diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6bd21a1e..2f4c0c71 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -31,6 +31,8 @@
   - `bedtools/bedtools_sort`: Sorts a feature file (bed/gff/vcf) by chromosome and other criteria (PR #98).
   - `bedtools/bedtools_bamtofastq`: Convert BAM alignments to FASTQ files (PR #101).
   - `bedtools/bedtools_bedtobam`: Converts genomic feature records (bed/gff/vcf) to BAM format (PR #111).
+ 
+* `qualimap/qualimap_rnaseq`: RNA-seq QC analysis using qualimap (PR #74). 
 
 ## MINOR CHANGES
 
diff --git a/src/qualimap/qualimap_rnaseq/config.vsh.yaml b/src/qualimap/qualimap_rnaseq/config.vsh.yaml
new file mode 100644
index 00000000..ffc807ab
--- /dev/null
+++ b/src/qualimap/qualimap_rnaseq/config.vsh.yaml
@@ -0,0 +1,103 @@
+name: qualimap_rnaseq
+namespace: qualimap
+keywords: [RNA-seq, quality control, QC Report]
+description: |
+  Qualimap RNA-seq QC reports quality control metrics and bias estimations 
+  which are specific for whole transcriptome sequencing, including reads genomic 
+  origin, junction analysis, transcript coverage and 5’-3’ bias computation.
+links:
+  homepage: http://qualimap.conesalab.org/
+  documentation: http://qualimap.conesalab.org/doc_html/analysis.html#rna-seq-qc
+  issue_tracker: https://bitbucket.org/kokonech/qualimap/issues?status=new&status=open
+  repository: https://bitbucket.org/kokonech/qualimap/commits/branch/master
+references:
+  doi: 10.1093/bioinformatics/btv566
+license: GPL-2.0
+authors:
+  - __merge__: /src/_authors/dorien_roosen.yaml
+    roles: [ author, maintainer ]
+argument_groups:
+  - name: "Input"
+    arguments: 
+    - name: "--bam"
+      type: file
+      required: true
+      example: alignment.bam
+      description: Path to the sequence alignment file in BAM format, produced by a splicing-aware aligner.
+    - name: "--gtf"
+      type: file
+      required: true
+      example: annotations.gtf
+      description: Path to genomic annotations in Ensembl GTF format.
+
+  - name: "Output"
+    arguments: 
+    - name: "--qc_results"
+      direction: output
+      type: file
+      required: true
+      example: rnaseq_qc_results.txt
+      description: Text file containing the RNAseq QC results.
+    - name: "--counts"
+      type: file
+      required: false
+      direction: output
+      description: Output file for computed counts.
+    - name: "--report"
+      type: file
+      direction: output
+      required: false
+      example: report.html
+      description: Report output file. Supported formats are PDF or HTML.
+
+  - name: "Optional"
+    arguments: 
+    - name: "--num_pr_bases"
+      type: integer
+      required: false
+      min: 1
+      description: Number of upstream/downstream nucleotide bases to compute 5'-3' bias (default = 100).
+    - name: "--num_tr_bias"
+      type: integer
+      required: false
+      min: 1
+      description: Number of top highly expressed transcripts to compute 5'-3' bias (default = 1000).
+    - name: "--algorithm"
+      type: string
+      required: false
+      choices: ["uniquely-mapped-reads", "proportional"]
+      description: Counting algorithm (uniquely-mapped-reads (default) or proportional).
+    - name: "--sequencing_protocol"
+      type: string
+      required: false
+      choices: ["non-strand-specific", "strand-specific-reverse", "strand-specific-forward"]
+      description: Sequencing library protocol (strand-specific-forward, strand-specific-reverse or non-strand-specific (default)).
+    - name: "--paired"
+      type: boolean_true
+      description: Setting this flag for paired-end experiments will result in counting fragments instead of reads.
+    - name: "--sorted"
+      type: boolean_true
+      description: Setting this flag indicates that the input file is already sorted by name. If flag is not set, additional sorting by name will be performed. Only requiredfor paired-end analysis.
+    - name: "--java_memory_size"
+      type: string
+      required: false
+      description: maximum Java heap memory size, default = 4G.
+
+resources:
+  - type: bash_script
+    path: script.sh
+test_resources:
+  - type: bash_script
+    path: test.sh
+  - path: test_data/
+
+engines:
+  - type: docker
+    image: quay.io/biocontainers/qualimap:2.3--hdfd78af_0
+    setup:   
+      - type: docker
+        run: |
+          echo QualiMap: $(qualimap 2>&1 | grep QualiMap | sed 's/^.*QualiMap//') > /var/software_versions.txt
+runners: 
+  - type: executable
+  - type: nextflow
diff --git a/src/qualimap/qualimap_rnaseq/help.txt b/src/qualimap/qualimap_rnaseq/help.txt
new file mode 100644
index 00000000..c6493ed9
--- /dev/null
+++ b/src/qualimap/qualimap_rnaseq/help.txt
@@ -0,0 +1,52 @@
+QualiMap v.2.3
+Built on 2023-05-19 16:57
+
+usage: qualimap <tool> [options]
+
+To launch GUI leave <tool> empty.
+
+Available tools:
+
+    bamqc            Evaluate NGS mapping to a reference genome
+    rnaseq           Evaluate RNA-seq alignment data
+    counts           Counts data analysis (further RNA-seq data evaluation)
+    multi-bamqc      Compare QC reports from multiple NGS mappings
+    clustering       Cluster epigenomic signals
+    comp-counts      Compute feature counts
+
+Special arguments: 
+
+    --java-mem-size  Use this argument to set Java memory heap size. Example:
+                     qualimap bamqc -bam very_large_alignment.bam --java-mem-size=4G
+                     
+usage: qualimap rnaseq [-a <arg>] -bam <arg> -gtf <arg> [-npb <arg>] [-ntb
+       <arg>] [-oc <arg>] [-outdir <arg>] [-outfile <arg>] [-outformat <arg>]
+       [-p <arg>] [-pe] [-s]
+ -a,--algorithm <arg>             Counting algorithm:
+                                  uniquely-mapped-reads(default) or
+                                  proportional.
+ -bam <arg>                       Input mapping file in BAM format.
+ -gtf <arg>                       Annotations file in Ensembl GTF format.
+ -npb,--num-pr-bases <arg>        Number of upstream/downstream nucleotide bases
+                                  to compute 5'-3' bias (default is 100).
+ -ntb,--num-tr-bias <arg>         Number of top highly expressed transcripts to
+                                  compute 5'-3' bias (default is 1000).
+ -oc <arg>                        Output file for computed counts. If only name
+                                  of the file is provided, then the file will be
+                                  saved in the output folder.
+ -outdir <arg>                    Output folder for HTML report and raw data.
+ -outfile <arg>                   Output file for PDF report (default value is
+                                  report.pdf).
+ -outformat <arg>                 Format of the output report (PDF, HTML or both
+                                  PDF:HTML, default is HTML).
+ -p,--sequencing-protocol <arg>   Sequencing library protocol:
+                                  strand-specific-forward,
+                                  strand-specific-reverse or non-strand-specific
+                                  (default)
+ -pe,--paired                     Setting this flag for paired-end experiments
+                                  will result in counting fragments instead of
+                                  reads
+ -s,--sorted                      This flag indicates that the input file is
+                                  already sorted by name. If not set, additional
+                                  sorting by name will be performed. Only
+                                  required for paired-end analysis.
\ No newline at end of file
diff --git a/src/qualimap/qualimap_rnaseq/script.sh b/src/qualimap/qualimap_rnaseq/script.sh
new file mode 100644
index 00000000..351e5159
--- /dev/null
+++ b/src/qualimap/qualimap_rnaseq/script.sh
@@ -0,0 +1,50 @@
+#!/bin/bash
+
+set -eo pipefail
+
+tmp_dir=$(mktemp -d -p "$meta_temp_dir" qualimap_XXXXXXXXX)
+
+# Handle output parameters
+if [ -n "$par_report" ]; then
+    outfile=$(basename "$par_report")
+    report_extension="${outfile##*.}"
+fi
+
+if [ -n "$par_counts" ]; then
+    counts=$(basename "$par_counts")
+fi
+
+# disable flags
+[[ "$par_paired" == "false" ]] && unset par_paired
+[[ "$par_sorted" == "false" ]] && unset par_sorted
+
+# Run qualimap
+qualimap rnaseq \
+    ${meta_memory_mb:+--java-mem-size=${meta_memory_mb}M} \
+    ${par_algorithm:+--algorithm $par_algorithm} \
+    ${par_sequencing_protocol:+--sequencing-protocol $par_sequencing_protocol} \
+    -bam $par_bam \
+    -gtf $par_gtf \
+    -outdir "$tmp_dir" \
+    ${par_num_pr_bases:+--num-pr-bases $par_num_pr_bases} \
+    ${par_num_tr_bias:+--num-tr-bias $par_num_tr_bias} \
+    ${par_report:+-outformat $report_extension} \
+    ${par_paired:+--paired} \
+    ${par_sorted:+--sorted} \
+    ${par_report:+-outfile "$outfile"} \
+    ${par_counts:+-oc "$counts"}
+
+# Move output files
+mv "$tmp_dir/rnaseq_qc_results.txt" "$par_qc_results"
+
+if [ -n "$par_report" ] && [ $report_extension = "html" ]; then
+    mv "$tmp_dir/qualimapReport.html" "$par_report"
+fi
+
+if [ -n "$par_report" ] && [ $report_extension = "pdf" ]; then
+    mv "$tmp_dir/$outfile" "$par_report"
+fi
+
+if [ -n "$par_counts" ]; then
+    mv "$tmp_dir/$counts" "$par_counts"
+fi
diff --git a/src/qualimap/qualimap_rnaseq/test.sh b/src/qualimap/qualimap_rnaseq/test.sh
new file mode 100755
index 00000000..2e1b647b
--- /dev/null
+++ b/src/qualimap/qualimap_rnaseq/test.sh
@@ -0,0 +1,112 @@
+set -e
+
+#############################################
+# helper functions
+assert_file_exists() {
+  [ -f "$1" ] || { echo "File '$1' does not exist" && exit 1; }
+}
+assert_file_doesnt_exist() {
+  [ ! -f "$1" ] || { echo "File '$1' exists but shouldn't" && exit 1; }
+}
+assert_file_not_empty() {
+  [ -s "$1" ] || { echo "File '$1' is empty but shouldn't be" && exit 1; }
+}
+assert_file_contains() {
+  grep -q "$2" "$1" || { echo "File '$1' does not contain '$2'" && exit 1; }
+}
+#############################################
+
+
+test_dir="$meta_resources_dir/test_data"
+
+mkdir "run_qualimap_rnaseq_html"
+cd "run_qualimap_rnaseq_html"
+
+echo "> Running qualimap with html output report"
+
+"$meta_executable" \
+    --bam $test_dir/a.bam \
+    --gtf $test_dir/annotation.gtf \
+    --report report.html \
+    --counts counts.txt \
+    --qc_results output.txt
+
+echo ">> Checking output"
+assert_file_exists "report.html"
+assert_file_exists "counts.txt"
+assert_file_exists "output.txt"
+assert_file_doesnt_exist "report.pdf"
+
+echo ">> Checking if output is empty"
+assert_file_not_empty "report.html"
+assert_file_not_empty "counts.txt"
+assert_file_not_empty "output.txt"
+
+echo ">> Checking output contents"
+assert_file_contains "output.txt" ">>>>>>> Input"
+assert_file_contains "output.txt" ">>>>>>> Reads alignment"
+assert_file_contains "output.txt" ">>>>>>> Reads genomic origin"
+assert_file_contains "output.txt" ">>>>>>> Transcript coverage profile"
+assert_file_contains "output.txt" ">>>>>>> Junction analysis"
+assert_file_contains "output.txt" ">>>>>>> Transcript coverage profile"
+
+assert_file_contains "counts.txt" "ENSG00000125841.12"
+
+assert_file_contains "report.html" "<title>Qualimap report: RNA Seq QC</title>"
+assert_file_contains "report.html" "<h3>Input</h3>"
+assert_file_contains "report.html" "<h3>Reads alignment</h3>"
+assert_file_contains "report.html" "<h3>Reads genomic origin</h3>"
+assert_file_contains "report.html" "<h3>Transcript coverage profile</h3>"
+assert_file_contains "report.html" "<h3>Junction analysis</h3>"
+
+
+cd ..
+rm -r run_qualimap_rnaseq_html
+
+mkdir "run_qualimap_rnaseq_pdf"
+cd "run_qualimap_rnaseq_pdf"
+
+echo "> Running qualimap with pdf output report"
+
+"$meta_executable" \
+    --bam $test_dir/a.bam \
+    --gtf $test_dir/annotation.gtf \
+    --report report.pdf \
+    --counts counts.txt \
+    --qc_results output.txt
+
+echo ">> Checking output"
+assert_file_exists "report.pdf"
+assert_file_exists "counts.txt"
+assert_file_exists "output.txt"
+assert_file_doesnt_exist "report.html"
+
+echo ">> Checking if output is empty"
+assert_file_not_empty "report.pdf"
+assert_file_not_empty "counts.txt"
+assert_file_not_empty "output.txt"
+
+cd ..
+rm -r run_qualimap_rnaseq_pdf
+
+mkdir "run_qualimap_rnaseq"
+cd "run_qualimap_rnaseq"
+
+echo "> Running qualimap without report and counts output"
+
+"$meta_executable" \
+    --bam $test_dir/a.bam \
+    --gtf $test_dir/annotation.gtf \
+    --qc_results output.txt
+
+echo ">> Checking output"
+assert_file_doesnt_exist "report.pdf"
+assert_file_doesnt_exist "report.html"
+assert_file_doesnt_exist "counts.txt"
+assert_file_exists "output.txt"
+
+echo ">> Checking if output is empty"
+assert_file_not_empty "output.txt"
+
+cd ..
+rm -r run_qualimap_rnaseq
\ No newline at end of file
diff --git a/src/qualimap/qualimap_rnaseq/test_data/a.bam b/src/qualimap/qualimap_rnaseq/test_data/a.bam
new file mode 100644
index 00000000..c8ea1065
Binary files /dev/null and b/src/qualimap/qualimap_rnaseq/test_data/a.bam differ
diff --git a/src/qualimap/qualimap_rnaseq/test_data/annotation.gtf b/src/qualimap/qualimap_rnaseq/test_data/annotation.gtf
new file mode 100644
index 00000000..976de753
--- /dev/null
+++ b/src/qualimap/qualimap_rnaseq/test_data/annotation.gtf
@@ -0,0 +1,10 @@
+chr20	HAVANA	transcript	347024	354868	.	+	.	gene_id "ENSG00000125841.12"; transcript_id "ENST00000382291.7"; gene_type "protein_coding"; gene_name "NRSN2"; transcript_type "protein_coding"; transcript_name "NRSN2-202"; level 2; protein_id "ENSP00000371728.3"; transcript_support_level "2"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS12996.1"; havana_gene "OTTHUMG00000031628.5"; havana_transcript "OTTHUMT00000077446.1";
+chr20	HAVANA	exon	347024	347142	.	+	.	gene_id "ENSG00000125841.12"; transcript_id "ENST00000382291.7"; gene_type "protein_coding"; gene_name "NRSN2"; transcript_type "protein_coding"; transcript_name "NRSN2-202"; exon_number 1; exon_id "ENSE00001831391.1"; level 2; protein_id "ENSP00000371728.3"; transcript_support_level "2"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS12996.1"; havana_gene "OTTHUMG00000031628.5"; havana_transcript "OTTHUMT00000077446.1";
+chr20	HAVANA	exon	349249	349363	.	+	.	gene_id "ENSG00000125841.12"; transcript_id "ENST00000382291.7"; gene_type "protein_coding"; gene_name "NRSN2"; transcript_type "protein_coding"; transcript_name "NRSN2-202"; exon_number 2; exon_id "ENSE00001491647.1"; level 2; protein_id "ENSP00000371728.3"; transcript_support_level "2"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS12996.1"; havana_gene "OTTHUMG00000031628.5"; havana_transcript "OTTHUMT00000077446.1";
+chr20	HAVANA	exon	349638	349832	.	+	.	gene_id "ENSG00000125841.12"; transcript_id "ENST00000382291.7"; gene_type "protein_coding"; gene_name "NRSN2"; transcript_type "protein_coding"; transcript_name "NRSN2-202"; exon_number 3; exon_id "ENSE00003710328.1"; level 2; protein_id "ENSP00000371728.3"; transcript_support_level "2"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS12996.1"; havana_gene "OTTHUMG00000031628.5"; havana_transcript "OTTHUMT00000077446.1";
+chr20	HAVANA	CDS	349644	349832	.	+	0	gene_id "ENSG00000125841.12"; transcript_id "ENST00000382291.7"; gene_type "protein_coding"; gene_name "NRSN2"; transcript_type "protein_coding"; transcript_name "NRSN2-202"; exon_number 3; exon_id "ENSE00003710328.1"; level 2; protein_id "ENSP00000371728.3"; transcript_support_level "2"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS12996.1"; havana_gene "OTTHUMG00000031628.5"; havana_transcript "OTTHUMT00000077446.1";
+chr20	HAVANA	start_codon	349644	349646	.	+	0	gene_id "ENSG00000125841.12"; transcript_id "ENST00000382291.7"; gene_type "protein_coding"; gene_name "NRSN2"; transcript_type "protein_coding"; transcript_name "NRSN2-202"; exon_number 3; exon_id "ENSE00003710328.1"; level 2; protein_id "ENSP00000371728.3"; transcript_support_level "2"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS12996.1"; havana_gene "OTTHUMG00000031628.5"; havana_transcript "OTTHUMT00000077446.1";
+chr20	HAVANA	exon	353210	354868	.	+	.	gene_id "ENSG00000125841.12"; transcript_id "ENST00000382291.7"; gene_type "protein_coding"; gene_name "NRSN2"; transcript_type "protein_coding"; transcript_name "NRSN2-202"; exon_number 4; exon_id "ENSE00001822456.1"; level 2; protein_id "ENSP00000371728.3"; transcript_support_level "2"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS12996.1"; havana_gene "OTTHUMG00000031628.5"; havana_transcript "OTTHUMT00000077446.1";
+chr20	HAVANA	CDS	353210	353632	.	+	0	gene_id "ENSG00000125841.12"; transcript_id "ENST00000382291.7"; gene_type "protein_coding"; gene_name "NRSN2"; transcript_type "protein_coding"; transcript_name "NRSN2-202"; exon_number 4; exon_id "ENSE00001822456.1"; level 2; protein_id "ENSP00000371728.3"; transcript_support_level "2"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS12996.1"; havana_gene "OTTHUMG00000031628.5"; havana_transcript "OTTHUMT00000077446.1";
+chr20	HAVANA	stop_codon	353633	353635	.	+	0	gene_id "ENSG00000125841.12"; transcript_id "ENST00000382291.7"; gene_type "protein_coding"; gene_name "NRSN2"; transcript_type "protein_coding"; transcript_name "NRSN2-202"; exon_number 4; exon_id "ENSE00001822456.1"; level 2; protein_id "ENSP00000371728.3"; transcript_support_level "2"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS12996.1"; havana_gene "OTTHUMG00000031628.5"; havana_transcript "OTTHUMT00000077446.1";
+chr20	HAVANA	UTR	347024	347142	.	+	.	gene_id "ENSG00000125841.12"; transcript_id "ENST00000382291.7"; gene_type "protein_coding"; gene_name "NRSN2"; transcript_type "protein_coding"; transcript_name "NRSN2-202"; exon_number 1; exon_id "ENSE00001831391.1"; level 2; protein_id "ENSP00000371728.3"; transcript_support_level "2"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS12996.1"; havana_gene "OTTHUMG00000031628.5"; havana_transcript "OTTHUMT00000077446.1";
diff --git a/src/qualimap/qualimap_rnaseq/test_data/script.sh b/src/qualimap/qualimap_rnaseq/test_data/script.sh
new file mode 100755
index 00000000..801fe405
--- /dev/null
+++ b/src/qualimap/qualimap_rnaseq/test_data/script.sh
@@ -0,0 +1,10 @@
+# qualimap test data
+
+# Test data was obtained from https://github.com/snakemake/snakemake-wrappers/raw/master/bio/qualimap/rnaseq/test
+
+if [ ! -d /tmp/snakemake-wrappers ]; then
+  git clone --depth 1 --single-branch --branch master https://github.com/snakemake/snakemake-wrappers /tmp/snakemake-wrappers
+fi
+
+cp -r /tmp/snakemake-wrappers/bio/qualimap/rnaseq/test/mapped/a.bam src/qualimap/qualimap_rnaseq/test_data
+cp -r /tmp/snakemake-wrappers/bio/qualimap/rnaseq/test/annotation.gtf src/qualimap/qualimap_rnaseq/test_data
diff --git a/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml b/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml
index 1c9be457..e4835e2c 100644
--- a/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml
@@ -235,7 +235,7 @@ build_info:
   output: "target/executable/agat/agat_convert_bed2gff"
   executable: "target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff b/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff
index ecf1708e..5ab1d981 100755
--- a/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff
+++ b/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff
@@ -514,9 +514,9 @@ 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="2024-08-14T20:58:52Z"
+LABEL org.opencontainers.image.created="2024-08-21T11:36:01Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="923a6da3898a832df96a0e17c8a3b74c2806d939"
+LABEL org.opencontainers.image.revision="766ab6c9c3059004c7c3f205621909b2d8b0b26d"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml b/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml
index e79ad73e..0bf07ed8 100644
--- a/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml
@@ -225,7 +225,7 @@ build_info:
   output: "target/executable/agat/agat_convert_embl2gff"
   executable: "target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff b/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff
index 4dff03cf..1504293c 100755
--- a/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff
+++ b/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff
@@ -504,9 +504,9 @@ 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="2024-08-14T20:58:52Z"
+LABEL org.opencontainers.image.created="2024-08-21T11:36:00Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="923a6da3898a832df96a0e17c8a3b74c2806d939"
+LABEL org.opencontainers.image.revision="766ab6c9c3059004c7c3f205621909b2d8b0b26d"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml b/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml
index 9450e730..7e0482d1 100644
--- a/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml
@@ -228,7 +228,7 @@ build_info:
   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-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf b/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf
index 95b2bcd9..8174a50b 100755
--- a/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf
+++ b/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf
@@ -518,9 +518,9 @@ 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="2024-08-14T20:58:53Z"
+LABEL org.opencontainers.image.created="2024-08-21T11:36:01Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="923a6da3898a832df96a0e17c8a3b74c2806d939"
+LABEL org.opencontainers.image.revision="766ab6c9c3059004c7c3f205621909b2d8b0b26d"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml b/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml
index f45d9631..8b31b2a2 100644
--- a/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml
@@ -188,7 +188,7 @@ build_info:
   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-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv b/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv
index 287f7cb8..4f562d66 100755
--- a/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv
+++ b/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv
@@ -483,9 +483,9 @@ 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="2024-08-14T20:58:52Z"
+LABEL org.opencontainers.image.created="2024-08-21T11:36:00Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="923a6da3898a832df96a0e17c8a3b74c2806d939"
+LABEL org.opencontainers.image.revision="766ab6c9c3059004c7c3f205621909b2d8b0b26d"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml b/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml
index ec2b5e9f..ba858099 100644
--- a/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml
@@ -195,7 +195,7 @@ build_info:
   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-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf b/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf
index 5beff467..9cdfad6f 100755
--- a/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf
+++ b/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf
@@ -492,9 +492,9 @@ 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="2024-08-14T20:58:51Z"
+LABEL org.opencontainers.image.created="2024-08-21T11:36:00Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="923a6da3898a832df96a0e17c8a3b74c2806d939"
+LABEL org.opencontainers.image.revision="766ab6c9c3059004c7c3f205621909b2d8b0b26d"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/arriba/.config.vsh.yaml b/target/executable/arriba/.config.vsh.yaml
index 1ecee512..e43ebec8 100644
--- a/target/executable/arriba/.config.vsh.yaml
+++ b/target/executable/arriba/.config.vsh.yaml
@@ -706,7 +706,7 @@ build_info:
   output: "target/executable/arriba"
   executable: "target/executable/arriba/arriba"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/arriba/arriba b/target/executable/arriba/arriba
index 71fdbbaa..6a35626c 100755
--- a/target/executable/arriba/arriba
+++ b/target/executable/arriba/arriba
@@ -753,9 +753,9 @@ RUN arriba -h | grep 'Version:' 2>&1 |  sed 's/Version:\s\(.*\)/arriba: "\1"/' >
 
 LABEL org.opencontainers.image.authors="Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component arriba"
-LABEL org.opencontainers.image.created="2024-08-14T20:58:44Z"
+LABEL org.opencontainers.image.created="2024-08-21T11:36:02Z"
 LABEL org.opencontainers.image.source="https://github.com/suhrig/arriba"
-LABEL org.opencontainers.image.revision="923a6da3898a832df96a0e17c8a3b74c2806d939"
+LABEL org.opencontainers.image.revision="766ab6c9c3059004c7c3f205621909b2d8b0b26d"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/bcl_convert/.config.vsh.yaml b/target/executable/bcl_convert/.config.vsh.yaml
index 81d67682..56921f80 100644
--- a/target/executable/bcl_convert/.config.vsh.yaml
+++ b/target/executable/bcl_convert/.config.vsh.yaml
@@ -418,7 +418,7 @@ build_info:
   output: "target/executable/bcl_convert"
   executable: "target/executable/bcl_convert/bcl_convert"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/bcl_convert/bcl_convert b/target/executable/bcl_convert/bcl_convert
index 9462c703..f033b570 100755
--- a/target/executable/bcl_convert/bcl_convert
+++ b/target/executable/bcl_convert/bcl_convert
@@ -598,9 +598,9 @@ 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="2024-08-14T20:58:45Z"
+LABEL org.opencontainers.image.created="2024-08-21T11:36:02Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="923a6da3898a832df96a0e17c8a3b74c2806d939"
+LABEL org.opencontainers.image.revision="766ab6c9c3059004c7c3f205621909b2d8b0b26d"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml
index ea4ce3ab..3a99e885 100644
--- a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml
+++ b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml
@@ -270,7 +270,7 @@ build_info:
   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-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference
index 0b614340..f4aa929e 100755
--- a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference
+++ b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference
@@ -548,9 +548,9 @@ RUN echo "bdgenomics/rhapsody: 2.2.1" > /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="2024-08-14T20:58:53Z"
+LABEL org.opencontainers.image.created="2024-08-21T11:36:05Z"
 LABEL org.opencontainers.image.source="https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1/Extra_Utilities/"
-LABEL org.opencontainers.image.revision="923a6da3898a832df96a0e17c8a3b74c2806d939"
+LABEL org.opencontainers.image.revision="766ab6c9c3059004c7c3f205621909b2d8b0b26d"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml b/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml
index db836704..320c4431 100644
