        | map{ tup ->
+          tup.take(4)
+        }
+
+      safeJoin(chPublishFiles, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, channel_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(2).take(3)
+        }
+        | publishFilesByConfig(key: key_, config: meta.config)
+    }
+    // Join the state from the events that were emitted from different channels
+    def chJoined = chInitialOutputProcessed
+      | map {tuple ->
+        def join_id = tuple[0]
+        def channel_id = tuple[1]
+        def id = tuple[2]
+        def other = tuple.drop(3)
+        // Below, groupTuple is used to join the events. To make sure resuming a workflow
+        // keeps working, the output state must be deterministic. This means the state needs to be
+        // sorted with groupTuple's has a 'sort' argument. This argument can be set to 'hash',
+        // but hashing the state when it is large can be problematic in terms of performance.
+        // Therefore, a custom comparator function is provided. We add the channel ID to the 
+        // states so that we can use the channel ID to sort the items. 
+        def stateWithChannelID = [[channel_id] * other.size(), other].transpose()
+        // A comparator that is provided to groupTuple's 'sort' argument is applied
+        // to all elements of the event tuple (that is not the 'id'). The comparator
+        // closure that is used below expects the input to be List. So the join_id and
+        // channel_id must also be wrapped in a list. 
+        [[join_id], [channel_id], id] + stateWithChannelID
+      }
+      | groupTuple(by: 2, sort: {a, b -> a[0] <=> b[0]}, size: chInitialOutputList.size(), remainder: true)
+      | map {join_ids, _, id, statesWithChannelID ->
+        // Remove the channel IDs from the states
+        def states = statesWithChannelID.collect{it[1]}
+        def newJoinId = join_ids.flatten().unique{a, b -> a <=> b}
+        assert newJoinId.size() == 1: "Multiple events were emitted for '$id'."
+        def newJoinIdUnique = newJoinId[0]
+        
+        // Merge the states from the different channels
+        def newState = states.inject([:]){ old_state, state_to_add ->
+          return old_state + state_to_add.collectEntries{k, v -> 
+            if (!multipleArgs.contains(k)) {
+              // if the key is not a multiple argument, we expect only one value
+              if (old_state.containsKey(k)) {
+                assert old_state[k] == v : "ID $id: multiple entries for argument $k were emitted."
+              }
+              [k, v]
+            } else {
+              // if the key is a multiple argument, append the different values into one list
+              def prevValue = old_state.getOrDefault(k, [])
+              def prevValueAsList = prevValue instanceof List ? prevValue : [prevValue]
+              [k, prevValueAsList + v]
+            }
+          }
+        }
+
+        _checkAllRequiredOuputsPresent(newState, meta.config, id, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && newState.size() == 1) {
+          newState = newState.values()[0]
+        }
+
+        return [newJoinIdUnique, id, newState]
+      }
+    
     // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
-    def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
+    def chNewState = safeJoin(chJoined, chRunFiltered, key_)
       // input tuple format: [join_id, id, output, prev_state, ...]
       // output tuple format: [join_id, id, new_state, ...]
       | map{ tup ->
@@ -2755,23 +2988,21 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
       }
 
     if (workflowArgs.auto.publish == "state") {
-      def chPublish = chNewState
+      def chPublishStates = chNewState
         // input tuple format: [join_id, id, new_state, ...]
         // output tuple format: [join_id, id, new_state]
         | map{ tup ->
           tup.take(3)
         }
 
-      safeJoin(chPublish, chArgsWithDefaults, key_)
+      safeJoin(chPublishStates, chArgsWithDefaults, key_)
         // input tuple format: [join_id, id, new_state, orig_state, ...]
         // output tuple format: [id, new_state, orig_state]
         | map { tup ->
           tup.drop(1).take(3)
-      }
+        }
         | publishStatesByConfig(key: key_, config: meta.config)
     }
-
-    // remove join_id and meta
     chReturn = chNewState
       | map { tup ->
         // input tuple format: [join_id, id, new_state, ...]
@@ -2997,6 +3228,10 @@ meta = [
     }
   ],
   "status" : "enabled",
+  "scope" : {
+    "image" : "public",
+    "target" : "public"
+  },
   "requirements" : {
     "commands" : [
       "ps"
@@ -3120,16 +3355,16 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/umi_tools/umi_tools_prepareforrsem",
-    "viash_version" : "0.9.0",
-    "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
-    "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-27-g952ff08"
+    "viash_version" : "0.9.2",
+    "git_commit" : "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde",
+    "git_remote" : "https://github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-30-g5f6516e"
   },
   "package_config" : {
     "name" : "biobox",
     "version" : "main",
     "description" : "A collection of bioinformatics tools for working with sequence data.\n",
-    "viash_version" : "0.9.0",
+    "viash_version" : "0.9.2",
     "source" : "src",
     "target" : "target",
     "config_mods" : [