Build branch main with version main (5f6516e)

Build pipeline: viash-hub.biobox.main-v9whr

Source commit: 5f6516e9c0

Source message: Bump viash version (#172)

* bump viash version

* fix agat requirements

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).

_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']

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 ]

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:

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:

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 ]

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:

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:

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:

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:

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:

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 ]

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:

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 ]

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

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"} \

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}"} \

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

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:

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=''
 

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:

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=''
 

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:

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=''
 

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:

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=''
 

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:

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=''
 

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:

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=''
 

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:

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=''
 

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:

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=''
 

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:

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=''
 

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:

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=''
 

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:

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=''
 

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:

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=''
 

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:

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=''
 

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:

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=''
 

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:

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=''
 

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:

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=''
 

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:

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=''
 

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:

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=''
 

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:

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=''
 

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:

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=''
 

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:

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"} \\

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:

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=''
 

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:

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=''
 

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:

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=''
 

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:

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=''
 

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:

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=''
 

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:

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=''
 

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:

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=''
 

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:

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=''
 

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:

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=''
 

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:

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=''
 

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:

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=''
 

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:

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=''
 

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:

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=''
 

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:

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=''
 

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:

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=''
 

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:

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=''
 

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:

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=''
 

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:

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=''
 

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:

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=''
 

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:

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=''