--- a/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml
@@ -187,7 +187,7 @@ build_info:
   output: "target/executable/bedtools/bedtools_bamtofastq"
   executable: "target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq b/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq
index 95624099..5723f757 100755
--- a/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq
+++ b/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq
@@ -482,9 +482,9 @@ 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="2024-08-14T20:58:47Z"
+LABEL org.opencontainers.image.created="2024-08-21T11:35:51Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="923a6da3898a832df96a0e17c8a3b74c2806d939"
+LABEL org.opencontainers.image.revision="766ab6c9c3059004c7c3f205621909b2d8b0b26d"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml b/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml
index ea2dbff5..1ee26d8e 100644
--- a/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml
@@ -214,7 +214,7 @@ build_info:
   output: "target/executable/bedtools/bedtools_bedtobam"
   executable: "target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam b/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam
index 5e1b0955..a7f37938 100755
--- a/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam
+++ b/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam
@@ -495,9 +495,9 @@ 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="2024-08-14T20:58:47Z"
+LABEL org.opencontainers.image.created="2024-08-21T11:35:51Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="923a6da3898a832df96a0e17c8a3b74c2806d939"
+LABEL org.opencontainers.image.revision="766ab6c9c3059004c7c3f205621909b2d8b0b26d"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml b/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml
index 11b0f864..585d1e3b 100644
--- a/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml
@@ -232,7 +232,7 @@ build_info:
   output: "target/executable/bedtools/bedtools_getfasta"
   executable: "target/executable/bedtools/bedtools_getfasta/bedtools_getfasta"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta b/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta
index cc53425c..cd873a08 100755
--- a/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta
+++ b/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta
@@ -525,9 +525,9 @@ 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="2024-08-14T20:58:47Z"
+LABEL org.opencontainers.image.created="2024-08-21T11:35:50Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="923a6da3898a832df96a0e17c8a3b74c2806d939"
+LABEL org.opencontainers.image.revision="766ab6c9c3059004c7c3f205621909b2d8b0b26d"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml b/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml
index 4de12853..71cbbe55 100644
--- a/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml
@@ -410,7 +410,7 @@ build_info:
   output: "target/executable/bedtools/bedtools_intersect"
   executable: "target/executable/bedtools/bedtools_intersect/bedtools_intersect"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/bedtools/bedtools_intersect/bedtools_intersect b/target/executable/bedtools/bedtools_intersect/bedtools_intersect
index bb865a49..61d28eed 100755
--- a/target/executable/bedtools/bedtools_intersect/bedtools_intersect
+++ b/target/executable/bedtools/bedtools_intersect/bedtools_intersect
@@ -632,9 +632,9 @@ 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="2024-08-14T20:58:48Z"
+LABEL org.opencontainers.image.created="2024-08-21T11:35:51Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="923a6da3898a832df96a0e17c8a3b74c2806d939"
+LABEL org.opencontainers.image.revision="766ab6c9c3059004c7c3f205621909b2d8b0b26d"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/bedtools/bedtools_sort/.config.vsh.yaml b/target/executable/bedtools/bedtools_sort/.config.vsh.yaml
index 86f9157a..0fbd5d4b 100644
--- a/target/executable/bedtools/bedtools_sort/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_sort/.config.vsh.yaml
@@ -222,7 +222,7 @@ build_info:
   output: "target/executable/bedtools/bedtools_sort"
   executable: "target/executable/bedtools/bedtools_sort/bedtools_sort"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/bedtools/bedtools_sort/bedtools_sort b/target/executable/bedtools/bedtools_sort/bedtools_sort
index 04fcce83..9c11f8ac 100755
--- a/target/executable/bedtools/bedtools_sort/bedtools_sort
+++ b/target/executable/bedtools/bedtools_sort/bedtools_sort
@@ -508,9 +508,9 @@ 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="2024-08-14T20:58:46Z"
+LABEL org.opencontainers.image.created="2024-08-21T11:35:51Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="923a6da3898a832df96a0e17c8a3b74c2806d939"
+LABEL org.opencontainers.image.revision="766ab6c9c3059004c7c3f205621909b2d8b0b26d"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/busco/busco_download_datasets/.config.vsh.yaml b/target/executable/busco/busco_download_datasets/.config.vsh.yaml
index 4321c877..cc54dddc 100644
--- a/target/executable/busco/busco_download_datasets/.config.vsh.yaml
+++ b/target/executable/busco/busco_download_datasets/.config.vsh.yaml
@@ -158,7 +158,7 @@ build_info:
   output: "target/executable/busco/busco_download_datasets"
   executable: "target/executable/busco/busco_download_datasets/busco_download_datasets"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/busco/busco_download_datasets/busco_download_datasets b/target/executable/busco/busco_download_datasets/busco_download_datasets
index 27312328..5cb56ccf 100755
--- a/target/executable/busco/busco_download_datasets/busco_download_datasets
+++ b/target/executable/busco/busco_download_datasets/busco_download_datasets
@@ -474,9 +474,9 @@ 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="2024-08-14T20:58:43Z"
+LABEL org.opencontainers.image.created="2024-08-21T11:35:59Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="923a6da3898a832df96a0e17c8a3b74c2806d939"
+LABEL org.opencontainers.image.revision="766ab6c9c3059004c7c3f205621909b2d8b0b26d"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/busco/busco_list_datasets/.config.vsh.yaml b/target/executable/busco/busco_list_datasets/.config.vsh.yaml
index aa106bfe..97a7be14 100644
--- a/target/executable/busco/busco_list_datasets/.config.vsh.yaml
+++ b/target/executable/busco/busco_list_datasets/.config.vsh.yaml
@@ -145,7 +145,7 @@ build_info:
   output: "target/executable/busco/busco_list_datasets"
   executable: "target/executable/busco/busco_list_datasets/busco_list_datasets"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/busco/busco_list_datasets/busco_list_datasets b/target/executable/busco/busco_list_datasets/busco_list_datasets
index 8dfbe802..4cecfc37 100755
--- a/target/executable/busco/busco_list_datasets/busco_list_datasets
+++ b/target/executable/busco/busco_list_datasets/busco_list_datasets
@@ -464,9 +464,9 @@ 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="2024-08-14T20:58:43Z"
+LABEL org.opencontainers.image.created="2024-08-21T11:35:59Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="923a6da3898a832df96a0e17c8a3b74c2806d939"
+LABEL org.opencontainers.image.revision="766ab6c9c3059004c7c3f205621909b2d8b0b26d"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/busco/busco_run/.config.vsh.yaml b/target/executable/busco/busco_run/.config.vsh.yaml
index d2fad983..54d7680e 100644
--- a/target/executable/busco/busco_run/.config.vsh.yaml
+++ b/target/executable/busco/busco_run/.config.vsh.yaml
@@ -423,7 +423,7 @@ build_info:
   output: "target/executable/busco/busco_run"
   executable: "target/executable/busco/busco_run/busco_run"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/busco/busco_run/busco_run b/target/executable/busco/busco_run/busco_run
index 1c4aab79..73649abc 100755
--- a/target/executable/busco/busco_run/busco_run
+++ b/target/executable/busco/busco_run/busco_run
@@ -631,9 +631,9 @@ 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="2024-08-14T20:58:44Z"
+LABEL org.opencontainers.image.created="2024-08-21T11:35:59Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="923a6da3898a832df96a0e17c8a3b74c2806d939"
+LABEL org.opencontainers.image.revision="766ab6c9c3059004c7c3f205621909b2d8b0b26d"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/cutadapt/.config.vsh.yaml b/target/executable/cutadapt/.config.vsh.yaml
index 697434e4..0067ea27 100644
--- a/target/executable/cutadapt/.config.vsh.yaml
+++ b/target/executable/cutadapt/.config.vsh.yaml
@@ -740,7 +740,7 @@ build_info:
   output: "target/executable/cutadapt"
   executable: "target/executable/cutadapt/cutadapt"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/cutadapt/cutadapt b/target/executable/cutadapt/cutadapt
index fa087008..98f91342 100755
--- a/target/executable/cutadapt/cutadapt
+++ b/target/executable/cutadapt/cutadapt
@@ -830,9 +830,9 @@ RUN cutadapt --version | sed 's/\(.*\)/cutadapt: "\1"/' > /var/software_versions
 
 LABEL org.opencontainers.image.authors="Toni Verbeiren"
 LABEL org.opencontainers.image.description="Companion container for running component cutadapt"
-LABEL org.opencontainers.image.created="2024-08-14T20:58:42Z"
+LABEL org.opencontainers.image.created="2024-08-21T11:36:03Z"
 LABEL org.opencontainers.image.source="https://github.com/marcelm/cutadapt"
-LABEL org.opencontainers.image.revision="923a6da3898a832df96a0e17c8a3b74c2806d939"
+LABEL org.opencontainers.image.revision="766ab6c9c3059004c7c3f205621909b2d8b0b26d"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/falco/.config.vsh.yaml b/target/executable/falco/.config.vsh.yaml
index fa2e830b..3b47c8c2 100644
--- a/target/executable/falco/.config.vsh.yaml
+++ b/target/executable/falco/.config.vsh.yaml
@@ -317,7 +317,7 @@ build_info:
   output: "target/executable/falco"
   executable: "target/executable/falco/falco"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/falco/falco b/target/executable/falco/falco
index 7efedcb2..803a8347 100755
--- a/target/executable/falco/falco
+++ b/target/executable/falco/falco
@@ -588,9 +588,9 @@ 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="2024-08-14T20:58:42Z"
+LABEL org.opencontainers.image.created="2024-08-21T11:36:04Z"
 LABEL org.opencontainers.image.source="https://github.com/smithlabcode/falco"
-LABEL org.opencontainers.image.revision="923a6da3898a832df96a0e17c8a3b74c2806d939"
+LABEL org.opencontainers.image.revision="766ab6c9c3059004c7c3f205621909b2d8b0b26d"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/fastp/.config.vsh.yaml b/target/executable/fastp/.config.vsh.yaml
index 8d8b7ae9..ea112e85 100644
--- a/target/executable/fastp/.config.vsh.yaml
+++ b/target/executable/fastp/.config.vsh.yaml
@@ -1083,7 +1083,7 @@ build_info:
   output: "target/executable/fastp"
   executable: "target/executable/fastp/fastp"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/fastp/fastp b/target/executable/fastp/fastp
index eb34d83a..3a2124be 100755
--- a/target/executable/fastp/fastp
+++ b/target/executable/fastp/fastp
@@ -1027,9 +1027,9 @@ 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="2024-08-14T20:58:48Z"
+LABEL org.opencontainers.image.created="2024-08-21T11:36:01Z"
 LABEL org.opencontainers.image.source="https://github.com/OpenGene/fastp"
-LABEL org.opencontainers.image.revision="923a6da3898a832df96a0e17c8a3b74c2806d939"
+LABEL org.opencontainers.image.revision="766ab6c9c3059004c7c3f205621909b2d8b0b26d"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/featurecounts/.config.vsh.yaml b/target/executable/featurecounts/.config.vsh.yaml
index 8f2d2765..1c8726b5 100644
--- a/target/executable/featurecounts/.config.vsh.yaml
+++ b/target/executable/featurecounts/.config.vsh.yaml
@@ -645,7 +645,7 @@ build_info:
   output: "target/executable/featurecounts"
   executable: "target/executable/featurecounts/featurecounts"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/featurecounts/featurecounts b/target/executable/featurecounts/featurecounts
index 36f439e8..1ec026f1 100755
--- a/target/executable/featurecounts/featurecounts
+++ b/target/executable/featurecounts/featurecounts
@@ -753,9 +753,9 @@ RUN featureCounts -v 2>&1 | sed 's/featureCounts v\([0-9.]*\)/featureCounts: \1/
 
 LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
 LABEL org.opencontainers.image.description="Companion container for running component featurecounts"
-LABEL org.opencontainers.image.created="2024-08-14T20:58:44Z"
+LABEL org.opencontainers.image.created="2024-08-21T11:35:57Z"
 LABEL org.opencontainers.image.source="https://github.com/ShiLab-Bioinformatics/subread"
-LABEL org.opencontainers.image.revision="923a6da3898a832df96a0e17c8a3b74c2806d939"
+LABEL org.opencontainers.image.revision="766ab6c9c3059004c7c3f205621909b2d8b0b26d"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/gffread/.config.vsh.yaml b/target/executable/gffread/.config.vsh.yaml
index 67aef5f9..99048d86 100644
--- a/target/executable/gffread/.config.vsh.yaml
+++ b/target/executable/gffread/.config.vsh.yaml
@@ -685,7 +685,7 @@ build_info:
   output: "target/executable/gffread"
   executable: "target/executable/gffread/gffread"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/gffread/gffread b/target/executable/gffread/gffread
index 4e64d015..68fa70fd 100755
--- a/target/executable/gffread/gffread
+++ b/target/executable/gffread/gffread
@@ -806,9 +806,9 @@ RUN echo "gffread: \"$(gffread --version 2>&1)\"" > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component gffread"
-LABEL org.opencontainers.image.created="2024-08-14T20:58:42Z"
+LABEL org.opencontainers.image.created="2024-08-21T11:35:49Z"
 LABEL org.opencontainers.image.source="https://github.com/gpertea/gffread"
-LABEL org.opencontainers.image.revision="923a6da3898a832df96a0e17c8a3b74c2806d939"
+LABEL org.opencontainers.image.revision="766ab6c9c3059004c7c3f205621909b2d8b0b26d"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/lofreq/lofreq_call/.config.vsh.yaml b/target/executable/lofreq/lofreq_call/.config.vsh.yaml
index b8e72d5d..82841437 100644
--- a/target/executable/lofreq/lofreq_call/.config.vsh.yaml
+++ b/target/executable/lofreq/lofreq_call/.config.vsh.yaml
@@ -507,7 +507,7 @@ build_info:
   output: "target/executable/lofreq/lofreq_call"
   executable: "target/executable/lofreq/lofreq_call/lofreq_call"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/lofreq/lofreq_call/lofreq_call b/target/executable/lofreq/lofreq_call/lofreq_call
index e0657616..478f8de3 100755
--- a/target/executable/lofreq/lofreq_call/lofreq_call
+++ b/target/executable/lofreq/lofreq_call/lofreq_call
@@ -655,9 +655,9 @@ echo "lofreq: $version" > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Kai Waldrant"
 LABEL org.opencontainers.image.description="Companion container for running component lofreq lofreq_call"
-LABEL org.opencontainers.image.created="2024-08-14T20:58:51Z"
+LABEL org.opencontainers.image.created="2024-08-21T11:35:57Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="923a6da3898a832df96a0e17c8a3b74c2806d939"
+LABEL org.opencontainers.image.revision="766ab6c9c3059004c7c3f205621909b2d8b0b26d"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml b/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml
index f14efeb3..bdaa51fa 100644
--- a/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml
+++ b/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml
@@ -215,7 +215,7 @@ build_info:
   output: "target/executable/lofreq/lofreq_indelqual"
   executable: "target/executable/lofreq/lofreq_indelqual/lofreq_indelqual"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual b/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual
index 072ababe..b46d4602 100755
--- a/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual
+++ b/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual
@@ -500,9 +500,9 @@ echo "lofreq: $version" > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Kai Waldrant"
 LABEL org.opencontainers.image.description="Companion container for running component lofreq lofreq_indelqual"
-LABEL org.opencontainers.image.created="2024-08-14T20:58:51Z"
+LABEL org.opencontainers.image.created="2024-08-21T11:35:57Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="923a6da3898a832df96a0e17c8a3b74c2806d939"
+LABEL org.opencontainers.image.revision="766ab6c9c3059004c7c3f205621909b2d8b0b26d"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/multiqc/.config.vsh.yaml b/target/executable/multiqc/.config.vsh.yaml
index f360b783..0d097e6d 100644
--- a/target/executable/multiqc/.config.vsh.yaml
+++ b/target/executable/multiqc/.config.vsh.yaml
@@ -456,7 +456,7 @@ build_info:
   output: "target/executable/multiqc"
   executable: "target/executable/multiqc/multiqc"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/multiqc/multiqc b/target/executable/multiqc/multiqc
index aa9a74ea..4b874ef1 100755
--- a/target/executable/multiqc/multiqc
+++ b/target/executable/multiqc/multiqc
@@ -636,9 +636,9 @@ RUN multiqc --version | sed 's/multiqc, version\s\(.*\)/multiqc: "\1"/' > /var/s
 
 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component multiqc"
-LABEL org.opencontainers.image.created="2024-08-14T20:58:45Z"
+LABEL org.opencontainers.image.created="2024-08-21T11:36:04Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="923a6da3898a832df96a0e17c8a3b74c2806d939"
+LABEL org.opencontainers.image.revision="766ab6c9c3059004c7c3f205621909b2d8b0b26d"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/pear/.config.vsh.yaml b/target/executable/pear/.config.vsh.yaml
index f4c00642..1e440ada 100644
--- a/target/executable/pear/.config.vsh.yaml
+++ b/target/executable/pear/.config.vsh.yaml
@@ -398,7 +398,7 @@ build_info:
   output: "target/executable/pear"
   executable: "target/executable/pear/pear"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/pear/pear b/target/executable/pear/pear
index 1a8e527a..f39adbd6 100755
--- a/target/executable/pear/pear
+++ b/target/executable/pear/pear
@@ -596,9 +596,9 @@ echo "pear: $version" > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Kai Waldrant"
 LABEL org.opencontainers.image.description="Companion container for running component pear"
-LABEL org.opencontainers.image.created="2024-08-14T20:58:50Z"
+LABEL org.opencontainers.image.created="2024-08-21T11:35:52Z"
 LABEL org.opencontainers.image.source="https://github.com/tseemann/PEAR"
-LABEL org.opencontainers.image.revision="923a6da3898a832df96a0e17c8a3b74c2806d939"
+LABEL org.opencontainers.image.revision="766ab6c9c3059004c7c3f205621909b2d8b0b26d"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml b/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml
new file mode 100644
index 00000000..d51b3b66
--- /dev/null
+++ b/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml
@@ -0,0 +1,290 @@
+name: "qualimap_rnaseq"
+namespace: "qualimap"
+version: "main"
+authors:
+- name: "Dorien Roosen"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      email: "dorien@data-intuitive.com"
+      github: "dorien-er"
+      linkedin: "dorien-roosen"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Scientist"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "file"
+    name: "--bam"
+    description: "Path to the sequence alignment file in BAM format, produced by a\
+      \ splicing-aware aligner."
+    info: null
+    example:
+    - "alignment.bam"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--gtf"
+    description: "Path to genomic annotations in Ensembl GTF format."
+    info: null
+    example:
+    - "annotations.gtf"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--qc_results"
+    description: "Text file containing the RNAseq QC results."
+    info: null
+    example:
+    - "rnaseq_qc_results.txt"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--counts"
+    description: "Output file for computed counts."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--report"
+    description: "Report output file. Supported formats are PDF or HTML."
+    info: null
+    example:
+    - "report.html"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Optional"
+  arguments:
+  - type: "integer"
+    name: "--num_pr_bases"
+    description: "Number of upstream/downstream nucleotide bases to compute 5'-3'\
+      \ bias (default = 100)."
+    info: null
+    required: false
+    min: 1
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--num_tr_bias"
+    description: "Number of top highly expressed transcripts to compute 5'-3' bias\
+      \ (default = 1000)."
+    info: null
+    required: false
+    min: 1
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--algorithm"
+    description: "Counting algorithm (uniquely-mapped-reads (default) or proportional)."
+    info: null
+    required: false
+    choices:
+    - "uniquely-mapped-reads"
+    - "proportional"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--sequencing_protocol"
+    description: "Sequencing library protocol (strand-specific-forward, strand-specific-reverse\
+      \ or non-strand-specific (default))."
+    info: null
+    required: false
+    choices:
+    - "non-strand-specific"
+    - "strand-specific-reverse"
+    - "strand-specific-forward"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--paired"
+    description: "Setting this flag for paired-end experiments will result in counting\
+      \ fragments instead of reads."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--sorted"
+    description: "Setting this flag indicates that the input file is already sorted\
+      \ by name. If flag is not set, additional sorting by name will be performed.\
+      \ Only requiredfor paired-end analysis."
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--java_memory_size"
+    description: "maximum Java heap memory size, default = 4G."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Qualimap RNA-seq QC reports quality control metrics and bias estimations\
+  \ \nwhich are specific for whole transcriptome sequencing, including reads genomic\
+  \ \norigin, junction analysis, transcript coverage and 5’-3’ bias computation.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test_data"
+info: null
+status: "enabled"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "RNA-seq"
+- "quality control"
+- "QC Report"
+license: "GPL-2.0"
+references:
+  doi:
+  - "10.1093/bioinformatics/btv566"
+links:
+  repository: "https://bitbucket.org/kokonech/qualimap/commits/branch/master"
+  homepage: "http://qualimap.conesalab.org/"
+  documentation: "http://qualimap.conesalab.org/doc_html/analysis.html#rna-seq-qc"
+  issue_tracker: "https://bitbucket.org/kokonech/qualimap/issues?status=new&status=open"
+runners:
+- type: "executable"
+  id: "executable"
+  docker_setup_strategy: "ifneedbepullelsecachedbuild"
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    tag: "$id"
+  auto:
+    simplifyInput: true
+    simplifyOutput: false
+    transcript: false
+    publish: false
+  config:
+    labels:
+      mem1gb: "memory = 1000000000.B"
+      mem2gb: "memory = 2000000000.B"
+      mem5gb: "memory = 5000000000.B"
+      mem10gb: "memory = 10000000000.B"
+      mem20gb: "memory = 20000000000.B"
+      mem50gb: "memory = 50000000000.B"
+      mem100gb: "memory = 100000000000.B"
+      mem200gb: "memory = 200000000000.B"
+      mem500gb: "memory = 500000000000.B"
+      mem1tb: "memory = 1000000000000.B"
+      mem2tb: "memory = 2000000000000.B"
+      mem5tb: "memory = 5000000000000.B"
+      mem10tb: "memory = 10000000000000.B"
+      mem20tb: "memory = 20000000000000.B"
+      mem50tb: "memory = 50000000000000.B"
+      mem100tb: "memory = 100000000000000.B"
+      mem200tb: "memory = 200000000000000.B"
+      mem500tb: "memory = 500000000000000.B"
+      mem1gib: "memory = 1073741824.B"
+      mem2gib: "memory = 2147483648.B"
+      mem4gib: "memory = 4294967296.B"
+      mem8gib: "memory = 8589934592.B"
+      mem16gib: "memory = 17179869184.B"
+      mem32gib: "memory = 34359738368.B"
+      mem64gib: "memory = 68719476736.B"
+      mem128gib: "memory = 137438953472.B"
+      mem256gib: "memory = 274877906944.B"
+      mem512gib: "memory = 549755813888.B"
+      mem1tib: "memory = 1099511627776.B"
+      mem2tib: "memory = 2199023255552.B"
+      mem4tib: "memory = 4398046511104.B"
+      mem8tib: "memory = 8796093022208.B"
+      mem16tib: "memory = 17592186044416.B"
+      mem32tib: "memory = 35184372088832.B"
+      mem64tib: "memory = 70368744177664.B"
+      mem128tib: "memory = 140737488355328.B"
+      mem256tib: "memory = 281474976710656.B"
+      mem512tib: "memory = 562949953421312.B"
+      cpu1: "cpus = 1"
+      cpu2: "cpus = 2"
+      cpu5: "cpus = 5"
+      cpu10: "cpus = 10"
+      cpu20: "cpus = 20"
+      cpu50: "cpus = 50"
+      cpu100: "cpus = 100"
+      cpu200: "cpus = 200"
+      cpu500: "cpus = 500"
+      cpu1000: "cpus = 1000"
+  debug: false
+  container: "docker"
+engines:
+- type: "docker"
+  id: "docker"
+  image: "quay.io/biocontainers/qualimap:2.3--hdfd78af_0"
+  target_registry: "images.viash-hub.com"
+  target_tag: "main"
+  namespace_separator: "/"
+  setup:
+  - type: "docker"
+    run:
+    - "echo QualiMap: $(qualimap 2>&1 | grep QualiMap | sed 's/^.*QualiMap//') > /var/software_versions.txt\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/qualimap/qualimap_rnaseq/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/qualimap/qualimap_rnaseq"
+  executable: "target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq"
+  viash_version: "0.9.0-RC6"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
+  git_remote: "https://github.com/viash-hub/biobox"
+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-RC6"
+  source: "src"
+  target: "target"
+  config_mods:
+  - ".requirements.commands := ['ps']\n"
+  - ".engines += { type: \"native\" }"
+  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
+  - ".engines[.type == 'docker'].target_tag := 'main'"
+  keywords:
+  - "bioinformatics"
+  - "modules"
+  - "sequencing"
+  license: "MIT"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/viash-hub/biobox"
+    issue_tracker: "https://github.com/viash-hub/biobox/issues"
diff --git a/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq b/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq
new file mode 100755
index 00000000..d7d58052
--- /dev/null
+++ b/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq
@@ -0,0 +1,1372 @@
+#!/usr/bin/env bash
+
+# qualimap_rnaseq main
+# 
+# This wrapper script is auto-generated by viash 0.9.0-RC6 and is thus a
+# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
+# Data Intuitive.
+# 
+# The component may contain files which fall under a different license. The
+# authors of this component should specify the license in the header of such
+# files, or include a separate license file detailing the licenses of all included
+# files.
+# 
+# Component authors:
+#  * Dorien Roosen (author, maintainer)
+
+set -e
+
+if [ -z "$VIASH_TEMP" ]; then
+  VIASH_TEMP=${VIASH_TEMP:-$VIASH_TMPDIR}
+  VIASH_TEMP=${VIASH_TEMP:-$VIASH_TEMPDIR}
+  VIASH_TEMP=${VIASH_TEMP:-$VIASH_TMP}
+  VIASH_TEMP=${VIASH_TEMP:-$TMPDIR}
+  VIASH_TEMP=${VIASH_TEMP:-$TMP}
+  VIASH_TEMP=${VIASH_TEMP:-$TEMPDIR}
+  VIASH_TEMP=${VIASH_TEMP:-$TEMP}
+  VIASH_TEMP=${VIASH_TEMP:-/tmp}
+fi
+
+# define helper functions
+# ViashQuote: put quotes around non flag values
+# $1     : unquoted string
+# return : possibly quoted string
+# examples:
+#   ViashQuote --foo      # returns --foo
+#   ViashQuote bar        # returns 'bar'
+#   Viashquote --foo=bar  # returns --foo='bar'
+function ViashQuote {
+  if [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+=.+$ ]]; then
+    echo "$1" | sed "s#=\(.*\)#='\1'#"
+  elif [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+$ ]]; then
+    echo "$1"
+  else
+    echo "'$1'"
+  fi
+}
+# ViashRemoveFlags: Remove leading flag
+# $1     : string with a possible leading flag
+# return : string without possible leading flag
+# examples:
+#   ViashRemoveFlags --foo=bar  # returns bar
+function ViashRemoveFlags {
+  echo "$1" | sed 's/^--*[a-zA-Z0-9_\-]*=//'
+}
+# ViashSourceDir: return the path of a bash file, following symlinks
+# usage   : ViashSourceDir ${BASH_SOURCE[0]}
+# $1      : Should always be set to ${BASH_SOURCE[0]}
+# returns : The absolute path of the bash file
+function ViashSourceDir {
+  SOURCE="$1"
+  while [ -h "$SOURCE" ]; do
+    DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )"
+    SOURCE="$(readlink "$SOURCE")"
+    [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE"
+  done
+  cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd
+}
+# ViashFindTargetDir: return the path of the '.build.yaml' file, following symlinks
+# usage   : ViashFindTargetDir 'ScriptPath'
+# $1      : The location from where to start the upward search
+# returns : The absolute path of the '.build.yaml' file
+function ViashFindTargetDir {
+  SOURCE="$1"
+  while [[ "$SOURCE" != "" && ! -e "$SOURCE/.build.yaml" ]]; do
+    SOURCE=${SOURCE%/*}
+  done
+  echo $SOURCE
+}
+# see https://en.wikipedia.org/wiki/Syslog#Severity_level
+VIASH_LOGCODE_EMERGENCY=0
+VIASH_LOGCODE_ALERT=1
+VIASH_LOGCODE_CRITICAL=2
+VIASH_LOGCODE_ERROR=3
+VIASH_LOGCODE_WARNING=4
+VIASH_LOGCODE_NOTICE=5
+VIASH_LOGCODE_INFO=6
+VIASH_LOGCODE_DEBUG=7
+VIASH_VERBOSITY=$VIASH_LOGCODE_NOTICE
+
+# ViashLog: Log events depending on the verbosity level
+# usage: ViashLog 1 alert Oh no something went wrong!
+# $1: required verbosity level
+# $2: display tag
+# $3+: messages to display
+# stdout: Your input, prepended by '[$2] '.
+function ViashLog {
+  local required_level="$1"
+  local display_tag="$2"
+  shift 2
+  if [ $VIASH_VERBOSITY -ge $required_level ]; then
+    >&2 echo "[$display_tag]" "$@"
+  fi
+}
+
+# ViashEmergency: log events when the system is unstable
+# usage: ViashEmergency Oh no something went wrong.
+# stdout: Your input, prepended by '[emergency] '.
+function ViashEmergency {
+  ViashLog $VIASH_LOGCODE_EMERGENCY emergency "$@"
+}
+
+# ViashAlert: log events when actions must be taken immediately (e.g. corrupted system database)
+# usage: ViashAlert Oh no something went wrong.
+# stdout: Your input, prepended by '[alert] '.
+function ViashAlert {
+  ViashLog $VIASH_LOGCODE_ALERT alert "$@"
+}
+
+# ViashCritical: log events when a critical condition occurs
+# usage: ViashCritical Oh no something went wrong.
+# stdout: Your input, prepended by '[critical] '.
+function ViashCritical {
+  ViashLog $VIASH_LOGCODE_CRITICAL critical "$@"
+}
+
+# ViashError: log events when an error condition occurs
+# usage: ViashError Oh no something went wrong.
+# stdout: Your input, prepended by '[error] '.
+function ViashError {
+  ViashLog $VIASH_LOGCODE_ERROR error "$@"
+}
+
+# ViashWarning: log potentially abnormal events
+# usage: ViashWarning Something may have gone wrong.
+# stdout: Your input, prepended by '[warning] '.
+function ViashWarning {
+  ViashLog $VIASH_LOGCODE_WARNING warning "$@"
+}
+
+# ViashNotice: log significant but normal events
+# usage: ViashNotice This just happened.
+# stdout: Your input, prepended by '[notice] '.
+function ViashNotice {
+  ViashLog $VIASH_LOGCODE_NOTICE notice "$@"
+}
+
+# ViashInfo: log normal events
+# usage: ViashInfo This just happened.
+# stdout: Your input, prepended by '[info] '.
+function ViashInfo {
+  ViashLog $VIASH_LOGCODE_INFO info "$@"
+}
+
+# ViashDebug: log all events, for debugging purposes
+# usage: ViashDebug This just happened.
+# stdout: Your input, prepended by '[debug] '.
+function ViashDebug {
+  ViashLog $VIASH_LOGCODE_DEBUG debug "$@"
+}
+
+# find source folder of this component
+VIASH_META_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}`
+
+# find the root of the built components & dependencies
+VIASH_TARGET_DIR=`ViashFindTargetDir $VIASH_META_RESOURCES_DIR`
+
+# define meta fields
+VIASH_META_NAME="qualimap_rnaseq"
+VIASH_META_FUNCTIONALITY_NAME="qualimap_rnaseq"
+VIASH_META_EXECUTABLE="$VIASH_META_RESOURCES_DIR/$VIASH_META_NAME"
+VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
+VIASH_META_TEMP_DIR="$VIASH_TEMP"
+
+
+# ViashHelp: Display helpful explanation about this executable
+function ViashHelp {
+  echo "qualimap_rnaseq main"
+  echo ""
+  echo "Qualimap RNA-seq QC reports quality control metrics and bias estimations"
+  echo "which are specific for whole transcriptome sequencing, including reads genomic"
+  echo "origin, junction analysis, transcript coverage and 5’-3’ bias computation."
+  echo ""
+  echo "Input:"
+  echo "    --bam"
+  echo "        type: file, required parameter, file must exist"
+  echo "        example: alignment.bam"
+  echo "        Path to the sequence alignment file in BAM format, produced by a"
+  echo "        splicing-aware aligner."
+  echo ""
+  echo "    --gtf"
+  echo "        type: file, required parameter, file must exist"
+  echo "        example: annotations.gtf"
+  echo "        Path to genomic annotations in Ensembl GTF format."
+  echo ""
+  echo "Output:"
+  echo "    --qc_results"
+  echo "        type: file, required parameter, output, file must exist"
+  echo "        example: rnaseq_qc_results.txt"
+  echo "        Text file containing the RNAseq QC results."
+  echo ""
+  echo "    --counts"
+  echo "        type: file, output, file must exist"
+  echo "        Output file for computed counts."
+  echo ""
+  echo "    --report"
+  echo "        type: file, output, file must exist"
+  echo "        example: report.html"
+  echo "        Report output file. Supported formats are PDF or HTML."
+  echo ""
+  echo "Optional:"
+  echo "    --num_pr_bases"
+  echo "        type: integer"
+  echo "        min: 1"
+  echo "        Number of upstream/downstream nucleotide bases to compute 5'-3' bias"
+  echo "        (default = 100)."
+  echo ""
+  echo "    --num_tr_bias"
+  echo "        type: integer"
+  echo "        min: 1"
+  echo "        Number of top highly expressed transcripts to compute 5'-3' bias"
+  echo "        (default = 1000)."
+  echo ""
+  echo "    --algorithm"
+  echo "        type: string"
+  echo "        choices: [ uniquely-mapped-reads, proportional ]"
+  echo "        Counting algorithm (uniquely-mapped-reads (default) or proportional)."
+  echo ""
+  echo "    --sequencing_protocol"
+  echo "        type: string"
+  echo "        choices: [ non-strand-specific, strand-specific-reverse,"
+  echo "strand-specific-forward ]"
+  echo "        Sequencing library protocol (strand-specific-forward,"
+  echo "        strand-specific-reverse or non-strand-specific (default))."
+  echo ""
+  echo "    --paired"
+  echo "        type: boolean_true"
+  echo "        Setting this flag for paired-end experiments will result in counting"
+  echo "        fragments instead of reads."
+  echo ""
+  echo "    --sorted"
+  echo "        type: boolean_true"
+  echo "        Setting this flag indicates that the input file is already sorted by"
+  echo "        name. If flag is not set, additional sorting by name will be performed."
+  echo "        Only requiredfor paired-end analysis."
+  echo ""
+  echo "    --java_memory_size"
+  echo "        type: string"
+  echo "        maximum Java heap memory size, default = 4G."
+}
+
+# initialise variables
+VIASH_MODE='run'
+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"
+  save=$-; set +e
+  docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
+  out=$?
+  [[ $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 $1 && return 0 || return 1
+  else
+    save=$-; set +e
+    docker pull $1 2> /dev/null > /dev/null
+    out=$?
+    [[ $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 '$1'"
+  save=$-; set +e
+  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
+#
+# $1                  : image identifier with format `[registry/]image[:tag]`
+# ViashDockerBuild    : a Bash function which builds a docker image, takes image identifier as argument.
+# examples:
+#   ViashDockerPullElseBuild mynewcomponent
+function ViashDockerPullElseBuild {
+  save=$-; set +e
+  ViashDockerPull $1
+  out=$?
+  [[ $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/qualimap:2.3--hdfd78af_0
+ENTRYPOINT []
+RUN echo QualiMap: $(qualimap 2>&1 | grep QualiMap | sed 's/^.*QualiMap//') > /var/software_versions.txt
+
+LABEL org.opencontainers.image.authors="Dorien Roosen"
+LABEL org.opencontainers.image.description="Companion container for running component qualimap qualimap_rnaseq"
+LABEL org.opencontainers.image.created="2024-08-21T11:35:55Z"
+LABEL org.opencontainers.image.source="https://bitbucket.org/kokonech/qualimap/commits/branch/master"
+LABEL org.opencontainers.image.revision="766ab6c9c3059004c7c3f205621909b2d8b0b26d"
+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
+  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
+# $VIASH_DIRECTORY_MOUNTS : Added another parameter to be passed to docker
+# examples:
+#   ViashDockerAutodetectMount /path/to/bar      # returns '/viash_automount/path/to/bar'
+#   ViashDockerAutodetectMountArg /path/to/bar   # returns '--volume="/path/to:/viash_automount/path/to"'
+function ViashDockerAutodetectMount {
+  abs_path=$(ViashAbsolutePath "$1")
+  if [ -d "$abs_path" ]; then
+    mount_source="$abs_path"
+    base_name=""
+  else
+    mount_source=`dirname "$abs_path"`
+    base_name=`basename "$abs_path"`
+  fi
+  mount_target="/viash_automount$mount_source"
+  if [ -z "$base_name" ]; then
+    echo "$mount_target"
+  else
+    echo "$mount_target/$base_name"
+  fi
+}
+function ViashDockerAutodetectMountArg {
+  abs_path=$(ViashAbsolutePath "$1")
+  if [ -d "$abs_path" ]; then
+    mount_source="$abs_path"
+    base_name=""
+  else
+    mount_source=`dirname "$abs_path"`
+    base_name=`basename "$abs_path"`
+  fi
+  mount_target="/viash_automount$mount_source"
+  ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target"
+  echo "--volume=\"$mount_source:$mount_target\""
+}
+function ViashDockerStripAutomount {
+  abs_path=$(ViashAbsolutePath "$1")
+  echo "${abs_path#/viash_automount}"
+}
+# initialise variables
+VIASH_DIRECTORY_MOUNTS=()
+
+# initialise docker variables
+VIASH_DOCKER_RUN_ARGS=(-i --rm)
+
+# initialise array
+VIASH_POSITIONAL_ARGS=''
+
+while [[ $# -gt 0 ]]; do
+    case "$1" in
+        -h|--help)
+            ViashHelp
+            exit
+            ;;
+        ---v|---verbose)
+            let "VIASH_VERBOSITY=VIASH_VERBOSITY+1"
+            shift 1
+            ;;
+        ---verbosity)
+            VIASH_VERBOSITY="$2"
+            shift 2
+            ;;
+        ---verbosity=*)
+            VIASH_VERBOSITY="$(ViashRemoveFlags "$1")"
+            shift 1
+            ;;
+        --version)
+            echo "qualimap_rnaseq main"
+            exit
+            ;;
+        --bam)
+            [ -n "$VIASH_PAR_BAM" ] && ViashError Bad arguments for option \'--bam\': \'$VIASH_PAR_BAM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_BAM="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --bam. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --bam=*)
+            [ -n "$VIASH_PAR_BAM" ] && ViashError Bad arguments for option \'--bam=*\': \'$VIASH_PAR_BAM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_BAM=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --gtf)
+            [ -n "$VIASH_PAR_GTF" ] && ViashError Bad arguments for option \'--gtf\': \'$VIASH_PAR_GTF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_GTF="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --gtf. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --gtf=*)
+            [ -n "$VIASH_PAR_GTF" ] && ViashError Bad arguments for option \'--gtf=*\': \'$VIASH_PAR_GTF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_GTF=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --qc_results)
+            [ -n "$VIASH_PAR_QC_RESULTS" ] && ViashError Bad arguments for option \'--qc_results\': \'$VIASH_PAR_QC_RESULTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_QC_RESULTS="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --qc_results. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --qc_results=*)
+            [ -n "$VIASH_PAR_QC_RESULTS" ] && ViashError Bad arguments for option \'--qc_results=*\': \'$VIASH_PAR_QC_RESULTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_QC_RESULTS=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --counts)
+            [ -n "$VIASH_PAR_COUNTS" ] && ViashError Bad arguments for option \'--counts\': \'$VIASH_PAR_COUNTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_COUNTS="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --counts. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --counts=*)
+            [ -n "$VIASH_PAR_COUNTS" ] && ViashError Bad arguments for option \'--counts=*\': \'$VIASH_PAR_COUNTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_COUNTS=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --report)
+            [ -n "$VIASH_PAR_REPORT" ] && ViashError Bad arguments for option \'--report\': \'$VIASH_PAR_REPORT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_REPORT="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --report. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --report=*)
+            [ -n "$VIASH_PAR_REPORT" ] && ViashError Bad arguments for option \'--report=*\': \'$VIASH_PAR_REPORT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_REPORT=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --num_pr_bases)
+            [ -n "$VIASH_PAR_NUM_PR_BASES" ] && ViashError Bad arguments for option \'--num_pr_bases\': \'$VIASH_PAR_NUM_PR_BASES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_NUM_PR_BASES="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --num_pr_bases. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --num_pr_bases=*)
+            [ -n "$VIASH_PAR_NUM_PR_BASES" ] && ViashError Bad arguments for option \'--num_pr_bases=*\': \'$VIASH_PAR_NUM_PR_BASES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_NUM_PR_BASES=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --num_tr_bias)
+            [ -n "$VIASH_PAR_NUM_TR_BIAS" ] && ViashError Bad arguments for option \'--num_tr_bias\': \'$VIASH_PAR_NUM_TR_BIAS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_NUM_TR_BIAS="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --num_tr_bias. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --num_tr_bias=*)
+            [ -n "$VIASH_PAR_NUM_TR_BIAS" ] && ViashError Bad arguments for option \'--num_tr_bias=*\': \'$VIASH_PAR_NUM_TR_BIAS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_NUM_TR_BIAS=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --algorithm)
+            [ -n "$VIASH_PAR_ALGORITHM" ] && ViashError Bad arguments for option \'--algorithm\': \'$VIASH_PAR_ALGORITHM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_ALGORITHM="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --algorithm. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --algorithm=*)
+            [ -n "$VIASH_PAR_ALGORITHM" ] && ViashError Bad arguments for option \'--algorithm=*\': \'$VIASH_PAR_ALGORITHM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_ALGORITHM=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --sequencing_protocol)
+            [ -n "$VIASH_PAR_SEQUENCING_PROTOCOL" ] && ViashError Bad arguments for option \'--sequencing_protocol\': \'$VIASH_PAR_SEQUENCING_PROTOCOL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_SEQUENCING_PROTOCOL="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --sequencing_protocol. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --sequencing_protocol=*)
+            [ -n "$VIASH_PAR_SEQUENCING_PROTOCOL" ] && ViashError Bad arguments for option \'--sequencing_protocol=*\': \'$VIASH_PAR_SEQUENCING_PROTOCOL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_SEQUENCING_PROTOCOL=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        --paired)
+            [ -n "$VIASH_PAR_PAIRED" ] && ViashError Bad arguments for option \'--paired\': \'$VIASH_PAR_PAIRED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_PAIRED=true
+            shift 1
+            ;;
+        --sorted)
+            [ -n "$VIASH_PAR_SORTED" ] && ViashError Bad arguments for option \'--sorted\': \'$VIASH_PAR_SORTED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_SORTED=true
+            shift 1
+            ;;
+        --java_memory_size)
+            [ -n "$VIASH_PAR_JAVA_MEMORY_SIZE" ] && ViashError Bad arguments for option \'--java_memory_size\': \'$VIASH_PAR_JAVA_MEMORY_SIZE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_JAVA_MEMORY_SIZE="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --java_memory_size. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --java_memory_size=*)
+            [ -n "$VIASH_PAR_JAVA_MEMORY_SIZE" ] && ViashError Bad arguments for option \'--java_memory_size=*\': \'$VIASH_PAR_JAVA_MEMORY_SIZE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_JAVA_MEMORY_SIZE=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        ---engine)
+            VIASH_ENGINE_ID="$2"
+            shift 2
+            ;;
+        ---engine=*)
+            VIASH_ENGINE_ID="$(ViashRemoveFlags "$1")"
+            shift 1
+            ;;
+        ---setup)
+            VIASH_MODE='setup'
+            VIASH_SETUP_STRATEGY="$2"
+            shift 2
+            ;;
+        ---setup=*)
+            VIASH_MODE='setup'
+            VIASH_SETUP_STRATEGY="$(ViashRemoveFlags "$1")"
+            shift 1
+            ;;
+        ---dockerfile)
+            VIASH_MODE='dockerfile'
+            shift 1
+            ;;
+        ---debug)
+            VIASH_MODE='debug'
+            shift 1
+            ;;
+        ---cpus)
+            [ -n "$VIASH_META_CPUS" ] && ViashError Bad arguments for option \'---cpus\': \'$VIASH_META_CPUS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_META_CPUS="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to ---cpus. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        ---cpus=*)
+            [ -n "$VIASH_META_CPUS" ] && ViashError Bad arguments for option \'---cpus=*\': \'$VIASH_META_CPUS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_META_CPUS=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        ---memory)
+            [ -n "$VIASH_META_MEMORY" ] && ViashError Bad arguments for option \'---memory\': \'$VIASH_META_MEMORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_META_MEMORY="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to ---memory. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        ---memory=*)
+            [ -n "$VIASH_META_MEMORY" ] && ViashError Bad arguments for option \'---memory=*\': \'$VIASH_META_MEMORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_META_MEMORY=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
+        *)  # positional arg or unknown option
+            # since the positional args will be eval'd, can we always quote, instead of using ViashQuote
+            VIASH_POSITIONAL_ARGS="$VIASH_POSITIONAL_ARGS '$1'"
+            [[ $1 == -* ]] && ViashWarning $1 looks like a parameter but is not a defined parameter and will instead be treated as a positional argument. Use "--help" to get more information on the parameters.
+            shift # past argument
+            ;;
+    esac
+done
+
+# parse positional parameters
+eval set -- $VIASH_POSITIONAL_ARGS
+
+
+if   [ "$VIASH_ENGINE_ID" == "native" ]  ; then
+  VIASH_ENGINE_TYPE='native'
+elif   [ "$VIASH_ENGINE_ID" == "docker" ]  ; then
+  VIASH_ENGINE_TYPE='docker'
+else
+  ViashError "Engine '$VIASH_ENGINE_ID' is not recognized. Options are: docker, native."
+  exit 1
+fi
+
+if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
+  # check if docker is installed properly
+  ViashDockerInstallationCheck
+
+  # determine docker image id
+  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/qualimap/qualimap_rnaseq:main'
+  fi
+
+  # print dockerfile
+  if [ "$VIASH_MODE" == "dockerfile" ]; then
+    ViashDockerfile "$VIASH_ENGINE_ID"
+    exit 0
+  
+  # enter docker container
+  elif [[ "$VIASH_MODE" == "debug" ]]; then
+    VIASH_CMD="docker run --entrypoint=bash ${VIASH_DOCKER_RUN_ARGS[@]} -v '$(pwd)':/pwd --workdir /pwd -t $VIASH_DOCKER_IMAGE_ID"
+    ViashNotice "+ $VIASH_CMD"
+    eval $VIASH_CMD
+    exit 
+
+  # build docker image
+  elif [ "$VIASH_MODE" == "setup" ]; then
+    ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY"
+    ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash'
+    exit 0
+  fi
+
+  # check if docker image exists
+  ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild
+  ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash'
+fi
+
+# setting computational defaults
+
+# helper function for parsing memory strings
+function ViashMemoryAsBytes {
+  local memory=`echo "$1" | tr '[:upper:]' '[:lower:]' | tr -d '[:space:]'`
+  local memory_regex='^([0-9]+)([kmgtp]i?b?|b)$'
+  if [[ $memory =~ $memory_regex ]]; then
+    local number=${memory/[^0-9]*/}
+    local symbol=${memory/*[0-9]/}
+    
+    case $symbol in
+      b)      memory_b=$number ;;
+      kb|k)   memory_b=$(( $number * 1000 )) ;;
+      mb|m)   memory_b=$(( $number * 1000 * 1000 )) ;;
+      gb|g)   memory_b=$(( $number * 1000 * 1000 * 1000 )) ;;
+      tb|t)   memory_b=$(( $number * 1000 * 1000 * 1000 * 1000 )) ;;
+      pb|p)   memory_b=$(( $number * 1000 * 1000 * 1000 * 1000 * 1000 )) ;;
+      kib|ki)   memory_b=$(( $number * 1024 )) ;;
+      mib|mi)   memory_b=$(( $number * 1024 * 1024 )) ;;
+      gib|gi)   memory_b=$(( $number * 1024 * 1024 * 1024 )) ;;
+      tib|ti)   memory_b=$(( $number * 1024 * 1024 * 1024 * 1024 )) ;;
+      pib|pi)   memory_b=$(( $number * 1024 * 1024 * 1024 * 1024 * 1024 )) ;;
+    esac
+    echo "$memory_b"
+  fi
+}
+# compute memory in different units
+if [ ! -z ${VIASH_META_MEMORY+x} ]; then
+  VIASH_META_MEMORY_B=`ViashMemoryAsBytes $VIASH_META_MEMORY`
+  # do not define other variables if memory_b is an empty string
+  if [ ! -z "$VIASH_META_MEMORY_B" ]; then
+    VIASH_META_MEMORY_KB=$(( ($VIASH_META_MEMORY_B+999) / 1000 ))
+    VIASH_META_MEMORY_MB=$(( ($VIASH_META_MEMORY_KB+999) / 1000 ))
+    VIASH_META_MEMORY_GB=$(( ($VIASH_META_MEMORY_MB+999) / 1000 ))
+    VIASH_META_MEMORY_TB=$(( ($VIASH_META_MEMORY_GB+999) / 1000 ))
+    VIASH_META_MEMORY_PB=$(( ($VIASH_META_MEMORY_TB+999) / 1000 ))
+    VIASH_META_MEMORY_KIB=$(( ($VIASH_META_MEMORY_B+1023) / 1024 ))
+    VIASH_META_MEMORY_MIB=$(( ($VIASH_META_MEMORY_KIB+1023) / 1024 ))
+    VIASH_META_MEMORY_GIB=$(( ($VIASH_META_MEMORY_MIB+1023) / 1024 ))
+    VIASH_META_MEMORY_TIB=$(( ($VIASH_META_MEMORY_GIB+1023) / 1024 ))
+    VIASH_META_MEMORY_PIB=$(( ($VIASH_META_MEMORY_TIB+1023) / 1024 ))
+  else
+    # unset memory if string is empty
+    unset $VIASH_META_MEMORY_B
+  fi
+fi
+# unset nproc if string is empty
+if [ -z "$VIASH_META_CPUS" ]; then
+  unset $VIASH_META_CPUS
+fi
+
+
+# check whether required parameters exist
+if [ -z ${VIASH_PAR_BAM+x} ]; then
+  ViashError '--bam' is a required argument. Use "--help" to get more information on the parameters.
+  exit 1
+fi
+if [ -z ${VIASH_PAR_GTF+x} ]; then
+  ViashError '--gtf' is a required argument. Use "--help" to get more information on the parameters.
+  exit 1
+fi
+if [ -z ${VIASH_PAR_QC_RESULTS+x} ]; then
+  ViashError '--qc_results' is a required argument. Use "--help" to get more information on the parameters.
+  exit 1
+fi
+if [ -z ${VIASH_META_NAME+x} ]; then
+  ViashError 'name' is a required argument. Use "--help" to get more information on the parameters.
+  exit 1
+fi
+if [ -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then
+  ViashError 'functionality_name' is a required argument. Use "--help" to get more information on the parameters.
+  exit 1
+fi
+if [ -z ${VIASH_META_RESOURCES_DIR+x} ]; then
+  ViashError 'resources_dir' is a required argument. Use "--help" to get more information on the parameters.
+  exit 1
+fi
+if [ -z ${VIASH_META_EXECUTABLE+x} ]; then
+  ViashError 'executable' is a required argument. Use "--help" to get more information on the parameters.
+  exit 1
+fi
+if [ -z ${VIASH_META_CONFIG+x} ]; then
+  ViashError 'config' is a required argument. Use "--help" to get more information on the parameters.
+  exit 1
+fi
+if [ -z ${VIASH_META_TEMP_DIR+x} ]; then
+  ViashError 'temp_dir' is a required argument. Use "--help" to get more information on the parameters.
+  exit 1
+fi
+
+# filling in defaults
+if [ -z ${VIASH_PAR_PAIRED+x} ]; then
+  VIASH_PAR_PAIRED="false"
+fi
+if [ -z ${VIASH_PAR_SORTED+x} ]; then
+  VIASH_PAR_SORTED="false"
+fi
+
+# check whether required files exist
+if [ ! -z "$VIASH_PAR_BAM" ] && [ ! -e "$VIASH_PAR_BAM" ]; then
+  ViashError "Input file '$VIASH_PAR_BAM' does not exist."
+  exit 1
+fi
+if [ ! -z "$VIASH_PAR_GTF" ] && [ ! -e "$VIASH_PAR_GTF" ]; then
+  ViashError "Input file '$VIASH_PAR_GTF' does not exist."
+  exit 1
+fi
+
+# check whether parameters values are of the right type
+if [[ -n "$VIASH_PAR_NUM_PR_BASES" ]]; then
+  if ! [[ "$VIASH_PAR_NUM_PR_BASES" =~ ^[-+]?[0-9]+$ ]]; then
+    ViashError '--num_pr_bases' has to be an integer. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+  if [[ $VIASH_PAR_NUM_PR_BASES -lt 1 ]]; then
+    ViashError '--num_pr_bases' has be more than or equal to 1. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_PAR_NUM_TR_BIAS" ]]; then
+  if ! [[ "$VIASH_PAR_NUM_TR_BIAS" =~ ^[-+]?[0-9]+$ ]]; then
+    ViashError '--num_tr_bias' has to be an integer. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+  if [[ $VIASH_PAR_NUM_TR_BIAS -lt 1 ]]; then
+    ViashError '--num_tr_bias' has be more than or equal to 1. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_PAR_PAIRED" ]]; then
+  if ! [[ "$VIASH_PAR_PAIRED" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
+    ViashError '--paired' has to be a boolean_true. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_PAR_SORTED" ]]; then
+  if ! [[ "$VIASH_PAR_SORTED" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
+    ViashError '--sorted' has to be a boolean_true. 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.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_META_MEMORY_B" ]]; then
+  if ! [[ "$VIASH_META_MEMORY_B" =~ ^[-+]?[0-9]+$ ]]; then
+    ViashError 'memory_b' has to be a long. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_META_MEMORY_KB" ]]; then
+  if ! [[ "$VIASH_META_MEMORY_KB" =~ ^[-+]?[0-9]+$ ]]; then
+    ViashError 'memory_kb' has to be a long. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_META_MEMORY_MB" ]]; then
+  if ! [[ "$VIASH_META_MEMORY_MB" =~ ^[-+]?[0-9]+$ ]]; then
+    ViashError 'memory_mb' has to be a long. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_META_MEMORY_GB" ]]; then
+  if ! [[ "$VIASH_META_MEMORY_GB" =~ ^[-+]?[0-9]+$ ]]; then
+    ViashError 'memory_gb' has to be a long. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_META_MEMORY_TB" ]]; then
+  if ! [[ "$VIASH_META_MEMORY_TB" =~ ^[-+]?[0-9]+$ ]]; then
+    ViashError 'memory_tb' has to be a long. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_META_MEMORY_PB" ]]; then
+  if ! [[ "$VIASH_META_MEMORY_PB" =~ ^[-+]?[0-9]+$ ]]; then
+    ViashError 'memory_pb' has to be a long. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_META_MEMORY_KIB" ]]; then
+  if ! [[ "$VIASH_META_MEMORY_KIB" =~ ^[-+]?[0-9]+$ ]]; then
+    ViashError 'memory_kib' has to be a long. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_META_MEMORY_MIB" ]]; then
+  if ! [[ "$VIASH_META_MEMORY_MIB" =~ ^[-+]?[0-9]+$ ]]; then
+    ViashError 'memory_mib' has to be a long. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_META_MEMORY_GIB" ]]; then
+  if ! [[ "$VIASH_META_MEMORY_GIB" =~ ^[-+]?[0-9]+$ ]]; then
+    ViashError 'memory_gib' has to be a long. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_META_MEMORY_TIB" ]]; then
+  if ! [[ "$VIASH_META_MEMORY_TIB" =~ ^[-+]?[0-9]+$ ]]; then
+    ViashError 'memory_tib' has to be a long. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+if [[ -n "$VIASH_META_MEMORY_PIB" ]]; then
+  if ! [[ "$VIASH_META_MEMORY_PIB" =~ ^[-+]?[0-9]+$ ]]; then
+    ViashError 'memory_pib' has to be a long. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+fi
+
+# check whether value is belongs to a set of choices
+if [ ! -z "$VIASH_PAR_ALGORITHM" ]; then
+  VIASH_PAR_ALGORITHM_CHOICES=("uniquely-mapped-reads;proportional")
+  IFS=';'
+  set -f
+  if ! [[ ";${VIASH_PAR_ALGORITHM_CHOICES[*]};" =~ ";$VIASH_PAR_ALGORITHM;" ]]; then
+    ViashError '--algorithm' specified value of \'$VIASH_PAR_ALGORITHM\' is not in the list of allowed values. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+  set +f
+  unset IFS
+fi
+
+if [ ! -z "$VIASH_PAR_SEQUENCING_PROTOCOL" ]; then
+  VIASH_PAR_SEQUENCING_PROTOCOL_CHOICES=("non-strand-specific;strand-specific-reverse;strand-specific-forward")
+  IFS=';'
+  set -f
+  if ! [[ ";${VIASH_PAR_SEQUENCING_PROTOCOL_CHOICES[*]};" =~ ";$VIASH_PAR_SEQUENCING_PROTOCOL;" ]]; then
+    ViashError '--sequencing_protocol' specified value of \'$VIASH_PAR_SEQUENCING_PROTOCOL\' is not in the list of allowed values. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+  set +f
+  unset IFS
+fi
+
+# create parent directories of output files, if so desired
+if [ ! -z "$VIASH_PAR_QC_RESULTS" ] && [ ! -d "$(dirname "$VIASH_PAR_QC_RESULTS")" ]; then
+  mkdir -p "$(dirname "$VIASH_PAR_QC_RESULTS")"
+fi
+if [ ! -z "$VIASH_PAR_COUNTS" ] && [ ! -d "$(dirname "$VIASH_PAR_COUNTS")" ]; then
+  mkdir -p "$(dirname "$VIASH_PAR_COUNTS")"
+fi
+if [ ! -z "$VIASH_PAR_REPORT" ] && [ ! -d "$(dirname "$VIASH_PAR_REPORT")" ]; then
+  mkdir -p "$(dirname "$VIASH_PAR_REPORT")"
+fi
+
+if  [ "$VIASH_ENGINE_ID" == "native" ]  ; then
+  if [ "$VIASH_MODE" == "run" ]; then
+    VIASH_CMD="bash"
+  else
+    ViashError "Engine '$VIASH_ENGINE_ID' does not support mode '$VIASH_MODE'."
+    exit 1
+  fi
+fi
+
+if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
+  # detect volumes from file arguments
+  VIASH_CHOWN_VARS=()
+if [ ! -z "$VIASH_PAR_BAM" ]; then
+  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_BAM")" )
+  VIASH_PAR_BAM=$(ViashDockerAutodetectMount "$VIASH_PAR_BAM")
+fi
+if [ ! -z "$VIASH_PAR_GTF" ]; then
+  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_GTF")" )
+  VIASH_PAR_GTF=$(ViashDockerAutodetectMount "$VIASH_PAR_GTF")
+fi
+if [ ! -z "$VIASH_PAR_QC_RESULTS" ]; then
+  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_QC_RESULTS")" )
+  VIASH_PAR_QC_RESULTS=$(ViashDockerAutodetectMount "$VIASH_PAR_QC_RESULTS")
+  VIASH_CHOWN_VARS+=( "$VIASH_PAR_QC_RESULTS" )
+fi
+if [ ! -z "$VIASH_PAR_COUNTS" ]; then
+  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_COUNTS")" )
+  VIASH_PAR_COUNTS=$(ViashDockerAutodetectMount "$VIASH_PAR_COUNTS")
+  VIASH_CHOWN_VARS+=( "$VIASH_PAR_COUNTS" )
+fi
+if [ ! -z "$VIASH_PAR_REPORT" ]; then
+  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_REPORT")" )
+  VIASH_PAR_REPORT=$(ViashDockerAutodetectMount "$VIASH_PAR_REPORT")
+  VIASH_CHOWN_VARS+=( "$VIASH_PAR_REPORT" )
+fi
+if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
+  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_RESOURCES_DIR")" )
+  VIASH_META_RESOURCES_DIR=$(ViashDockerAutodetectMount "$VIASH_META_RESOURCES_DIR")
+fi
+if [ ! -z "$VIASH_META_EXECUTABLE" ]; then
+  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_EXECUTABLE")" )
+  VIASH_META_EXECUTABLE=$(ViashDockerAutodetectMount "$VIASH_META_EXECUTABLE")
+fi
+if [ ! -z "$VIASH_META_CONFIG" ]; then
+  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_CONFIG")" )
+  VIASH_META_CONFIG=$(ViashDockerAutodetectMount "$VIASH_META_CONFIG")
+fi
+if [ ! -z "$VIASH_META_TEMP_DIR" ]; then
+  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_TEMP_DIR")" )
+  VIASH_META_TEMP_DIR=$(ViashDockerAutodetectMount "$VIASH_META_TEMP_DIR")
+fi
+  
+  # get unique mounts
+  VIASH_UNIQUE_MOUNTS=($(for val in "${VIASH_DIRECTORY_MOUNTS[@]}"; do echo "$val"; done | sort -u))
+fi
+
+if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
+  # change file ownership
+  function ViashPerformChown {
+    if (( ${#VIASH_CHOWN_VARS[@]} )); then
+      set +e
+      VIASH_CMD="docker run --entrypoint=bash --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_DOCKER_IMAGE_ID -c 'chown $(id -u):$(id -g) --silent --recursive ${VIASH_CHOWN_VARS[@]}'"
+      ViashDebug "+ $VIASH_CMD"
+      eval $VIASH_CMD
+      set -e
+    fi
+  }
+  trap ViashPerformChown EXIT
+fi
+
+if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
+  # helper function for filling in extra docker args
+  if [ ! -z "$VIASH_META_MEMORY_B" ]; then
+    VIASH_DOCKER_RUN_ARGS+=("--memory=${VIASH_META_MEMORY_B}")
+  fi
+  if [ ! -z "$VIASH_META_CPUS" ]; then
+    VIASH_DOCKER_RUN_ARGS+=("--cpus=${VIASH_META_CPUS}")
+  fi
+fi
+
+if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
+  VIASH_CMD="docker run --entrypoint=bash ${VIASH_DOCKER_RUN_ARGS[@]} ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_DOCKER_IMAGE_ID"
+fi
+
+
+# set dependency paths
+
+
+ViashDebug "Running command: $(echo $VIASH_CMD)"
+cat << VIASHEOF | eval $VIASH_CMD
+set -e
+tempscript=\$(mktemp "$VIASH_META_TEMP_DIR/viash-run-qualimap_rnaseq-XXXXXX").sh
+function clean_up {
+  rm "\$tempscript"
+}
+function interrupt {
+  echo -e "\nCTRL-C Pressed..."
+  exit 1
+}
+trap clean_up EXIT
+trap interrupt INT SIGINT
+cat > "\$tempscript" << 'VIASHMAIN'
+## VIASH START
+# The following code has been auto-generated by Viash.
+$( if [ ! -z ${VIASH_PAR_BAM+x} ]; then echo "${VIASH_PAR_BAM}" | sed "s#'#'\"'\"'#g;s#.*#par_bam='&'#" ; else echo "# par_bam="; fi )
+$( if [ ! -z ${VIASH_PAR_GTF+x} ]; then echo "${VIASH_PAR_GTF}" | sed "s#'#'\"'\"'#g;s#.*#par_gtf='&'#" ; else echo "# par_gtf="; fi )
+$( if [ ! -z ${VIASH_PAR_QC_RESULTS+x} ]; then echo "${VIASH_PAR_QC_RESULTS}" | sed "s#'#'\"'\"'#g;s#.*#par_qc_results='&'#" ; else echo "# par_qc_results="; fi )
+$( if [ ! -z ${VIASH_PAR_COUNTS+x} ]; then echo "${VIASH_PAR_COUNTS}" | sed "s#'#'\"'\"'#g;s#.*#par_counts='&'#" ; else echo "# par_counts="; fi )
+$( if [ ! -z ${VIASH_PAR_REPORT+x} ]; then echo "${VIASH_PAR_REPORT}" | sed "s#'#'\"'\"'#g;s#.*#par_report='&'#" ; else echo "# par_report="; fi )
+$( if [ ! -z ${VIASH_PAR_NUM_PR_BASES+x} ]; then echo "${VIASH_PAR_NUM_PR_BASES}" | sed "s#'#'\"'\"'#g;s#.*#par_num_pr_bases='&'#" ; else echo "# par_num_pr_bases="; fi )
+$( if [ ! -z ${VIASH_PAR_NUM_TR_BIAS+x} ]; then echo "${VIASH_PAR_NUM_TR_BIAS}" | sed "s#'#'\"'\"'#g;s#.*#par_num_tr_bias='&'#" ; else echo "# par_num_tr_bias="; fi )
+$( if [ ! -z ${VIASH_PAR_ALGORITHM+x} ]; then echo "${VIASH_PAR_ALGORITHM}" | sed "s#'#'\"'\"'#g;s#.*#par_algorithm='&'#" ; else echo "# par_algorithm="; fi )
+$( if [ ! -z ${VIASH_PAR_SEQUENCING_PROTOCOL+x} ]; then echo "${VIASH_PAR_SEQUENCING_PROTOCOL}" | sed "s#'#'\"'\"'#g;s#.*#par_sequencing_protocol='&'#" ; else echo "# par_sequencing_protocol="; fi )
+$( if [ ! -z ${VIASH_PAR_PAIRED+x} ]; then echo "${VIASH_PAR_PAIRED}" | sed "s#'#'\"'\"'#g;s#.*#par_paired='&'#" ; else echo "# par_paired="; fi )
+$( if [ ! -z ${VIASH_PAR_SORTED+x} ]; then echo "${VIASH_PAR_SORTED}" | sed "s#'#'\"'\"'#g;s#.*#par_sorted='&'#" ; else echo "# par_sorted="; fi )
+$( if [ ! -z ${VIASH_PAR_JAVA_MEMORY_SIZE+x} ]; then echo "${VIASH_PAR_JAVA_MEMORY_SIZE}" | sed "s#'#'\"'\"'#g;s#.*#par_java_memory_size='&'#" ; else echo "# par_java_memory_size="; 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 )
+$( if [ ! -z ${VIASH_META_EXECUTABLE+x} ]; then echo "${VIASH_META_EXECUTABLE}" | sed "s#'#'\"'\"'#g;s#.*#meta_executable='&'#" ; else echo "# meta_executable="; fi )
+$( if [ ! -z ${VIASH_META_CONFIG+x} ]; then echo "${VIASH_META_CONFIG}" | sed "s#'#'\"'\"'#g;s#.*#meta_config='&'#" ; else echo "# meta_config="; fi )
+$( if [ ! -z ${VIASH_META_TEMP_DIR+x} ]; then echo "${VIASH_META_TEMP_DIR}" | sed "s#'#'\"'\"'#g;s#.*#meta_temp_dir='&'#" ; else echo "# meta_temp_dir="; fi )
+$( if [ ! -z ${VIASH_META_CPUS+x} ]; then echo "${VIASH_META_CPUS}" | sed "s#'#'\"'\"'#g;s#.*#meta_cpus='&'#" ; else echo "# meta_cpus="; fi )
+$( if [ ! -z ${VIASH_META_MEMORY_B+x} ]; then echo "${VIASH_META_MEMORY_B}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_b='&'#" ; else echo "# meta_memory_b="; fi )
+$( if [ ! -z ${VIASH_META_MEMORY_KB+x} ]; then echo "${VIASH_META_MEMORY_KB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_kb='&'#" ; else echo "# meta_memory_kb="; fi )
+$( if [ ! -z ${VIASH_META_MEMORY_MB+x} ]; then echo "${VIASH_META_MEMORY_MB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_mb='&'#" ; else echo "# meta_memory_mb="; fi )
+$( if [ ! -z ${VIASH_META_MEMORY_GB+x} ]; then echo "${VIASH_META_MEMORY_GB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_gb='&'#" ; else echo "# meta_memory_gb="; fi )
+$( if [ ! -z ${VIASH_META_MEMORY_TB+x} ]; then echo "${VIASH_META_MEMORY_TB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_tb='&'#" ; else echo "# meta_memory_tb="; fi )
+$( if [ ! -z ${VIASH_META_MEMORY_PB+x} ]; then echo "${VIASH_META_MEMORY_PB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_pb='&'#" ; else echo "# meta_memory_pb="; fi )
+$( if [ ! -z ${VIASH_META_MEMORY_KIB+x} ]; then echo "${VIASH_META_MEMORY_KIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_kib='&'#" ; else echo "# meta_memory_kib="; fi )
+$( if [ ! -z ${VIASH_META_MEMORY_MIB+x} ]; then echo "${VIASH_META_MEMORY_MIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_mib='&'#" ; else echo "# meta_memory_mib="; fi )
+$( if [ ! -z ${VIASH_META_MEMORY_GIB+x} ]; then echo "${VIASH_META_MEMORY_GIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_gib='&'#" ; else echo "# meta_memory_gib="; fi )
+$( if [ ! -z ${VIASH_META_MEMORY_TIB+x} ]; then echo "${VIASH_META_MEMORY_TIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_tib='&'#" ; else echo "# meta_memory_tib="; fi )
+$( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_pib='&'#" ; else echo "# meta_memory_pib="; fi )
+
+## VIASH END
+#!/bin/bash
+
+set -eo pipefail
+
+tmp_dir=\$(mktemp -d -p "\$meta_temp_dir" qualimap_XXXXXXXXX)
+
+# Handle output parameters
+if [ -n "\$par_report" ]; then
+    outfile=\$(basename "\$par_report")
+    report_extension="\${outfile##*.}"
+fi
+
+if [ -n "\$par_counts" ]; then
+    counts=\$(basename "\$par_counts")
+fi
+
+# disable flags
+[[ "\$par_paired" == "false" ]] && unset par_paired
+[[ "\$par_sorted" == "false" ]] && unset par_sorted
+
+# Run qualimap
+qualimap rnaseq \\
+    \${meta_memory_mb:+--java-mem-size=\${meta_memory_mb}M} \\
+    \${par_algorithm:+--algorithm \$par_algorithm} \\
+    \${par_sequencing_protocol:+--sequencing-protocol \$par_sequencing_protocol} \\
+    -bam \$par_bam \\
+    -gtf \$par_gtf \\
+    -outdir "\$tmp_dir" \\
+    \${par_num_pr_bases:+--num-pr-bases \$par_num_pr_bases} \\
+    \${par_num_tr_bias:+--num-tr-bias \$par_num_tr_bias} \\
+    \${par_report:+-outformat \$report_extension} \\
+    \${par_paired:+--paired} \\
+    \${par_sorted:+--sorted} \\
+    \${par_report:+-outfile "\$outfile"} \\
+    \${par_counts:+-oc "\$counts"}
+
+# Move output files
+mv "\$tmp_dir/rnaseq_qc_results.txt" "\$par_qc_results"
+
+if [ -n "\$par_report" ] && [ \$report_extension = "html" ]; then
+    mv "\$tmp_dir/qualimapReport.html" "\$par_report"
+fi
+
+if [ -n "\$par_report" ] && [ \$report_extension = "pdf" ]; then
+    mv "\$tmp_dir/\$outfile" "\$par_report"
+fi
+
+if [ -n "\$par_counts" ]; then
+    mv "\$tmp_dir/\$counts" "\$par_counts"
+fi
+VIASHMAIN
+bash "\$tempscript" &
+wait "\$!"
+
+VIASHEOF
+
+
+if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
+  # strip viash automount from file paths
+  
+  if [ ! -z "$VIASH_PAR_BAM" ]; then
+    VIASH_PAR_BAM=$(ViashDockerStripAutomount "$VIASH_PAR_BAM")
+  fi
+  if [ ! -z "$VIASH_PAR_GTF" ]; then
+    VIASH_PAR_GTF=$(ViashDockerStripAutomount "$VIASH_PAR_GTF")
+  fi
+  if [ ! -z "$VIASH_PAR_QC_RESULTS" ]; then
+    VIASH_PAR_QC_RESULTS=$(ViashDockerStripAutomount "$VIASH_PAR_QC_RESULTS")
+  fi
+  if [ ! -z "$VIASH_PAR_COUNTS" ]; then
+    VIASH_PAR_COUNTS=$(ViashDockerStripAutomount "$VIASH_PAR_COUNTS")
+  fi
+  if [ ! -z "$VIASH_PAR_REPORT" ]; then
+    VIASH_PAR_REPORT=$(ViashDockerStripAutomount "$VIASH_PAR_REPORT")
+  fi
+  if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
+    VIASH_META_RESOURCES_DIR=$(ViashDockerStripAutomount "$VIASH_META_RESOURCES_DIR")
+  fi
+  if [ ! -z "$VIASH_META_EXECUTABLE" ]; then
+    VIASH_META_EXECUTABLE=$(ViashDockerStripAutomount "$VIASH_META_EXECUTABLE")
+  fi
+  if [ ! -z "$VIASH_META_CONFIG" ]; then
+    VIASH_META_CONFIG=$(ViashDockerStripAutomount "$VIASH_META_CONFIG")
+  fi
+  if [ ! -z "$VIASH_META_TEMP_DIR" ]; then
+    VIASH_META_TEMP_DIR=$(ViashDockerStripAutomount "$VIASH_META_TEMP_DIR")
+  fi
+fi
+
+
+# check whether required files exist
+if [ ! -z "$VIASH_PAR_QC_RESULTS" ] && [ ! -e "$VIASH_PAR_QC_RESULTS" ]; then
+  ViashError "Output file '$VIASH_PAR_QC_RESULTS' does not exist."
+  exit 1
+fi
+if [ ! -z "$VIASH_PAR_COUNTS" ] && [ ! -e "$VIASH_PAR_COUNTS" ]; then
+  ViashError "Output file '$VIASH_PAR_COUNTS' does not exist."
+  exit 1
+fi
+if [ ! -z "$VIASH_PAR_REPORT" ] && [ ! -e "$VIASH_PAR_REPORT" ]; then
+  ViashError "Output file '$VIASH_PAR_REPORT' does not exist."
+  exit 1
+fi
+
+
+exit 0
diff --git a/target/executable/salmon/salmon_index/.config.vsh.yaml b/target/executable/salmon/salmon_index/.config.vsh.yaml
index eef91767..e5d4f46f 100644
--- a/target/executable/salmon/salmon_index/.config.vsh.yaml
+++ b/target/executable/salmon/salmon_index/.config.vsh.yaml
@@ -277,7 +277,7 @@ build_info:
   output: "target/executable/salmon/salmon_index"
   executable: "target/executable/salmon/salmon_index/salmon_index"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/salmon/salmon_index/salmon_index b/target/executable/salmon/salmon_index/salmon_index
index 63d92e6a..bc1f2ba0 100755
--- a/target/executable/salmon/salmon_index/salmon_index
+++ b/target/executable/salmon/salmon_index/salmon_index
@@ -545,9 +545,9 @@ RUN salmon index -v 2>&1 | sed 's/salmon \([0-9.]*\)/salmon: \1/' > /var/softwar
 
 LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
 LABEL org.opencontainers.image.description="Companion container for running component salmon salmon_index"
-LABEL org.opencontainers.image.created="2024-08-14T20:58:46Z"
+LABEL org.opencontainers.image.created="2024-08-21T11:36:03Z"
 LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon"
-LABEL org.opencontainers.image.revision="923a6da3898a832df96a0e17c8a3b74c2806d939"
+LABEL org.opencontainers.image.revision="766ab6c9c3059004c7c3f205621909b2d8b0b26d"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/salmon/salmon_quant/.config.vsh.yaml b/target/executable/salmon/salmon_quant/.config.vsh.yaml
index eb00cb58..f185c964 100644
--- a/target/executable/salmon/salmon_quant/.config.vsh.yaml
+++ b/target/executable/salmon/salmon_quant/.config.vsh.yaml
@@ -1173,7 +1173,7 @@ build_info:
   output: "target/executable/salmon/salmon_quant"
   executable: "target/executable/salmon/salmon_quant/salmon_quant"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/salmon/salmon_quant/salmon_quant b/target/executable/salmon/salmon_quant/salmon_quant
index 50c365e2..0af7704a 100755
--- a/target/executable/salmon/salmon_quant/salmon_quant
+++ b/target/executable/salmon/salmon_quant/salmon_quant
@@ -1167,9 +1167,9 @@ RUN salmon index -v 2>&1 | sed 's/salmon \([0-9.]*\)/salmon: \1/' > /var/softwar
 
 LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
 LABEL org.opencontainers.image.description="Companion container for running component salmon salmon_quant"
-LABEL org.opencontainers.image.created="2024-08-14T20:58:46Z"
+LABEL org.opencontainers.image.created="2024-08-21T11:36:03Z"
 LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon"
-LABEL org.opencontainers.image.revision="923a6da3898a832df96a0e17c8a3b74c2806d939"
+LABEL org.opencontainers.image.revision="766ab6c9c3059004c7c3f205621909b2d8b0b26d"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/samtools/samtools_collate/.config.vsh.yaml b/target/executable/samtools/samtools_collate/.config.vsh.yaml
index 84e2e7b1..8d9dcd3b 100644
--- a/target/executable/samtools/samtools_collate/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_collate/.config.vsh.yaml
@@ -264,7 +264,7 @@ build_info:
   output: "target/executable/samtools/samtools_collate"
   executable: "target/executable/samtools/samtools_collate/samtools_collate"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/samtools/samtools_collate/samtools_collate b/target/executable/samtools/samtools_collate/samtools_collate
index 16e351bc..0da2dc4c 100755
--- a/target/executable/samtools/samtools_collate/samtools_collate
+++ b/target/executable/samtools/samtools_collate/samtools_collate
@@ -518,9 +518,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_collate"
-LABEL org.opencontainers.image.created="2024-08-14T20:58:55Z"
+LABEL org.opencontainers.image.created="2024-08-21T11:35:54Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="923a6da3898a832df96a0e17c8a3b74c2806d939"
+LABEL org.opencontainers.image.revision="766ab6c9c3059004c7c3f205621909b2d8b0b26d"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/samtools/samtools_faidx/.config.vsh.yaml b/target/executable/samtools/samtools_faidx/.config.vsh.yaml
index afe0ed61..06c00810 100644
--- a/target/executable/samtools/samtools_faidx/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_faidx/.config.vsh.yaml
@@ -243,7 +243,7 @@ build_info:
   output: "target/executable/samtools/samtools_faidx"
   executable: "target/executable/samtools/samtools_faidx/samtools_faidx"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/samtools/samtools_faidx/samtools_faidx b/target/executable/samtools/samtools_faidx/samtools_faidx
index ed4ec7c0..5de56cf9 100755
--- a/target/executable/samtools/samtools_faidx/samtools_faidx
+++ b/target/executable/samtools/samtools_faidx/samtools_faidx
@@ -511,9 +511,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_faidx"
-LABEL org.opencontainers.image.created="2024-08-14T20:58:56Z"
+LABEL org.opencontainers.image.created="2024-08-21T11:35:54Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="923a6da3898a832df96a0e17c8a3b74c2806d939"
+LABEL org.opencontainers.image.revision="766ab6c9c3059004c7c3f205621909b2d8b0b26d"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/samtools/samtools_fasta/.config.vsh.yaml b/target/executable/samtools/samtools_fasta/.config.vsh.yaml
index 3d1a5e0b..e3107328 100644
--- a/target/executable/samtools/samtools_fasta/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_fasta/.config.vsh.yaml
@@ -433,7 +433,7 @@ build_info:
   output: "target/executable/samtools/samtools_fasta"
   executable: "target/executable/samtools/samtools_fasta/samtools_fasta"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/samtools/samtools_fasta/samtools_fasta b/target/executable/samtools/samtools_fasta/samtools_fasta
index 1aa23b32..c4936296 100755
--- a/target/executable/samtools/samtools_fasta/samtools_fasta
+++ b/target/executable/samtools/samtools_fasta/samtools_fasta
@@ -624,9 +624,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_fasta"
-LABEL org.opencontainers.image.created="2024-08-14T20:58:54Z"
+LABEL org.opencontainers.image.created="2024-08-21T11:35:54Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="923a6da3898a832df96a0e17c8a3b74c2806d939"
+LABEL org.opencontainers.image.revision="766ab6c9c3059004c7c3f205621909b2d8b0b26d"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/samtools/samtools_fastq/.config.vsh.yaml b/target/executable/samtools/samtools_fastq/.config.vsh.yaml
index e61730de..9d149fd0 100644
--- a/target/executable/samtools/samtools_fastq/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_fastq/.config.vsh.yaml
@@ -433,7 +433,7 @@ build_info:
   output: "target/executable/samtools/samtools_fastq"
   executable: "target/executable/samtools/samtools_fastq/samtools_fastq"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/samtools/samtools_fastq/samtools_fastq b/target/executable/samtools/samtools_fastq/samtools_fastq
index 58948be0..183a1897 100755
--- a/target/executable/samtools/samtools_fastq/samtools_fastq
+++ b/target/executable/samtools/samtools_fastq/samtools_fastq
@@ -625,9 +625,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_fastq"
-LABEL org.opencontainers.image.created="2024-08-14T20:58:56Z"
+LABEL org.opencontainers.image.created="2024-08-21T11:35:53Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="923a6da3898a832df96a0e17c8a3b74c2806d939"
+LABEL org.opencontainers.image.revision="766ab6c9c3059004c7c3f205621909b2d8b0b26d"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/samtools/samtools_flagstat/.config.vsh.yaml b/target/executable/samtools/samtools_flagstat/.config.vsh.yaml
index 3e65a348..31cdef96 100644
--- a/target/executable/samtools/samtools_flagstat/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_flagstat/.config.vsh.yaml
@@ -173,7 +173,7 @@ build_info:
   output: "target/executable/samtools/samtools_flagstat"
   executable: "target/executable/samtools/samtools_flagstat/samtools_flagstat"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/samtools/samtools_flagstat/samtools_flagstat b/target/executable/samtools/samtools_flagstat/samtools_flagstat
index 0485b374..c715ce64 100755
--- a/target/executable/samtools/samtools_flagstat/samtools_flagstat
+++ b/target/executable/samtools/samtools_flagstat/samtools_flagstat
@@ -473,9 +473,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_flagstat"
-LABEL org.opencontainers.image.created="2024-08-14T20:58:54Z"
+LABEL org.opencontainers.image.created="2024-08-21T11:35:53Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="923a6da3898a832df96a0e17c8a3b74c2806d939"
+LABEL org.opencontainers.image.revision="766ab6c9c3059004c7c3f205621909b2d8b0b26d"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/samtools/samtools_idxstats/.config.vsh.yaml b/target/executable/samtools/samtools_idxstats/.config.vsh.yaml
index 2085d11f..9e86142c 100644
--- a/target/executable/samtools/samtools_idxstats/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_idxstats/.config.vsh.yaml
@@ -183,7 +183,7 @@ build_info:
   output: "target/executable/samtools/samtools_idxstats"
   executable: "target/executable/samtools/samtools_idxstats/samtools_idxstats"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/samtools/samtools_idxstats/samtools_idxstats b/target/executable/samtools/samtools_idxstats/samtools_idxstats
index 3391b324..683a6eec 100755
--- a/target/executable/samtools/samtools_idxstats/samtools_idxstats
+++ b/target/executable/samtools/samtools_idxstats/samtools_idxstats
@@ -477,9 +477,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_idxstats"
-LABEL org.opencontainers.image.created="2024-08-14T20:58:55Z"
+LABEL org.opencontainers.image.created="2024-08-21T11:35:52Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="923a6da3898a832df96a0e17c8a3b74c2806d939"
+LABEL org.opencontainers.image.revision="766ab6c9c3059004c7c3f205621909b2d8b0b26d"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/samtools/samtools_index/.config.vsh.yaml b/target/executable/samtools/samtools_index/.config.vsh.yaml
index afc62cf3..4ba2537d 100644
--- a/target/executable/samtools/samtools_index/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_index/.config.vsh.yaml
@@ -189,7 +189,7 @@ build_info:
   output: "target/executable/samtools/samtools_index"
   executable: "target/executable/samtools/samtools_index/samtools_index"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/samtools/samtools_index/samtools_index b/target/executable/samtools/samtools_index/samtools_index
index de2505f9..83e9bf11 100755
--- a/target/executable/samtools/samtools_index/samtools_index
+++ b/target/executable/samtools/samtools_index/samtools_index
@@ -484,9 +484,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_index"
-LABEL org.opencontainers.image.created="2024-08-14T20:58:55Z"
+LABEL org.opencontainers.image.created="2024-08-21T11:35:52Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="923a6da3898a832df96a0e17c8a3b74c2806d939"
+LABEL org.opencontainers.image.revision="766ab6c9c3059004c7c3f205621909b2d8b0b26d"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/samtools/samtools_sort/.config.vsh.yaml b/target/executable/samtools/samtools_sort/.config.vsh.yaml
index 7db09619..af1e162c 100644
--- a/target/executable/samtools/samtools_sort/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_sort/.config.vsh.yaml
@@ -332,7 +332,7 @@ build_info:
   output: "target/executable/samtools/samtools_sort"
   executable: "target/executable/samtools/samtools_sort/samtools_sort"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/samtools/samtools_sort/samtools_sort b/target/executable/samtools/samtools_sort/samtools_sort
index d9a4e0c9..ea44e2cb 100755
--- a/target/executable/samtools/samtools_sort/samtools_sort
+++ b/target/executable/samtools/samtools_sort/samtools_sort
@@ -555,9 +555,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_sort"
-LABEL org.opencontainers.image.created="2024-08-14T20:58:56Z"
+LABEL org.opencontainers.image.created="2024-08-21T11:35:55Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="923a6da3898a832df96a0e17c8a3b74c2806d939"
+LABEL org.opencontainers.image.revision="766ab6c9c3059004c7c3f205621909b2d8b0b26d"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/samtools/samtools_stats/.config.vsh.yaml b/target/executable/samtools/samtools_stats/.config.vsh.yaml
index 8acf3b43..441c07f1 100644
--- a/target/executable/samtools/samtools_stats/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_stats/.config.vsh.yaml
@@ -401,7 +401,7 @@ build_info:
   output: "target/executable/samtools/samtools_stats"
   executable: "target/executable/samtools/samtools_stats/samtools_stats"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/samtools/samtools_stats/samtools_stats b/target/executable/samtools/samtools_stats/samtools_stats
index b81a8be2..a637c4e4 100755
--- a/target/executable/samtools/samtools_stats/samtools_stats
+++ b/target/executable/samtools/samtools_stats/samtools_stats
@@ -574,9 +574,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_stats"
-LABEL org.opencontainers.image.created="2024-08-14T20:58:54Z"
+LABEL org.opencontainers.image.created="2024-08-21T11:35:55Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="923a6da3898a832df96a0e17c8a3b74c2806d939"
+LABEL org.opencontainers.image.revision="766ab6c9c3059004c7c3f205621909b2d8b0b26d"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/samtools/samtools_view/.config.vsh.yaml b/target/executable/samtools/samtools_view/.config.vsh.yaml
index ad58dd84..66e3768e 100644
--- a/target/executable/samtools/samtools_view/.config.vsh.yaml
+++ b/target/executable/samtools/samtools_view/.config.vsh.yaml
@@ -665,7 +665,7 @@ build_info:
   output: "target/executable/samtools/samtools_view"
   executable: "target/executable/samtools/samtools_view/samtools_view"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/samtools/samtools_view/samtools_view b/target/executable/samtools/samtools_view/samtools_view
index b830edcf..9def3cc3 100755
--- a/target/executable/samtools/samtools_view/samtools_view
+++ b/target/executable/samtools/samtools_view/samtools_view
@@ -824,9 +824,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_view"
-LABEL org.opencontainers.image.created="2024-08-14T20:58:53Z"
+LABEL org.opencontainers.image.created="2024-08-21T11:35:53Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="923a6da3898a832df96a0e17c8a3b74c2806d939"
+LABEL org.opencontainers.image.revision="766ab6c9c3059004c7c3f205621909b2d8b0b26d"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/seqtk/seqtk_sample/.config.vsh.yaml b/target/executable/seqtk/seqtk_sample/.config.vsh.yaml
index dc60b87f..f96f6d3b 100644
--- a/target/executable/seqtk/seqtk_sample/.config.vsh.yaml
+++ b/target/executable/seqtk/seqtk_sample/.config.vsh.yaml
@@ -173,7 +173,7 @@ build_info:
   output: "target/executable/seqtk/seqtk_sample"
   executable: "target/executable/seqtk/seqtk_sample/seqtk_sample"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/seqtk/seqtk_sample/seqtk_sample b/target/executable/seqtk/seqtk_sample/seqtk_sample
index a6529881..fbed128a 100755
--- a/target/executable/seqtk/seqtk_sample/seqtk_sample
+++ b/target/executable/seqtk/seqtk_sample/seqtk_sample
@@ -480,9 +480,9 @@ FROM quay.io/biocontainers/seqtk:1.4--he4a0461_2
 ENTRYPOINT []
 LABEL org.opencontainers.image.authors="Jakub Majercik"
 LABEL org.opencontainers.image.description="Companion container for running component seqtk seqtk_sample"
-LABEL org.opencontainers.image.created="2024-08-14T20:58:49Z"
+LABEL org.opencontainers.image.created="2024-08-21T11:36:05Z"
 LABEL org.opencontainers.image.source="https://github.com/lh3/seqtk/tree/v1.4"
-LABEL org.opencontainers.image.revision="923a6da3898a832df96a0e17c8a3b74c2806d939"
+LABEL org.opencontainers.image.revision="766ab6c9c3059004c7c3f205621909b2d8b0b26d"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml b/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml
index bc14a41a..14f425b6 100644
--- a/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml
+++ b/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml
@@ -196,7 +196,7 @@ build_info:
   output: "target/executable/seqtk/seqtk_subseq"
   executable: "target/executable/seqtk/seqtk_subseq/seqtk_subseq"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/seqtk/seqtk_subseq/seqtk_subseq b/target/executable/seqtk/seqtk_subseq/seqtk_subseq
index 6e79c144..70ad29aa 100755
--- a/target/executable/seqtk/seqtk_subseq/seqtk_subseq
+++ b/target/executable/seqtk/seqtk_subseq/seqtk_subseq
@@ -490,9 +490,9 @@ RUN echo $(echo $(seqtk 2>&1) | sed -n 's/.*\(Version: [^ ]*\).*/\1/p') > /var/s
 
 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component seqtk seqtk_subseq"
-LABEL org.opencontainers.image.created="2024-08-14T20:58:49Z"
+LABEL org.opencontainers.image.created="2024-08-21T11:36:05Z"
 LABEL org.opencontainers.image.source="https://github.com/lh3/seqtk/tree/v1.4"
-LABEL org.opencontainers.image.revision="923a6da3898a832df96a0e17c8a3b74c2806d939"
+LABEL org.opencontainers.image.revision="766ab6c9c3059004c7c3f205621909b2d8b0b26d"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/star/star_align_reads/.config.vsh.yaml b/target/executable/star/star_align_reads/.config.vsh.yaml
index 85958512..bd6707d4 100644
--- a/target/executable/star/star_align_reads/.config.vsh.yaml
+++ b/target/executable/star/star_align_reads/.config.vsh.yaml
@@ -2663,7 +2663,7 @@ build_info:
   output: "target/executable/star/star_align_reads"
   executable: "target/executable/star/star_align_reads/star_align_reads"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/star/star_align_reads/star_align_reads b/target/executable/star/star_align_reads/star_align_reads
index 6c8ab379..391fdccb 100755
--- a/target/executable/star/star_align_reads/star_align_reads
+++ b/target/executable/star/star_align_reads/star_align_reads
@@ -1919,9 +1919,9 @@ RUN STAR --version | sed 's#\(.*\)#star: "\1"#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component star star_align_reads"
-LABEL org.opencontainers.image.created="2024-08-14T20:58:50Z"
+LABEL org.opencontainers.image.created="2024-08-21T11:35:58Z"
 LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR"
-LABEL org.opencontainers.image.revision="923a6da3898a832df96a0e17c8a3b74c2806d939"
+LABEL org.opencontainers.image.revision="766ab6c9c3059004c7c3f205621909b2d8b0b26d"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/star/star_genome_generate/.config.vsh.yaml b/target/executable/star/star_genome_generate/.config.vsh.yaml
index 75d57b52..2b739f42 100644
--- a/target/executable/star/star_genome_generate/.config.vsh.yaml
+++ b/target/executable/star/star_genome_generate/.config.vsh.yaml
@@ -333,7 +333,7 @@ build_info:
   output: "target/executable/star/star_genome_generate"
   executable: "target/executable/star/star_genome_generate/star_genome_generate"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/star/star_genome_generate/star_genome_generate b/target/executable/star/star_genome_generate/star_genome_generate
index a731ee64..3ebc41be 100755
--- a/target/executable/star/star_genome_generate/star_genome_generate
+++ b/target/executable/star/star_genome_generate/star_genome_generate
@@ -576,9 +576,9 @@ RUN STAR --version | sed 's#\(.*\)#star: "\1"#' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
 LABEL org.opencontainers.image.description="Companion container for running component star star_genome_generate"
-LABEL org.opencontainers.image.created="2024-08-14T20:58:49Z"
+LABEL org.opencontainers.image.created="2024-08-21T11:35:58Z"
 LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR"
-LABEL org.opencontainers.image.revision="923a6da3898a832df96a0e17c8a3b74c2806d939"
+LABEL org.opencontainers.image.revision="766ab6c9c3059004c7c3f205621909b2d8b0b26d"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml b/target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml
index 86088dae..afd0164e 100644
--- a/target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml
+++ b/target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml
@@ -611,7 +611,7 @@ build_info:
   output: "target/executable/umi_tools/umi_tools_dedup"
   executable: "target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup b/target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup
index 397a78e7..b99ca5b3 100755
--- a/target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup
+++ b/target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup
@@ -769,9 +769,9 @@ RUN umi_tools -v | sed 's/ version//g' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.authors="Emma Rousseau"
 LABEL org.opencontainers.image.description="Companion container for running component umi_tools umi_tools_dedup"
-LABEL org.opencontainers.image.created="2024-08-14T20:58:57Z"
+LABEL org.opencontainers.image.created="2024-08-21T11:35:56Z"
 LABEL org.opencontainers.image.source="https://github.com/CGATOxford/UMI-tools"
-LABEL org.opencontainers.image.revision="923a6da3898a832df96a0e17c8a3b74c2806d939"
+LABEL org.opencontainers.image.revision="766ab6c9c3059004c7c3f205621909b2d8b0b26d"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml b/target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml
index f6e16c07..19fc3e13 100644
--- a/target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml
+++ b/target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml
@@ -449,7 +449,7 @@ build_info:
   output: "target/executable/umi_tools/umi_tools_extract"
   executable: "target/executable/umi_tools/umi_tools_extract/umi_tools_extract"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/executable/umi_tools/umi_tools_extract/umi_tools_extract b/target/executable/umi_tools/umi_tools_extract/umi_tools_extract
index edf03d9d..61a66eba 100755
--- a/target/executable/umi_tools/umi_tools_extract/umi_tools_extract
+++ b/target/executable/umi_tools/umi_tools_extract/umi_tools_extract
@@ -636,9 +636,9 @@ ENTRYPOINT []
 RUN umi_tools -v | sed 's/ version//g' > /var/software_versions.txt
 
 LABEL org.opencontainers.image.description="Companion container for running component umi_tools umi_tools_extract"
-LABEL org.opencontainers.image.created="2024-08-14T20:58:57Z"
+LABEL org.opencontainers.image.created="2024-08-21T11:35:56Z"
 LABEL org.opencontainers.image.source="https://github.com/CGATOxford/UMI-tools"
-LABEL org.opencontainers.image.revision="923a6da3898a832df96a0e17c8a3b74c2806d939"
+LABEL org.opencontainers.image.revision="766ab6c9c3059004c7c3f205621909b2d8b0b26d"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/nextflow/agat/agat_convert_bed2gff/.config.vsh.yaml b/target/nextflow/agat/agat_convert_bed2gff/.config.vsh.yaml
index 35e7df8b..ba20050a 100644
--- a/target/nextflow/agat/agat_convert_bed2gff/.config.vsh.yaml
+++ b/target/nextflow/agat/agat_convert_bed2gff/.config.vsh.yaml
@@ -235,7 +235,7 @@ build_info:
   output: "target/nextflow/agat/agat_convert_bed2gff"
   executable: "target/nextflow/agat/agat_convert_bed2gff/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/agat/agat_convert_bed2gff/main.nf b/target/nextflow/agat/agat_convert_bed2gff/main.nf
index 18863948..1a9d0c14 100644
--- a/target/nextflow/agat/agat_convert_bed2gff/main.nf
+++ b/target/nextflow/agat/agat_convert_bed2gff/main.nf
@@ -3066,7 +3066,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/agat/agat_convert_bed2gff",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "923a6da3898a832df96a0e17c8a3b74c2806d939",
+    "git_commit" : "766ab6c9c3059004c7c3f205621909b2d8b0b26d",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml b/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml
index d4019792..b4be3e72 100644
--- a/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml
+++ b/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml
@@ -225,7 +225,7 @@ build_info:
   output: "target/nextflow/agat/agat_convert_embl2gff"
   executable: "target/nextflow/agat/agat_convert_embl2gff/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/agat/agat_convert_embl2gff/main.nf b/target/nextflow/agat/agat_convert_embl2gff/main.nf
index 7d7fb77f..8e73dc48 100644
--- a/target/nextflow/agat/agat_convert_embl2gff/main.nf
+++ b/target/nextflow/agat/agat_convert_embl2gff/main.nf
@@ -3059,7 +3059,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/agat/agat_convert_embl2gff",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "923a6da3898a832df96a0e17c8a3b74c2806d939",
+    "git_commit" : "766ab6c9c3059004c7c3f205621909b2d8b0b26d",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml b/target/nextflow/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml
index e64c6fec..50247564 100644
--- a/target/nextflow/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml
+++ b/target/nextflow/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml
@@ -228,7 +228,7 @@ build_info:
   output: "target/nextflow/agat/agat_convert_sp_gff2gtf"
   executable: "target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf b/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf
index 0c5de57f..09ec6503 100644
--- a/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf
+++ b/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf
@@ -3042,7 +3042,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/agat/agat_convert_sp_gff2gtf",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "923a6da3898a832df96a0e17c8a3b74c2806d939",
+    "git_commit" : "766ab6c9c3059004c7c3f205621909b2d8b0b26d",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml b/target/nextflow/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml
index 61bfa22e..00d06376 100644
--- a/target/nextflow/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml
+++ b/target/nextflow/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml
@@ -188,7 +188,7 @@ build_info:
   output: "target/nextflow/agat/agat_convert_sp_gff2tsv"
   executable: "target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf b/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf
index 6058b608..f9bcbbd5 100644
--- a/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf
+++ b/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf
@@ -3020,7 +3020,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/agat/agat_convert_sp_gff2tsv",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "923a6da3898a832df96a0e17c8a3b74c2806d939",
+    "git_commit" : "766ab6c9c3059004c7c3f205621909b2d8b0b26d",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml b/target/nextflow/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml
index cb844e3c..9101e247 100644
--- a/target/nextflow/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml
+++ b/target/nextflow/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml
@@ -195,7 +195,7 @@ build_info:
   output: "target/nextflow/agat/agat_convert_sp_gxf2gxf"
   executable: "target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf b/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf
index 1f5e6dd6..f0a12b36 100644
--- a/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf
+++ b/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf
@@ -3020,7 +3020,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/agat/agat_convert_sp_gxf2gxf",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "923a6da3898a832df96a0e17c8a3b74c2806d939",
+    "git_commit" : "766ab6c9c3059004c7c3f205621909b2d8b0b26d",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/arriba/.config.vsh.yaml b/target/nextflow/arriba/.config.vsh.yaml
index e146cbe2..ea0bdd83 100644
--- a/target/nextflow/arriba/.config.vsh.yaml
+++ b/target/nextflow/arriba/.config.vsh.yaml
@@ -706,7 +706,7 @@ build_info:
   output: "target/nextflow/arriba"
   executable: "target/nextflow/arriba/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/arriba/main.nf b/target/nextflow/arriba/main.nf
index 42721c59..a9c482b3 100644
--- a/target/nextflow/arriba/main.nf
+++ b/target/nextflow/arriba/main.nf
@@ -3566,7 +3566,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/arriba",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "923a6da3898a832df96a0e17c8a3b74c2806d939",
+    "git_commit" : "766ab6c9c3059004c7c3f205621909b2d8b0b26d",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/bcl_convert/.config.vsh.yaml b/target/nextflow/bcl_convert/.config.vsh.yaml
index eccb7a87..bbed5a1e 100644
--- a/target/nextflow/bcl_convert/.config.vsh.yaml
+++ b/target/nextflow/bcl_convert/.config.vsh.yaml
@@ -418,7 +418,7 @@ build_info:
   output: "target/nextflow/bcl_convert"
   executable: "target/nextflow/bcl_convert/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/bcl_convert/main.nf b/target/nextflow/bcl_convert/main.nf
index 2d2b9751..32f94280 100644
--- a/target/nextflow/bcl_convert/main.nf
+++ b/target/nextflow/bcl_convert/main.nf
@@ -3303,7 +3303,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/bcl_convert",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "923a6da3898a832df96a0e17c8a3b74c2806d939",
+    "git_commit" : "766ab6c9c3059004c7c3f205621909b2d8b0b26d",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml
index 4bb348e2..96f7a8de 100644
--- a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml
+++ b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml
@@ -270,7 +270,7 @@ build_info:
   output: "target/nextflow/bd_rhapsody/bd_rhapsody_make_reference"
   executable: "target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf
index e8dedd5e..9cf164be 100644
--- a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf
+++ b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf
@@ -3116,7 +3116,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/bd_rhapsody/bd_rhapsody_make_reference",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "923a6da3898a832df96a0e17c8a3b74c2806d939",
+    "git_commit" : "766ab6c9c3059004c7c3f205621909b2d8b0b26d",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml
index 1285e8dd..c830f6c5 100644
--- a/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml
+++ b/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml
@@ -187,7 +187,7 @@ build_info:
   output: "target/nextflow/bedtools/bedtools_bamtofastq"
   executable: "target/nextflow/bedtools/bedtools_bamtofastq/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/bedtools/bedtools_bamtofastq/main.nf b/target/nextflow/bedtools/bedtools_bamtofastq/main.nf
index ef29b827..a839ee9b 100644
--- a/target/nextflow/bedtools/bedtools_bamtofastq/main.nf
+++ b/target/nextflow/bedtools/bedtools_bamtofastq/main.nf
@@ -3024,7 +3024,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/bedtools/bedtools_bamtofastq",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "923a6da3898a832df96a0e17c8a3b74c2806d939",
+    "git_commit" : "766ab6c9c3059004c7c3f205621909b2d8b0b26d",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml
index 14d8fcfd..6430b5a8 100644
--- a/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml
+++ b/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml
@@ -214,7 +214,7 @@ build_info:
   output: "target/nextflow/bedtools/bedtools_bedtobam"
   executable: "target/nextflow/bedtools/bedtools_bedtobam/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/bedtools/bedtools_bedtobam/main.nf b/target/nextflow/bedtools/bedtools_bedtobam/main.nf
index 51abddf9..e1522b33 100644
--- a/target/nextflow/bedtools/bedtools_bedtobam/main.nf
+++ b/target/nextflow/bedtools/bedtools_bedtobam/main.nf
@@ -3057,7 +3057,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/bedtools/bedtools_bedtobam",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "923a6da3898a832df96a0e17c8a3b74c2806d939",
+    "git_commit" : "766ab6c9c3059004c7c3f205621909b2d8b0b26d",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml
index 945b8e07..6b575393 100644
--- a/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml
+++ b/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml
@@ -232,7 +232,7 @@ build_info:
   output: "target/nextflow/bedtools/bedtools_getfasta"
   executable: "target/nextflow/bedtools/bedtools_getfasta/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/bedtools/bedtools_getfasta/main.nf b/target/nextflow/bedtools/bedtools_getfasta/main.nf
index ed94158e..99019b44 100644
--- a/target/nextflow/bedtools/bedtools_getfasta/main.nf
+++ b/target/nextflow/bedtools/bedtools_getfasta/main.nf
@@ -3060,7 +3060,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/bedtools/bedtools_getfasta",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "923a6da3898a832df96a0e17c8a3b74c2806d939",
+    "git_commit" : "766ab6c9c3059004c7c3f205621909b2d8b0b26d",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/bedtools/bedtools_getfasta/nextflow_schema.json b/target/nextflow/bedtools/bedtools_getfasta/nextflow_schema.json
new file mode 100644
index 00000000..c3f7e079
--- /dev/null
+++ b/target/nextflow/bedtools/bedtools_getfasta/nextflow_schema.json
@@ -0,0 +1,207 @@
+{
+"$schema": "http://json-schema.org/draft-07/schema",
+"title": "bedtools_getfasta",
+"description": "Extract sequences from a FASTA file for each of the intervals defined in a BED/GFF/VCF file.",
+"type": "object",
+"definitions": {
+
+    
+    
+    "input arguments" : {
+    "title": "Input arguments",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "input_fasta": {
+                "type":
+                "string",
+                "description": "Type: `file`. FASTA file containing sequences for each interval specified in the input BED file",
+                "help_text": "Type: `file`. FASTA file containing sequences for each interval specified in the input BED file.\nThe headers in the input FASTA file must exactly match the chromosome column in the BED file.\n"
+            
+            }
+    
+
+        ,
+                "input_bed": {
+                "type":
+                "string",
+                "description": "Type: `file`. BED file containing intervals to extract from the FASTA file",
+                "help_text": "Type: `file`. BED file containing intervals to extract from the FASTA file.\nBED files containing a single region require a newline character\nat the end of the line, otherwise a blank output file is produced.\n"
+            
+            }
+    
+
+        ,
+                "rna": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. The FASTA is RNA not DNA",
+                "help_text": "Type: `boolean_true`, default: `false`. The FASTA is RNA not DNA. Reverse complementation handled accordingly.\n"
+            ,
+                "default": "False"
+            }
+    
+
+}
+},
+    
+    
+    "run arguments" : {
+    "title": "Run arguments",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "strandedness": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Force strandedness",
+                "help_text": "Type: `boolean_true`, default: `false`. Force strandedness. If the feature occupies the antisense strand, the output sequence will\nbe reverse complemented. By default strandedness is not taken into account.\n"
+            ,
+                "default": "False"
+            }
+    
+
+}
+},
+    
+    
+    "output arguments" : {
+    "title": "Output arguments",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "output": {
+                "type":
+                "string",
+                "description": "Type: `file`, required, default: `$id.$key.output.output`. Output file where the output from the \u0027bedtools getfasta\u0027 commend will\nbe written to",
+                "help_text": "Type: `file`, required, default: `$id.$key.output.output`. Output file where the output from the \u0027bedtools getfasta\u0027 commend will\nbe written to.\n"
+            ,
+                "default": "$id.$key.output.output"
+            }
+    
+
+        ,
+                "tab": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Report extract sequences in a tab-delimited format instead of in FASTA format",
+                "help_text": "Type: `boolean_true`, default: `false`. Report extract sequences in a tab-delimited format instead of in FASTA format.\n"
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "bed_out": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Report extract sequences in a tab-delimited BED format instead of in FASTA format",
+                "help_text": "Type: `boolean_true`, default: `false`. Report extract sequences in a tab-delimited BED format instead of in FASTA format.\n"
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "name": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Set the FASTA header for each extracted sequence to be the \"name\" and coordinate columns from the BED feature",
+                "help_text": "Type: `boolean_true`, default: `false`. Set the FASTA header for each extracted sequence to be the \"name\" and coordinate columns from the BED feature.\n"
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "name_only": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Set the FASTA header for each extracted sequence to be the \"name\" columns from the BED feature",
+                "help_text": "Type: `boolean_true`, default: `false`. Set the FASTA header for each extracted sequence to be the \"name\" columns from the BED feature.\n"
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "split": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. When --input is in BED12 format, create a separate fasta entry for each block in a BED12 record,\nblocks being described in the 11th and 12th column of the BED",
+                "help_text": "Type: `boolean_true`, default: `false`. When --input is in BED12 format, create a separate fasta entry for each block in a BED12 record,\nblocks being described in the 11th and 12th column of the BED.\n"
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "full_header": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Use full fasta header",
+                "help_text": "Type: `boolean_true`, default: `false`. Use full fasta header. By default, only the word before the first space or tab is used.\n"
+            ,
+                "default": "False"
+            }
+    
+
+}
+},
+    
+    
+    "nextflow input-output arguments" : {
+    "title": "Nextflow input-output arguments",
+    "type": "object",
+    "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
+    "properties": {
+    
+        
+                "publish_dir": {
+                "type":
+                "string",
+                "description": "Type: `string`, required, example: `output/`. Path to an output directory",
+                "help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
+            
+            }
+    
+
+        ,
+                "param_list": {
+                "type":
+                "string",
+                "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
+                "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.",
+                "hidden": true
+            
+            }
+    
+
+}
+}
+},
+"allOf": [
+
+    {
+    "$ref": "#/definitions/input arguments"
+    },
+
+    {
+    "$ref": "#/definitions/run arguments"
+    },
+
+    {
+    "$ref": "#/definitions/output arguments"
+    },
+
+    {
+    "$ref": "#/definitions/nextflow input-output arguments"
+    }
+]
+}
diff --git a/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml
index cad25689..a6340d80 100644
--- a/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml
+++ b/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml
@@ -410,7 +410,7 @@ build_info:
   output: "target/nextflow/bedtools/bedtools_intersect"
   executable: "target/nextflow/bedtools/bedtools_intersect/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/bedtools/bedtools_intersect/main.nf b/target/nextflow/bedtools/bedtools_intersect/main.nf
index 2134053c..10af2709 100644
--- a/target/nextflow/bedtools/bedtools_intersect/main.nf
+++ b/target/nextflow/bedtools/bedtools_intersect/main.nf
@@ -3256,7 +3256,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/bedtools/bedtools_intersect",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "923a6da3898a832df96a0e17c8a3b74c2806d939",
+    "git_commit" : "766ab6c9c3059004c7c3f205621909b2d8b0b26d",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml
index 2a3701c4..b7b639a6 100644
--- a/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml
+++ b/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml
@@ -222,7 +222,7 @@ build_info:
   output: "target/nextflow/bedtools/bedtools_sort"
   executable: "target/nextflow/bedtools/bedtools_sort/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/bedtools/bedtools_sort/main.nf b/target/nextflow/bedtools/bedtools_sort/main.nf
index 37f080c1..ef6322d6 100644
--- a/target/nextflow/bedtools/bedtools_sort/main.nf
+++ b/target/nextflow/bedtools/bedtools_sort/main.nf
@@ -3066,7 +3066,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/bedtools/bedtools_sort",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "923a6da3898a832df96a0e17c8a3b74c2806d939",
+    "git_commit" : "766ab6c9c3059004c7c3f205621909b2d8b0b26d",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml b/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml
index c61be1b4..0bf38cc9 100644
--- a/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml
+++ b/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml
@@ -158,7 +158,7 @@ build_info:
   output: "target/nextflow/busco/busco_download_datasets"
   executable: "target/nextflow/busco/busco_download_datasets/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/busco/busco_download_datasets/main.nf b/target/nextflow/busco/busco_download_datasets/main.nf
index 4cba66c4..02a60944 100644
--- a/target/nextflow/busco/busco_download_datasets/main.nf
+++ b/target/nextflow/busco/busco_download_datasets/main.nf
@@ -2985,7 +2985,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/busco/busco_download_datasets",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "923a6da3898a832df96a0e17c8a3b74c2806d939",
+    "git_commit" : "766ab6c9c3059004c7c3f205621909b2d8b0b26d",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml b/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml
index 0f221099..37b6716b 100644
--- a/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml
+++ b/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml
@@ -145,7 +145,7 @@ build_info:
   output: "target/nextflow/busco/busco_list_datasets"
   executable: "target/nextflow/busco/busco_list_datasets/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/busco/busco_list_datasets/main.nf b/target/nextflow/busco/busco_list_datasets/main.nf
index 2bd87c65..fc971cb4 100644
--- a/target/nextflow/busco/busco_list_datasets/main.nf
+++ b/target/nextflow/busco/busco_list_datasets/main.nf
@@ -2971,7 +2971,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/busco/busco_list_datasets",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "923a6da3898a832df96a0e17c8a3b74c2806d939",
+    "git_commit" : "766ab6c9c3059004c7c3f205621909b2d8b0b26d",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/busco/busco_list_datasets/nextflow_schema.json b/target/nextflow/busco/busco_list_datasets/nextflow_schema.json
new file mode 100644
index 00000000..c2f65754
--- /dev/null
+++ b/target/nextflow/busco/busco_list_datasets/nextflow_schema.json
@@ -0,0 +1,71 @@
+{
+"$schema": "http://json-schema.org/draft-07/schema",
+"title": "busco_list_datasets",
+"description": "Lists the available busco datasets",
+"type": "object",
+"definitions": {
+
+    
+    
+    "outputs" : {
+    "title": "Outputs",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "output": {
+                "type":
+                "string",
+                "description": "Type: `file`, default: `$id.$key.output.txt`, example: `file.txt`. Output file of the available busco datasets\n",
+                "help_text": "Type: `file`, default: `$id.$key.output.txt`, example: `file.txt`. Output file of the available busco datasets\n"
+            ,
+                "default": "$id.$key.output.txt"
+            }
+    
+
+}
+},
+    
+    
+    "nextflow input-output arguments" : {
+    "title": "Nextflow input-output arguments",
+    "type": "object",
+    "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
+    "properties": {
+    
+        
+                "publish_dir": {
+                "type":
+                "string",
+                "description": "Type: `string`, required, example: `output/`. Path to an output directory",
+                "help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
+            
+            }
+    
+
+        ,
+                "param_list": {
+                "type":
+                "string",
+                "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
+                "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.",
+                "hidden": true
+            
+            }
+    
+
+}
+}
+},
+"allOf": [
+
+    {
+    "$ref": "#/definitions/outputs"
+    },
+
+    {
+    "$ref": "#/definitions/nextflow input-output arguments"
+    }
+]
+}
diff --git a/target/nextflow/busco/busco_run/.config.vsh.yaml b/target/nextflow/busco/busco_run/.config.vsh.yaml
index 353a6f7a..a8fadb6b 100644
--- a/target/nextflow/busco/busco_run/.config.vsh.yaml
+++ b/target/nextflow/busco/busco_run/.config.vsh.yaml
@@ -423,7 +423,7 @@ build_info:
   output: "target/nextflow/busco/busco_run"
   executable: "target/nextflow/busco/busco_run/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/busco/busco_run/main.nf b/target/nextflow/busco/busco_run/main.nf
index 6bc9ba38..878dc89d 100644
--- a/target/nextflow/busco/busco_run/main.nf
+++ b/target/nextflow/busco/busco_run/main.nf
@@ -3283,7 +3283,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/busco/busco_run",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "923a6da3898a832df96a0e17c8a3b74c2806d939",
+    "git_commit" : "766ab6c9c3059004c7c3f205621909b2d8b0b26d",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/cutadapt/.config.vsh.yaml b/target/nextflow/cutadapt/.config.vsh.yaml
index 59424cc3..488c11c7 100644
--- a/target/nextflow/cutadapt/.config.vsh.yaml
+++ b/target/nextflow/cutadapt/.config.vsh.yaml
@@ -740,7 +740,7 @@ build_info:
   output: "target/nextflow/cutadapt"
   executable: "target/nextflow/cutadapt/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/cutadapt/main.nf b/target/nextflow/cutadapt/main.nf
index f04b4c3f..a9a17e2e 100644
--- a/target/nextflow/cutadapt/main.nf
+++ b/target/nextflow/cutadapt/main.nf
@@ -3593,7 +3593,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/cutadapt",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "923a6da3898a832df96a0e17c8a3b74c2806d939",
+    "git_commit" : "766ab6c9c3059004c7c3f205621909b2d8b0b26d",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/falco/.config.vsh.yaml b/target/nextflow/falco/.config.vsh.yaml
index 1da2720d..ec4bbf23 100644
--- a/target/nextflow/falco/.config.vsh.yaml
+++ b/target/nextflow/falco/.config.vsh.yaml
@@ -317,7 +317,7 @@ build_info:
   output: "target/nextflow/falco"
   executable: "target/nextflow/falco/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/falco/main.nf b/target/nextflow/falco/main.nf
index ddde22db..6acc35c7 100644
--- a/target/nextflow/falco/main.nf
+++ b/target/nextflow/falco/main.nf
@@ -3144,7 +3144,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/falco",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "923a6da3898a832df96a0e17c8a3b74c2806d939",
+    "git_commit" : "766ab6c9c3059004c7c3f205621909b2d8b0b26d",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/fastp/.config.vsh.yaml b/target/nextflow/fastp/.config.vsh.yaml
index 28f262b8..78fd615e 100644
--- a/target/nextflow/fastp/.config.vsh.yaml
+++ b/target/nextflow/fastp/.config.vsh.yaml
@@ -1083,7 +1083,7 @@ build_info:
   output: "target/nextflow/fastp"
   executable: "target/nextflow/fastp/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/fastp/main.nf b/target/nextflow/fastp/main.nf
index 1b9685d0..b5493232 100644
--- a/target/nextflow/fastp/main.nf
+++ b/target/nextflow/fastp/main.nf
@@ -3997,7 +3997,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/fastp",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "923a6da3898a832df96a0e17c8a3b74c2806d939",
+    "git_commit" : "766ab6c9c3059004c7c3f205621909b2d8b0b26d",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/featurecounts/.config.vsh.yaml b/target/nextflow/featurecounts/.config.vsh.yaml
index 4ba020bd..0a48a279 100644
--- a/target/nextflow/featurecounts/.config.vsh.yaml
+++ b/target/nextflow/featurecounts/.config.vsh.yaml
@@ -645,7 +645,7 @@ build_info:
   output: "target/nextflow/featurecounts"
   executable: "target/nextflow/featurecounts/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/featurecounts/main.nf b/target/nextflow/featurecounts/main.nf
index 4383b6d0..f140dca6 100644
--- a/target/nextflow/featurecounts/main.nf
+++ b/target/nextflow/featurecounts/main.nf
@@ -3523,7 +3523,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/featurecounts",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "923a6da3898a832df96a0e17c8a3b74c2806d939",
+    "git_commit" : "766ab6c9c3059004c7c3f205621909b2d8b0b26d",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/gffread/.config.vsh.yaml b/target/nextflow/gffread/.config.vsh.yaml
index 208da938..d7099025 100644
--- a/target/nextflow/gffread/.config.vsh.yaml
+++ b/target/nextflow/gffread/.config.vsh.yaml
@@ -685,7 +685,7 @@ build_info:
   output: "target/nextflow/gffread"
   executable: "target/nextflow/gffread/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/gffread/main.nf b/target/nextflow/gffread/main.nf
index 2c58fc24..1ef70a9e 100644
--- a/target/nextflow/gffread/main.nf
+++ b/target/nextflow/gffread/main.nf
@@ -3580,7 +3580,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/gffread",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "923a6da3898a832df96a0e17c8a3b74c2806d939",
+    "git_commit" : "766ab6c9c3059004c7c3f205621909b2d8b0b26d",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml b/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml
index 6ceb7a35..4ccd35a5 100644
--- a/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml
+++ b/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml
@@ -507,7 +507,7 @@ build_info:
   output: "target/nextflow/lofreq/lofreq_call"
   executable: "target/nextflow/lofreq/lofreq_call/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/lofreq/lofreq_call/main.nf b/target/nextflow/lofreq/lofreq_call/main.nf
index 1141d34c..48c0387f 100644
--- a/target/nextflow/lofreq/lofreq_call/main.nf
+++ b/target/nextflow/lofreq/lofreq_call/main.nf
@@ -3388,7 +3388,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/lofreq/lofreq_call",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "923a6da3898a832df96a0e17c8a3b74c2806d939",
+    "git_commit" : "766ab6c9c3059004c7c3f205621909b2d8b0b26d",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml b/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml
index 3566bc19..b3d80488 100644
--- a/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml
+++ b/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml
@@ -215,7 +215,7 @@ build_info:
   output: "target/nextflow/lofreq/lofreq_indelqual"
   executable: "target/nextflow/lofreq/lofreq_indelqual/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/lofreq/lofreq_indelqual/main.nf b/target/nextflow/lofreq/lofreq_indelqual/main.nf
index 3b0658ec..88188ad0 100644
--- a/target/nextflow/lofreq/lofreq_indelqual/main.nf
+++ b/target/nextflow/lofreq/lofreq_indelqual/main.nf
@@ -3051,7 +3051,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/lofreq/lofreq_indelqual",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "923a6da3898a832df96a0e17c8a3b74c2806d939",
+    "git_commit" : "766ab6c9c3059004c7c3f205621909b2d8b0b26d",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/multiqc/.config.vsh.yaml b/target/nextflow/multiqc/.config.vsh.yaml
index 9d2c2581..8bfe5fc0 100644
--- a/target/nextflow/multiqc/.config.vsh.yaml
+++ b/target/nextflow/multiqc/.config.vsh.yaml
@@ -456,7 +456,7 @@ build_info:
   output: "target/nextflow/multiqc"
   executable: "target/nextflow/multiqc/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/multiqc/main.nf b/target/nextflow/multiqc/main.nf
index 5cfc4eb0..010f178c 100644
--- a/target/nextflow/multiqc/main.nf
+++ b/target/nextflow/multiqc/main.nf
@@ -3340,7 +3340,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/multiqc",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "923a6da3898a832df96a0e17c8a3b74c2806d939",
+    "git_commit" : "766ab6c9c3059004c7c3f205621909b2d8b0b26d",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/pear/.config.vsh.yaml b/target/nextflow/pear/.config.vsh.yaml
index 2b1ec956..9e76fcb4 100644
--- a/target/nextflow/pear/.config.vsh.yaml
+++ b/target/nextflow/pear/.config.vsh.yaml
@@ -398,7 +398,7 @@ build_info:
   output: "target/nextflow/pear"
   executable: "target/nextflow/pear/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/pear/main.nf b/target/nextflow/pear/main.nf
index 853fb1c4..0a0f8086 100644
--- a/target/nextflow/pear/main.nf
+++ b/target/nextflow/pear/main.nf
@@ -3233,7 +3233,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/pear",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "923a6da3898a832df96a0e17c8a3b74c2806d939",
+    "git_commit" : "766ab6c9c3059004c7c3f205621909b2d8b0b26d",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml b/target/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml
new file mode 100644
index 00000000..c5ee581d
--- /dev/null
+++ b/target/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml
@@ -0,0 +1,290 @@
+name: "qualimap_rnaseq"
+namespace: "qualimap"
+version: "main"
+authors:
+- name: "Dorien Roosen"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      email: "dorien@data-intuitive.com"
+      github: "dorien-er"
+      linkedin: "dorien-roosen"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Scientist"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "file"
+    name: "--bam"
+    description: "Path to the sequence alignment file in BAM format, produced by a\
+      \ splicing-aware aligner."
+    info: null
+    example:
+    - "alignment.bam"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--gtf"
+    description: "Path to genomic annotations in Ensembl GTF format."
+    info: null
+    example:
+    - "annotations.gtf"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--qc_results"
+    description: "Text file containing the RNAseq QC results."
+    info: null
+    example:
+    - "rnaseq_qc_results.txt"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--counts"
+    description: "Output file for computed counts."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--report"
+    description: "Report output file. Supported formats are PDF or HTML."
+    info: null
+    example:
+    - "report.html"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Optional"
+  arguments:
+  - type: "integer"
+    name: "--num_pr_bases"
+    description: "Number of upstream/downstream nucleotide bases to compute 5'-3'\
+      \ bias (default = 100)."
+    info: null
+    required: false
+    min: 1
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--num_tr_bias"
+    description: "Number of top highly expressed transcripts to compute 5'-3' bias\
+      \ (default = 1000)."
+    info: null
+    required: false
+    min: 1
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--algorithm"
+    description: "Counting algorithm (uniquely-mapped-reads (default) or proportional)."
+    info: null
+    required: false
+    choices:
+    - "uniquely-mapped-reads"
+    - "proportional"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--sequencing_protocol"
+    description: "Sequencing library protocol (strand-specific-forward, strand-specific-reverse\
+      \ or non-strand-specific (default))."
+    info: null
+    required: false
+    choices:
+    - "non-strand-specific"
+    - "strand-specific-reverse"
+    - "strand-specific-forward"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--paired"
+    description: "Setting this flag for paired-end experiments will result in counting\
+      \ fragments instead of reads."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--sorted"
+    description: "Setting this flag indicates that the input file is already sorted\
+      \ by name. If flag is not set, additional sorting by name will be performed.\
+      \ Only requiredfor paired-end analysis."
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--java_memory_size"
+    description: "maximum Java heap memory size, default = 4G."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Qualimap RNA-seq QC reports quality control metrics and bias estimations\
+  \ \nwhich are specific for whole transcriptome sequencing, including reads genomic\
+  \ \norigin, junction analysis, transcript coverage and 5’-3’ bias computation.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test_data"
+info: null
+status: "enabled"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "RNA-seq"
+- "quality control"
+- "QC Report"
+license: "GPL-2.0"
+references:
+  doi:
+  - "10.1093/bioinformatics/btv566"
+links:
+  repository: "https://bitbucket.org/kokonech/qualimap/commits/branch/master"
+  homepage: "http://qualimap.conesalab.org/"
+  documentation: "http://qualimap.conesalab.org/doc_html/analysis.html#rna-seq-qc"
+  issue_tracker: "https://bitbucket.org/kokonech/qualimap/issues?status=new&status=open"
+runners:
+- type: "executable"
+  id: "executable"
+  docker_setup_strategy: "ifneedbepullelsecachedbuild"
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    tag: "$id"
+  auto:
+    simplifyInput: true
+    simplifyOutput: false
+    transcript: false
+    publish: false
+  config:
+    labels:
+      mem1gb: "memory = 1000000000.B"
+      mem2gb: "memory = 2000000000.B"
+      mem5gb: "memory = 5000000000.B"
+      mem10gb: "memory = 10000000000.B"
+      mem20gb: "memory = 20000000000.B"
+      mem50gb: "memory = 50000000000.B"
+      mem100gb: "memory = 100000000000.B"
+      mem200gb: "memory = 200000000000.B"
+      mem500gb: "memory = 500000000000.B"
+      mem1tb: "memory = 1000000000000.B"
+      mem2tb: "memory = 2000000000000.B"
+      mem5tb: "memory = 5000000000000.B"
+      mem10tb: "memory = 10000000000000.B"
+      mem20tb: "memory = 20000000000000.B"
+      mem50tb: "memory = 50000000000000.B"
+      mem100tb: "memory = 100000000000000.B"
+      mem200tb: "memory = 200000000000000.B"
+      mem500tb: "memory = 500000000000000.B"
+      mem1gib: "memory = 1073741824.B"
+      mem2gib: "memory = 2147483648.B"
+      mem4gib: "memory = 4294967296.B"
+      mem8gib: "memory = 8589934592.B"
+      mem16gib: "memory = 17179869184.B"
+      mem32gib: "memory = 34359738368.B"
+      mem64gib: "memory = 68719476736.B"
+      mem128gib: "memory = 137438953472.B"
+      mem256gib: "memory = 274877906944.B"
+      mem512gib: "memory = 549755813888.B"
+      mem1tib: "memory = 1099511627776.B"
+      mem2tib: "memory = 2199023255552.B"
+      mem4tib: "memory = 4398046511104.B"
+      mem8tib: "memory = 8796093022208.B"
+      mem16tib: "memory = 17592186044416.B"
+      mem32tib: "memory = 35184372088832.B"
+      mem64tib: "memory = 70368744177664.B"
+      mem128tib: "memory = 140737488355328.B"
+      mem256tib: "memory = 281474976710656.B"
+      mem512tib: "memory = 562949953421312.B"
+      cpu1: "cpus = 1"
+      cpu2: "cpus = 2"
+      cpu5: "cpus = 5"
+      cpu10: "cpus = 10"
+      cpu20: "cpus = 20"
+      cpu50: "cpus = 50"
+      cpu100: "cpus = 100"
+      cpu200: "cpus = 200"
+      cpu500: "cpus = 500"
+      cpu1000: "cpus = 1000"
+  debug: false
+  container: "docker"
+engines:
+- type: "docker"
+  id: "docker"
+  image: "quay.io/biocontainers/qualimap:2.3--hdfd78af_0"
+  target_registry: "images.viash-hub.com"
+  target_tag: "main"
+  namespace_separator: "/"
+  setup:
+  - type: "docker"
+    run:
+    - "echo QualiMap: $(qualimap 2>&1 | grep QualiMap | sed 's/^.*QualiMap//') > /var/software_versions.txt\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/qualimap/qualimap_rnaseq/config.vsh.yaml"
+  runner: "nextflow"
+  engine: "docker|native"
+  output: "target/nextflow/qualimap/qualimap_rnaseq"
+  executable: "target/nextflow/qualimap/qualimap_rnaseq/main.nf"
+  viash_version: "0.9.0-RC6"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
+  git_remote: "https://github.com/viash-hub/biobox"
+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-RC6"
+  source: "src"
+  target: "target"
+  config_mods:
+  - ".requirements.commands := ['ps']\n"
+  - ".engines += { type: \"native\" }"
+  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
+  - ".engines[.type == 'docker'].target_tag := 'main'"
+  keywords:
+  - "bioinformatics"
+  - "modules"
+  - "sequencing"
+  license: "MIT"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/viash-hub/biobox"
+    issue_tracker: "https://github.com/viash-hub/biobox/issues"
diff --git a/target/nextflow/qualimap/qualimap_rnaseq/main.nf b/target/nextflow/qualimap/qualimap_rnaseq/main.nf
new file mode 100644
index 00000000..286420d2
--- /dev/null
+++ b/target/nextflow/qualimap/qualimap_rnaseq/main.nf
@@ -0,0 +1,3705 @@
+// qualimap_rnaseq main
+// 
+// This wrapper script is auto-generated by viash 0.9.0-RC6 and is thus a
+// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
+// Data Intuitive.
+// 
+// The component may contain files which fall under a different license. The
+// authors of this component should specify the license in the header of such
+// files, or include a separate license file detailing the licenses of all included
+// files.
+// 
+// Component authors:
+//  * Dorien Roosen (author, maintainer)
+
+////////////////////////////
+// VDSL3 helper functions //
+////////////////////////////
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_checkArgumentType.nf'
+class UnexpectedArgumentTypeException extends Exception {
+  String errorIdentifier
+  String stage
+  String plainName
+  String expectedClass
+  String foundClass
+  
+  // ${key ? " in module '$key'" : ""}${id ? " id '$id'" : ""}
+  UnexpectedArgumentTypeException(String errorIdentifier, String stage, String plainName, String expectedClass, String foundClass) {
+    super("Error${errorIdentifier ? " $errorIdentifier" : ""}:${stage ? " $stage" : "" } argument '${plainName}' has the wrong type. " +
+      "Expected type: ${expectedClass}. Found type: ${foundClass}")
+    this.errorIdentifier = errorIdentifier
+    this.stage = stage
+    this.plainName = plainName
+    this.expectedClass = expectedClass
+    this.foundClass = foundClass
+  }
+}
+
+/**
+  * Checks if the given value is of the expected type. If not, an exception is thrown.
+  *
+  * @param stage The stage of the argument (input or output)
+  * @param par The parameter definition
+  * @param value The value to check
+  * @param errorIdentifier The identifier to use in the error message
+  * @return The value, if it is of the expected type
+  * @throws UnexpectedArgumentTypeException If the value is not of the expected type
+*/
+def _checkArgumentType(String stage, Map par, Object value, String errorIdentifier) {
+  // expectedClass will only be != null if value is not of the expected type
+  def expectedClass = null
+  def foundClass = null
+  
+  // todo: split if need be
+  
+  if (!par.required && value == null) {
+    expectedClass = null
+  } else if (par.multiple) {
+    if (value !instanceof Collection) {
+      value = [value]
+    }
+    
+    // split strings
+    value = value.collectMany{ val ->
+      if (val instanceof String) {
+        // collect() to ensure that the result is a List and not simply an array
+        val.split(par.multiple_sep).collect()
+      } else {
+        [val]
+      }
+    }
+
+    // process globs
+    if (par.type == "file" && par.direction == "input") {
+      value = value.collect{ it instanceof String ? file(it, hidden: true) : it }.flatten()
+    }
+
+    // check types of elements in list
+    try {
+      value = value.collect { listVal ->
+        _checkArgumentType(stage, par + [multiple: false], listVal, errorIdentifier)
+      }
+    } catch (UnexpectedArgumentTypeException e) {
+      expectedClass = "List[${e.expectedClass}]"
+      foundClass = "List[${e.foundClass}]"
+    }
+  } else if (par.type == "string") {
+    // cast to string if need be
+    if (value instanceof GString) {
+      value = value.toString()
+    }
+    expectedClass = value instanceof String ? null : "String"
+  } else if (par.type == "integer") {
+    // cast to integer if need be
+    if (value instanceof String) {
+      try {
+        value = value.toInteger()
+      } catch (NumberFormatException e) {
+        // do nothing
+      }
+    }
+    if (value instanceof java.math.BigInteger) {
+      value = value.intValue()
+    }
+    expectedClass = value instanceof Integer ? null : "Integer"
+  } else if (par.type == "long") {
+    // cast to long if need be
+    if (value instanceof String) {
+      try {
+        value = value.toLong()
+      } catch (NumberFormatException e) {
+        // do nothing
+      }
+    }
+    if (value instanceof Integer) {
+      value = value.toLong()
+    }
+    expectedClass = value instanceof Long ? null : "Long"
+  } else if (par.type == "double") {
+    // cast to double if need be
+    if (value instanceof String) {
+      try {
+        value = value.toDouble()
+      } catch (NumberFormatException e) {
+        // do nothing
+      }
+    }
+    if (value instanceof java.math.BigDecimal) {
+      value = value.doubleValue()
+    }
+    if (value instanceof Float) {
+      value = value.toDouble()
+    }
+    expectedClass = value instanceof Double ? null : "Double"
+  } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
+    // cast to boolean if need be
+    if (value instanceof String) {
+      def valueLower = value.toLowerCase()
+      if (valueLower == "true") {
+        value = true
+      } else if (valueLower == "false") {
+        value = false
+      }
+    }
+    expectedClass = value instanceof Boolean ? null : "Boolean"
+  } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
+    // cast to path if need be
+    if (value instanceof String) {
+      value = file(value, hidden: true)
+    }
+    if (value instanceof File) {
+      value = value.toPath()
+    }
+    expectedClass = value instanceof Path ? null : "Path"
+  } else if (par.type == "file" && stage == "input" && par.direction == "output") {
+    // cast to string if need be
+    if (value instanceof GString) {
+      value = value.toString()
+    }
+    expectedClass = value instanceof String ? null : "String"
+  } else {
+    // didn't find a match for par.type
+    expectedClass = par.type
+  }
+
+  if (expectedClass != null) {
+    if (foundClass == null) {
+      foundClass = value.getClass().getName()
+    }
+    throw new UnexpectedArgumentTypeException(errorIdentifier, stage, par.plainName, expectedClass, foundClass)
+  }
+  
+  return value
+}
+// helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processInputValues.nf'
+Map _processInputValues(Map inputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.required) {
+        assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing"
+      }
+    }
+
+    inputs = inputs.collectEntries { name, value ->
+      def par = config.allArguments.find { it.plainName == name && (it.direction == "input" || it.type == "file") }
+      assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid input argument"
+
+      value = _checkArgumentType("input", par, value, "in module '$key' id '$id'")
+
+      [ name, value ]
+    }
+  }
+  return inputs
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf'
+Map _processOutputValues(Map outputs, Map config, String id, String key) {
+  if (!workflow.stubRun) {
+    config.allArguments.each { arg ->
+      if (arg.direction == "output" && arg.required) {
+        assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : 
+          "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing"
+      }
+    }
+
+    outputs = outputs.collectEntries { name, value ->
+      def par = config.allArguments.find { it.plainName == name && it.direction == "output" }
+      assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument"
+      
+      value = _checkArgumentType("output", par, value, "in module '$key' id '$id'")
+      
+      [ name, value ]
+    }
+  }
+  return outputs
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf'
+class IDChecker {
+  final def items = [] as Set
+
+  @groovy.transform.WithWriteLock
+  boolean observe(String item) {
+    if (items.contains(item)) {
+      return false
+    } else {
+      items << item
+      return true
+    }
+  }
+
+  @groovy.transform.WithReadLock
+  boolean contains(String item) {
+    return items.contains(item)
+  }
+
+  @groovy.transform.WithReadLock
+  Set getItems() {
+    return items.clone()
+  }
+}
+// helper file: 'src/main/resources/io/viash/runners/nextflow/channel/_checkUniqueIds.nf'
+
+/**
+ * Check if the ids are unique across parameter sets
+ *
+ * @param parameterSets a list of parameter sets.
+ */
+private void _checkUniqueIds(List<Tuple2<String, Map<String, Object>>> parameterSets) {
+  def ppIds = parameterSets.collect{it[0]}
+  assert ppIds.size() == ppIds.unique().size() : "All argument sets should have unique ids. Detected ids: $ppIds"
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/channel/_getChild.nf'
+
+// helper functions for reading params from file //
+def _getChild(parent, child) {
+  if (child.contains("://") || java.nio.file.Paths.get(child).isAbsolute()) {
+    child
+  } else {
+    def parentAbsolute = java.nio.file.Paths.get(parent).toAbsolutePath().toString()
+    parentAbsolute.replaceAll('/[^/]*$', "/") + child
+  }
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/channel/_parseParamList.nf'
+/**
+  * Figure out the param list format based on the file extension
+  *
+  * @param param_list A String containing the path to the parameter list file.
+  *
+  * @return A String containing the format of the parameter list file.
+  */
+def _paramListGuessFormat(param_list) {
+  if (param_list !instanceof String) {
+    "asis"
+  } else if (param_list.endsWith(".csv")) {
+    "csv"
+  } else if (param_list.endsWith(".json") || param_list.endsWith(".jsn")) {
+    "json"
+  } else if (param_list.endsWith(".yaml") || param_list.endsWith(".yml")) {
+    "yaml"
+  } else {
+    "yaml_blob"
+  }
+}
+
+
+/**
+  * Read the param list
+  * 
+  * @param param_list One of the following:
+  *   - A String containing the path to the parameter list file (csv, json or yaml),
+  *   - A yaml blob of a list of maps (yaml_blob),
+  *   - Or a groovy list of maps (asis).
+  * @param config A Map of the Viash configuration.
+  * 
+  * @return A List of Maps containing the parameters.
+  */
+def _parseParamList(param_list, Map config) {
+  // first determine format by extension
+  def paramListFormat = _paramListGuessFormat(param_list)
+
+  def paramListPath = (paramListFormat != "asis" && paramListFormat != "yaml_blob") ?
+    file(param_list, hidden: true) :
+    null
+
+  // get the correct parser function for the detected params_list format
+  def paramSets = []
+  if (paramListFormat == "asis") {
+    paramSets = param_list
+  } else if (paramListFormat == "yaml_blob") {
+    paramSets = readYamlBlob(param_list)
+  } else if (paramListFormat == "yaml") {
+    paramSets = readYaml(paramListPath)
+  } else if (paramListFormat == "json") {
+    paramSets = readJson(paramListPath)
+  } else if (paramListFormat == "csv") {
+    paramSets = readCsv(paramListPath)
+  } else {
+    error "Format of provided --param_list not recognised.\n" +
+    "Found: '$paramListFormat'.\n" +
+    "Expected: a csv file, a json file, a yaml file,\n" +
+    "a yaml blob or a groovy list of maps."
+  }
+
+  // data checks
+  assert paramSets instanceof List: "--param_list should contain a list of maps"
+  for (value in paramSets) {
+    assert value instanceof Map: "--param_list should contain a list of maps"
+  }
+
+  // id is argument
+  def idIsArgument = config.allArguments.any{it.plainName == "id"}
+
+  // Reformat from List<Map> to List<Tuple2<String, Map>> by adding the ID as first element of a Tuple2
+  paramSets = paramSets.collect({ data ->
+    def id = data.id
+    if (!idIsArgument) {
+      data = data.findAll{k, v -> k != "id"}
+    }
+    [id, data]
+  })
+
+  // Split parameters with 'multiple: true'
+  paramSets = paramSets.collect({ id, data ->
+    data = _splitParams(data, config)
+    [id, data]
+  })
+  
+  // The paths of input files inside a param_list file may have been specified relatively to the
+  // location of the param_list file. These paths must be made absolute.
+  if (paramListPath) {
+    paramSets = paramSets.collect({ id, data ->
+      def new_data = data.collectEntries{ parName, parValue ->
+        def par = config.allArguments.find{it.plainName == parName}
+        if (par && par.type == "file" && par.direction == "input") {
+          if (parValue instanceof Collection) {
+            parValue = parValue.collectMany{path -> 
+              def x = _resolveSiblingIfNotAbsolute(path, paramListPath)
+              x instanceof Collection ? x : [x]
+            }
+          } else {
+            parValue = _resolveSiblingIfNotAbsolute(parValue, paramListPath) 
+          }
+        }
+        [parName, parValue]
+      }
+      [id, new_data]
+    })
+  }
+
+  return paramSets
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/channel/_splitParams.nf'
+/**
+ * Split parameters for arguments that accept multiple values using their separator
+ *
+ * @param paramList A Map containing parameters to split.
+ * @param config A Map of the Viash configuration. This Map can be generated from the config file
+ *               using the readConfig() function.
+ *
+ * @return A Map of parameters where the parameter values have been split into a list using
+ *         their seperator.
+ */
+Map<String, Object> _splitParams(Map<String, Object> parValues, Map config){
+  def parsedParamValues = parValues.collectEntries { parName, parValue ->
+    def parameterSettings = config.allArguments.find({it.plainName == parName})
+
+    if (!parameterSettings) {
+      // if argument is not found, do not alter 
+      return [parName, parValue]
+    }
+    if (parameterSettings.multiple) { // Check if parameter can accept multiple values
+      if (parValue instanceof Collection) {
+        parValue = parValue.collect{it instanceof String ? it.split(parameterSettings.multiple_sep) : it }
+      } else if (parValue instanceof String) {
+        parValue = parValue.split(parameterSettings.multiple_sep)
+      } else if (parValue == null) {
+        parValue = []
+      } else {
+        parValue = [ parValue ]
+      }
+      parValue = parValue.flatten()
+    }
+    // For all parameters check if multiple values are only passed for
+    // arguments that allow it. Quietly simplify lists of length 1.
+    if (!parameterSettings.multiple && parValue instanceof Collection) {
+      assert parValue.size() == 1 : 
+      "Error: argument ${parName} has too many values.\n" +
+      "  Expected amount: 1. Found: ${parValue.size()}"
+      parValue = parValue[0]
+    }
+    [parName, parValue]
+  }
+  return parsedParamValues
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/channel/channelFromParams.nf'
+/**
+ * Parse nextflow parameters based on settings defined in a viash config.
+ * Return a list of parameter sets, each parameter set corresponding to 
+ * an event in a nextflow channel. The output from this function can be used
+ * with Channel.fromList to create a nextflow channel with Vdsl3 formatted 
+ * events.
+ *
+ * This function performs:
+ *   - A filtering of the params which can be found in the config file.
+ *   - Process the params_list argument which allows a user to to initialise 
+ *     a Vsdl3 channel with multiple parameter sets. Possible formats are 
+ *     csv, json, yaml, or simply a yaml_blob. A csv should have column names 
+ *     which correspond to the different arguments of this pipeline. A json or a yaml
+ *     file should be a list of maps, each of which has keys corresponding to the
+ *     arguments of the pipeline. A yaml blob can also be passed directly as a parameter.
+ *     When passing a csv, json or yaml, relative path names are relativized to the
+ *     location of the parameter file.
+ *   - Combine the parameter sets into a vdsl3 Channel.
+ *
+ * @param params Input parameters. Can optionaly contain a 'param_list' key that
+ *               provides a list of arguments that can be split up into multiple events
+ *               in the output channel possible formats of param_lists are: a csv file, 
+ *               json file, a yaml file or a yaml blob. Each parameters set (event) must
+ *               have a unique ID.
+ * @param config A Map of the Viash configuration. This Map can be generated from the config file
+ *               using the readConfig() function.
+ * 
+ * @return A list of parameters with the first element of the event being
+ *         the event ID and the second element containing a map of the parsed parameters.
+ */
+ 
+private List<Tuple2<String, Map<String, Object>>> _paramsToParamSets(Map params, Map config){
+  // todo: fetch key from run args
+  def key_ = config.name
+  
+  /* parse regular parameters (not in param_list)  */
+  /*************************************************/
+  def globalParams = config.allArguments
+    .findAll { params.containsKey(it.plainName) }
+    .collectEntries { [ it.plainName, params[it.plainName] ] }
+  def globalID = params.get("id", null)
+
+  /* process params_list arguments */
+  /*********************************/
+  def paramList = params.containsKey("param_list") && params.param_list != null ?
+    params.param_list : []
+  // if (paramList instanceof String) {
+  //   paramList = [paramList]
+  // }
+  // def paramSets = paramList.collectMany{ _parseParamList(it, config) }
+  // TODO: be able to process param_list when it is a list of strings
+  def paramSets = _parseParamList(paramList, config)
+  if (paramSets.isEmpty()) {
+    paramSets = [[null, [:]]]
+  }
+
+  /* combine arguments into channel */
+  /**********************************/
+  def processedParams = paramSets.indexed().collect{ index, tup ->
+    // Process ID
+    def id = tup[0] ?: globalID
+  
+    if (workflow.stubRun && !id) {
+      // if stub run, explicitly add an id if missing
+      id = "stub${index}"
+    }
+    assert id != null: "Each parameter set should have at least an 'id'"
+
+    // Process params
+    def parValues = globalParams + tup[1]
+    // // Remove parameters which are null, if the default is also null
+    // parValues = parValues.collectEntries{paramName, paramValue ->
+    //   parameterSettings = config.functionality.allArguments.find({it.plainName == paramName})
+    //   if ( paramValue != null || parameterSettings.get("default", null) != null ) {
+    //     [paramName, paramValue]
+    //   }
+    // }
+    parValues = parValues.collectEntries { name, value ->
+      def par = config.allArguments.find { it.plainName == name && (it.direction == "input" || it.type == "file") }
+      assert par != null : "Error in module '${key_}' id '${id}': '${name}' is not a valid input argument"
+
+      if (par == null) {
+        return [:]
+      }
+      value = _checkArgumentType("input", par, value, "in module '$key_' id '$id'")
+
+      [ name, value ]
+    }
+
+    [id, parValues]
+  }
+
+  // Check if ids (first element of each list) is unique
+  _checkUniqueIds(processedParams)
+  return processedParams
+}
+
+/**
+ * Parse nextflow parameters based on settings defined in a viash config 
+ * and return a nextflow channel.
+ * 
+ * @param params Input parameters. Can optionaly contain a 'param_list' key that
+ *               provides a list of arguments that can be split up into multiple events
+ *               in the output channel possible formats of param_lists are: a csv file, 
+ *               json file, a yaml file or a yaml blob. Each parameters set (event) must
+ *               have a unique ID.
+ * @param config A Map of the Viash configuration. This Map can be generated from the config file
+ *               using the readConfig() function.
+ * 
+ * @return A nextflow Channel with events. Events are formatted as a tuple that contains 
+ *         first contains the ID of the event and as second element holds a parameter map.
+ *       
+ *
+ */
+def channelFromParams(Map params, Map config) {
+  def processedParams = _paramsToParamSets(params, config)
+  return Channel.fromList(processedParams)
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/channel/checkUniqueIds.nf'
+def checkUniqueIds(Map args) {
+  def stopOnError = args.stopOnError == null ? args.stopOnError : true
+
+  def idChecker = new IDChecker()
+
+  return filter { tup ->
+    if (!idChecker.observe(tup[0])) {
+      if (stopOnError) {
+        error "Duplicate id: ${tup[0]}"
+      } else {
+        log.warn "Duplicate id: ${tup[0]}, removing duplicate entry"
+        return false
+      }
+    }
+    return true
+  }
+}
+// helper file: 'src/main/resources/io/viash/runners/nextflow/channel/preprocessInputs.nf'
+// This helper file will be deprecated soon
+preprocessInputsDeprecationWarningPrinted = false
+
+def preprocessInputsDeprecationWarning() {
+  if (!preprocessInputsDeprecationWarningPrinted) {
+    preprocessInputsDeprecationWarningPrinted = true
+    System.err.println("Warning: preprocessInputs() is deprecated and will be removed in Viash 0.9.0.")
+  }
+}
+
+/**
+ * Generate a nextflow Workflow that allows processing a channel of 
+ * Vdsl3 formatted events and apply a Viash config to them:
+ *    - Gather default parameters from the Viash config and make 
+ *      sure that they are correctly formatted (see applyConfig method).
+ *    - Format the input parameters (also using the applyConfig method).
+ *    - Apply the default parameter to the input parameters.
+ *    - Do some assertions:
+ *        ~ Check if the event IDs in the channel are unique.
+ * 
+ * The events in the channel are formatted as tuples, with the 
+ * first element of the tuples being a unique id of the parameter set, 
+ * and the second element containg the the parameters themselves.
+ * Optional extra elements of the tuples will be passed to the output as is.
+ *
+ * @param args A map that must contain a 'config' key that points
+ *              to a parsed config (see readConfig()). Optionally, a
+ *              'key' key can be provided which can be used to create a unique
+ *              name for the workflow process.
+ *
+ * @return A workflow that allows processing a channel of Vdsl3 formatted events
+ * and apply a Viash config to them.
+ */
+def preprocessInputs(Map args) {
+  preprocessInputsDeprecationWarning()
+
+  def config = args.config
+  assert config instanceof Map : 
+    "Error in preprocessInputs: config must be a map. " +
+    "Expected class: Map. Found: config.getClass() is ${config.getClass()}"
+  def key_ = args.key ?: config.name
+
+  // Get different parameter types (used throughout this function)
+  def defaultArgs = config.allArguments
+    .findAll { it.containsKey("default") }
+    .collectEntries { [ it.plainName, it.default ] }
+
+  map { tup ->
+    def id = tup[0]
+    def data = tup[1]
+    def passthrough = tup.drop(2)
+
+    def new_data = (defaultArgs + data).collectEntries { name, value ->
+      def par = config.allArguments.find { it.plainName == name && (it.direction == "input" || it.type == "file") }
+      
+      if (par != null) {
+        value = _checkArgumentType("input", par, value, "in module '$key_' id '$id'")
+      }
+
+      [ name, value ]
+    }
+
+    [ id, new_data ] + passthrough
+  }
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/channel/runComponents.nf'
+/**
+ * Run a list of components on a stream of data.
+ * 
+ * @param components: list of Viash VDSL3 modules to run
+ * @param fromState: a closure, a map or a list of keys to extract from the input data.
+ *   If a closure, it will be called with the id, the data and the component config.
+ * @param toState: a closure, a map or a list of keys to extract from the output data
+ *   If a closure, it will be called with the id, the output data, the old state and the component config.
+ * @param filter: filter function to apply to the input.
+ *   It will be called with the id, the data and the component config.
+ * @param id: id to use for the output data
+ *   If a closure, it will be called with the id, the data and the component config.
+ * @param auto: auto options to pass to the components
+ *
+ * @return: a workflow that runs the components
+ **/
+def runComponents(Map args) {
+  log.warn("runComponents is deprecated, use runEach instead")
+  assert args.components: "runComponents should be passed a list of components to run"
+
+  def components_ = args.components
+  if (components_ !instanceof List) {
+    components_ = [ components_ ]
+  }
+  assert components_.size() > 0: "pass at least one component to runComponents"
+
+  def fromState_ = args.fromState
+  def toState_ = args.toState
+  def filter_ = args.filter
+  def id_ = args.id
+
+  workflow runComponentsWf {
+    take: input_ch
+    main:
+
+    // generate one channel per method
+    out_chs = components_.collect{ comp_ ->
+      def comp_config = comp_.config
+
+      def filter_ch = filter_
+        ? input_ch | filter{tup ->
+          filter_(tup[0], tup[1], comp_config)
+        }
+        : input_ch
+      def id_ch = id_
+        ? filter_ch | map{tup ->
+          // def new_id = id_(tup[0], tup[1], comp_config)
+          def new_id = tup[0]
+          if (id_ instanceof String) {
+            new_id = id_
+          } else if (id_ instanceof Closure) {
+            new_id = id_(new_id, tup[1], comp_config)
+          }
+          [new_id] + tup.drop(1)
+        }
+        : filter_ch
+      def data_ch = id_ch | map{tup ->
+          def new_data = tup[1]
+          if (fromState_ instanceof Map) {
+            new_data = fromState_.collectEntries{ key0, key1 ->
+              [key0, new_data[key1]]
+            }
+          } else if (fromState_ instanceof List) {
+            new_data = fromState_.collectEntries{ key ->
+              [key, new_data[key]]
+            }
+          } else if (fromState_ instanceof Closure) {
+            new_data = fromState_(tup[0], new_data, comp_config)
+          }
+          tup.take(1) + [new_data] + tup.drop(1)
+        }
+      def out_ch = data_ch
+        | comp_.run(
+          auto: (args.auto ?: [:]) + [simplifyInput: false, simplifyOutput: false]
+        )
+      def post_ch = toState_
+        ? out_ch | map{tup ->
+          def output = tup[1]
+          def old_state = tup[2]
+          def new_state = null
+          if (toState_ instanceof Map) {
+            new_state = old_state + toState_.collectEntries{ key0, key1 ->
+              [key0, output[key1]]
+            }
+          } else if (toState_ instanceof List) {
+            new_state = old_state + toState_.collectEntries{ key ->
+              [key, output[key]]
+            }
+          } else if (toState_ instanceof Closure) {
+            new_state = toState_(tup[0], output, old_state, comp_config)
+          }
+          [tup[0], new_state] + tup.drop(3)
+        }
+        : out_ch
+      
+      post_ch
+    }
+
+    // mix all results
+    output_ch =
+      (out_chs.size == 1)
+        ? out_chs[0]
+        : out_chs[0].mix(*out_chs.drop(1))
+
+    emit: output_ch
+  }
+
+  return runComponentsWf
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/channel/runEach.nf'
+/**
+ * Run a list of components on a stream of data.
+ * 
+ * @param components: list of Viash VDSL3 modules to run
+ * @param fromState: a closure, a map or a list of keys to extract from the input data.
+ *   If a closure, it will be called with the id, the data and the component itself.
+ * @param toState: a closure, a map or a list of keys to extract from the output data
+ *   If a closure, it will be called with the id, the output data, the old state and the component itself.
+ * @param filter: filter function to apply to the input.
+ *   It will be called with the id, the data and the component itself.
+ * @param id: id to use for the output data
+ *   If a closure, it will be called with the id, the data and the component itself.
+ * @param auto: auto options to pass to the components
+ *
+ * @return: a workflow that runs the components
+ **/
+def runEach(Map args) {
+  assert args.components: "runEach should be passed a list of components to run"
+
+  def components_ = args.components
+  if (components_ !instanceof List) {
+    components_ = [ components_ ]
+  }
+  assert components_.size() > 0: "pass at least one component to runEach"
+
+  def fromState_ = args.fromState
+  def toState_ = args.toState
+  def filter_ = args.filter
+  def id_ = args.id
+
+  workflow runEachWf {
+    take: input_ch
+    main:
+
+    // generate one channel per method
+    out_chs = components_.collect{ comp_ ->
+      def filter_ch = filter_
+        ? input_ch | filter{tup ->
+          filter_(tup[0], tup[1], comp_)
+        }
+        : input_ch
+      def id_ch = id_
+        ? filter_ch | map{tup ->
+          def new_id = id_
+          if (new_id instanceof Closure) {
+            new_id = new_id(tup[0], tup[1], comp_)
+          }
+          assert new_id instanceof String : "Error in runEach: id should be a String or a Closure that returns a String. Expected: id instanceof String. Found: ${new_id.getClass()}"
+          [new_id] + tup.drop(1)
+        }
+        : filter_ch
+      def data_ch = id_ch | map{tup ->
+          def new_data = tup[1]
+          if (fromState_ instanceof Map) {
+            new_data = fromState_.collectEntries{ key0, key1 ->
+              [key0, new_data[key1]]
+            }
+          } else if (fromState_ instanceof List) {
+            new_data = fromState_.collectEntries{ key ->
+              [key, new_data[key]]
+            }
+          } else if (fromState_ instanceof Closure) {
+            new_data = fromState_(tup[0], new_data, comp_)
+          }
+          tup.take(1) + [new_data] + tup.drop(1)
+        }
+      def out_ch = data_ch
+        | comp_.run(
+          auto: (args.auto ?: [:]) + [simplifyInput: false, simplifyOutput: false]
+        )
+      def post_ch = toState_
+        ? out_ch | map{tup ->
+          def output = tup[1]
+          def old_state = tup[2]
+          def new_state = null
+          if (toState_ instanceof Map) {
+            new_state = old_state + toState_.collectEntries{ key0, key1 ->
+              [key0, output[key1]]
+            }
+          } else if (toState_ instanceof List) {
+            new_state = old_state + toState_.collectEntries{ key ->
+              [key, output[key]]
+            }
+          } else if (toState_ instanceof Closure) {
+            new_state = toState_(tup[0], output, old_state, comp_)
+          }
+          [tup[0], new_state] + tup.drop(3)
+        }
+        : out_ch
+      
+      post_ch
+    }
+
+    // mix all results
+    output_ch =
+      (out_chs.size == 1)
+        ? out_chs[0]
+        : out_chs[0].mix(*out_chs.drop(1))
+
+    emit: output_ch
+  }
+
+  return runEachWf
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/channel/safeJoin.nf'
+/**
+ * Join sourceChannel to targetChannel
+ * 
+ * This function joins the sourceChannel to the targetChannel. 
+ * However, each id in the targetChannel must be present in the
+ * sourceChannel. If _meta.join_id exists in the targetChannel, that is 
+ * used as an id instead. If the id doesn't match any id in the sourceChannel,
+ * an error is thrown.
+ */
+
+def safeJoin(targetChannel, sourceChannel, key) {
+  def sourceIDs = new IDChecker()
+
+  def sourceCheck = sourceChannel
+    | map { tup ->
+      sourceIDs.observe(tup[0])
+      tup
+    }
+  def targetCheck = targetChannel
+    | map { tup ->
+      def id = tup[0]
+      
+      if (!sourceIDs.contains(id)) {
+        error (
+          "Error in module '${key}' when merging output with original state.\n" +
+          "  Reason: output with id '${id}' could not be joined with source channel.\n" +
+          "    If the IDs in the output channel differ from the input channel,\n" + 
+          "    please set `tup[1]._meta.join_id to the original ID.\n" +
+          "  Original IDs in input channel: ['${sourceIDs.getItems().join("', '")}'].\n" + 
+          "  Unexpected ID in the output channel: '${id}'.\n" +
+          "  Example input event: [\"id\", [input: file(...)]],\n" +
+          "  Example output event: [\"newid\", [output: file(...), _meta: [join_id: \"id\"]]]"
+        )
+      }
+      // TODO: add link to our documentation on how to fix this
+
+      tup
+    }
+  
+  sourceCheck.cross(targetChannel)
+    | map{ left, right ->
+      right + left.drop(1)
+    }
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/config/_processArgument.nf'
+def _processArgument(arg) {
+  arg.multiple = arg.multiple != null ? arg.multiple : false
+  arg.required = arg.required != null ? arg.required : false
+  arg.direction = arg.direction != null ? arg.direction : "input"
+  arg.multiple_sep = arg.multiple_sep != null ? arg.multiple_sep : ";"
+  arg.plainName = arg.name.replaceAll("^-*", "")
+
+  if (arg.type == "file") {
+    arg.must_exist = arg.must_exist != null ? arg.must_exist : true
+    arg.create_parent = arg.create_parent != null ? arg.create_parent : true
+  }
+
+  // add default values to output files which haven't already got a default
+  if (arg.type == "file" && arg.direction == "output" && arg.default == null) {
+    def mult = arg.multiple ? "_*" : ""
+    def extSearch = ""
+    if (arg.default != null) {
+      extSearch = arg.default
+    } else if (arg.example != null) {
+      extSearch = arg.example
+    }
+    if (extSearch instanceof List) {
+      extSearch = extSearch[0]
+    }
+    def extSearchResult = extSearch.find("\\.[^\\.]+\$")
+    def ext = extSearchResult != null ? extSearchResult : ""
+    arg.default = "\$id.\$key.${arg.plainName}${mult}${ext}"
+    if (arg.multiple) {
+      arg.default = [arg.default]
+    }
+  }
+
+  if (!arg.multiple) {
+    if (arg.default != null && arg.default instanceof List) {
+      arg.default = arg.default[0]
+    }
+    if (arg.example != null && arg.example instanceof List) {
+      arg.example = arg.example[0]
+    }
+  }
+
+  if (arg.type == "boolean_true") {
+    arg.default = false
+  }
+  if (arg.type == "boolean_false") {
+    arg.default = true
+  }
+
+  arg
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/config/addGlobalParams.nf'
+def addGlobalArguments(config) {
+  def localConfig = [
+    "argument_groups": [
+      [
+        "name": "Nextflow input-output arguments",
+        "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
+        "arguments" : [
+          [
+            'name': '--publish_dir',
+            'required': true,
+            'type': 'string',
+            'description': 'Path to an output directory.',
+            'example': 'output/',
+            'multiple': false
+          ],
+          [
+            'name': '--param_list',
+            'required': false,
+            'type': 'string',
+            'description': '''Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.
+            |
+            |* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ ['id': 'foo', 'input': 'foo.txt'], ['id': 'bar', 'input': 'bar.txt'] ]`.
+            |* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.
+            |* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {'id': 'foo', 'input': 'foo.txt'}, {'id': 'bar', 'input': 'bar.txt'} ]`.
+            |* A yaml blob can also be passed directly as a string. Example: `--param_list "[ {'id': 'foo', 'input': 'foo.txt'}, {'id': 'bar', 'input': 'bar.txt'} ]"`.
+            |
+            |When passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.'''.stripMargin(),
+            'example': 'my_params.yaml',
+            'multiple': false,
+            'hidden': true
+          ]
+          // TODO: allow multiple: true in param_list?
+          // TODO: allow to specify a --param_list_regex to filter the param_list?
+          // TODO: allow to specify a --param_list_from_state to remap entries in the param_list?
+        ]
+      ]
+    ]
+  ]
+
+  return processConfig(_mergeMap(config, localConfig))
+}
+
+def _mergeMap(Map lhs, Map rhs) {
+  return rhs.inject(lhs.clone()) { map, entry ->
+    if (map[entry.key] instanceof Map && entry.value instanceof Map) {
+      map[entry.key] = _mergeMap(map[entry.key], entry.value)
+    } else if (map[entry.key] instanceof Collection && entry.value instanceof Collection) {
+      map[entry.key] += entry.value
+    } else {
+      map[entry.key] = entry.value
+    }
+    return map
+  }
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/config/generateHelp.nf'
+def _generateArgumentHelp(param) {
+  // alternatives are not supported
+  // def names = param.alternatives ::: List(param.name)
+
+  def unnamedProps = [
+    ["required parameter", param.required],
+    ["multiple values allowed", param.multiple],
+    ["output", param.direction.toLowerCase() == "output"],
+    ["file must exist", param.type == "file" && param.must_exist]
+  ].findAll{it[1]}.collect{it[0]}
+  
+  def dflt = null
+  if (param.default != null) {
+    if (param.default instanceof List) {
+      dflt = param.default.join(param.multiple_sep != null ? param.multiple_sep : ", ")
+    } else {
+      dflt = param.default.toString()
+    }
+  }
+  def example = null
+  if (param.example != null) {
+    if (param.example instanceof List) {
+      example = param.example.join(param.multiple_sep != null ? param.multiple_sep : ", ")
+    } else {
+      example = param.example.toString()
+    }
+  }
+  def min = param.min?.toString()
+  def max = param.max?.toString()
+
+  def escapeChoice = { choice ->
+    def s1 = choice.replaceAll("\\n", "\\\\n")
+    def s2 = s1.replaceAll("\"", """\\\"""")
+    s2.contains(",") || s2 != choice ? "\"" + s2 + "\"" : s2
+  }
+  def choices = param.choices == null ? 
+    null : 
+    "[ " + param.choices.collect{escapeChoice(it.toString())}.join(", ") + " ]"
+
+  def namedPropsStr = [
+    ["type", ([param.type] + unnamedProps).join(", ")],
+    ["default", dflt],
+    ["example", example],
+    ["choices", choices],
+    ["min", min],
+    ["max", max]
+  ]
+    .findAll{it[1]}
+    .collect{"\n        " + it[0] + ": " + it[1].replaceAll("\n", "\\n")}
+    .join("")
+  
+  def descStr = param.description == null ?
+    "" :
+    _paragraphWrap("\n" + param.description.trim(), 80 - 8).join("\n        ")
+  
+  "\n    --" + param.plainName +
+    namedPropsStr +
+    descStr
+}
+
+// Based on Helper.generateHelp() in Helper.scala
+def _generateHelp(config) {
+  def fun = config
+
+  // PART 1: NAME AND VERSION
+  def nameStr = fun.name + 
+    (fun.version == null ? "" : " " + fun.version)
+
+  // PART 2: DESCRIPTION
+  def descrStr = fun.description == null ? 
+    "" :
+    "\n\n" + _paragraphWrap(fun.description.trim(), 80).join("\n")
+
+  // PART 3: Usage
+  def usageStr = fun.usage == null ? 
+    "" :
+    "\n\nUsage:\n" + fun.usage.trim()
+
+  // PART 4: Options
+  def argGroupStrs = fun.allArgumentGroups.collect{argGroup ->
+    def name = argGroup.name
+    def descriptionStr = argGroup.description == null ?
+      "" :
+      "\n    " + _paragraphWrap(argGroup.description.trim(), 80-4).join("\n    ") + "\n"
+    def arguments = argGroup.arguments.collect{arg -> 
+      arg instanceof String ? fun.allArguments.find{it.plainName == arg} : arg
+    }.findAll{it != null}
+    def argumentStrs = arguments.collect{param -> _generateArgumentHelp(param)}
+    
+    "\n\n$name:" +
+      descriptionStr +
+      argumentStrs.join("\n")
+  }
+
+  // FINAL: combine
+  def out = nameStr + 
+    descrStr +
+    usageStr + 
+    argGroupStrs.join("")
+
+  return out
+}
+
+// based on Format._paragraphWrap
+def _paragraphWrap(str, maxLength) {
+  def outLines = []
+  str.split("\n").each{par ->
+    def words = par.split("\\s").toList()
+
+    def word = null
+    def line = words.pop()
+    while(!words.isEmpty()) {
+      word = words.pop()
+      if (line.length() + word.length() + 1 <= maxLength) {
+        line = line + " " + word
+      } else {
+        outLines.add(line)
+        line = word
+      }
+    }
+    if (words.isEmpty()) {
+      outLines.add(line)
+    }
+  }
+  return outLines
+}
+
+def helpMessage(config) {
+  if (params.containsKey("help") && params.help) {
+    def mergedConfig = addGlobalArguments(config)
+    def helpStr = _generateHelp(mergedConfig)
+    println(helpStr)
+    exit 0
+  }
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/config/processConfig.nf'
+def processConfig(config) {
+  // set defaults for arguments
+  config.arguments = 
+    (config.arguments ?: []).collect{_processArgument(it)}
+
+  // set defaults for argument_group arguments
+  config.argument_groups =
+    (config.argument_groups ?: []).collect{grp ->
+      grp.arguments = (grp.arguments ?: []).collect{_processArgument(it)}
+      grp
+    }
+
+  // create combined arguments list
+  config.allArguments = 
+    config.arguments +
+    config.argument_groups.collectMany{it.arguments}
+
+  // add missing argument groups (based on Functionality::allArgumentGroups())
+  def argGroups = config.argument_groups
+  if (argGroups.any{it.name.toLowerCase() == "arguments"}) {
+    argGroups = argGroups.collect{ grp ->
+      if (grp.name.toLowerCase() == "arguments") {
+        grp = grp + [
+          arguments: grp.arguments + config.arguments
+        ]
+      }
+      grp
+    }
+  } else {
+    argGroups = argGroups + [
+      name: "Arguments",
+      arguments: config.arguments
+    ]
+  }
+  config.allArgumentGroups = argGroups
+
+  config
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/config/readConfig.nf'
+
+def readConfig(file) {
+  def config = readYaml(file ?: moduleDir.resolve("config.vsh.yaml"))
+  processConfig(config)
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/functions/_resolveSiblingIfNotAbsolute.nf'
+/**
+  * Resolve a path relative to the current file.
+  * 
+  * @param str The path to resolve, as a String.
+  * @param parentPath The path to resolve relative to, as a Path.
+  *
+  * @return The path that may have been resovled, as a Path.
+  */
+def _resolveSiblingIfNotAbsolute(str, parentPath) {
+  if (str !instanceof String) {
+    return str
+  }
+  if (!_stringIsAbsolutePath(str)) {
+    return parentPath.resolveSibling(str)
+  } else {
+    return file(str, hidden: true)
+  }
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/functions/_stringIsAbsolutePath.nf'
+/**
+  * Check whether a path as a string is absolute.
+  *
+  * In the past, we tried using `file(., relative: true).isAbsolute()`,
+  * but the 'relative' option was added in 22.10.0.
+  *
+  * @param path The path to check, as a String.
+  *
+  * @return Whether the path is absolute, as a boolean.
+  */
+def _stringIsAbsolutePath(path) {
+  def _resolve_URL_PROTOCOL = ~/^([a-zA-Z][a-zA-Z0-9]*:)?\\/.+/
+
+  assert path instanceof String
+  return _resolve_URL_PROTOCOL.matcher(path).matches()
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/functions/collectTraces.nf'
+class CustomTraceObserver implements nextflow.trace.TraceObserver {
+  List traces
+
+  CustomTraceObserver(List traces) {
+    this.traces = traces
+  }
+
+  @Override
+  void onProcessComplete(nextflow.processor.TaskHandler handler, nextflow.trace.TraceRecord trace) {
+    def trace2 = trace.store.clone()
+    trace2.script = null
+    traces.add(trace2)
+  }
+
+  @Override
+  void onProcessCached(nextflow.processor.TaskHandler handler, nextflow.trace.TraceRecord trace) {
+    def trace2 = trace.store.clone()
+    trace2.script = null
+    traces.add(trace2)
+  }
+}
+
+def collectTraces() {
+  def traces = Collections.synchronizedList([])
+
+  // add custom trace observer which stores traces in the traces object
+  session.observers.add(new CustomTraceObserver(traces))
+
+  traces
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/functions/deepClone.nf'
+/**
+  * Performs a deep clone of the given object.
+  * @param x an object
+  */
+def deepClone(x) {
+  iterateMap(x, {it instanceof Cloneable ? it.clone() : it})
+}
+// helper file: 'src/main/resources/io/viash/runners/nextflow/functions/getPublishDir.nf'
+def getPublishDir() {
+  return params.containsKey("publish_dir") ? params.publish_dir : 
+    params.containsKey("publishDir") ? params.publishDir : 
+    null
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/functions/getRootDir.nf'
+
+// Recurse upwards until we find a '.build.yaml' file
+def _findBuildYamlFile(pathPossiblySymlink) {
+  def path = pathPossiblySymlink.toRealPath()
+  def child = path.resolve(".build.yaml")
+  if (java.nio.file.Files.isDirectory(path) && java.nio.file.Files.exists(child)) {
+    return child
+  } else {
+    def parent = path.getParent()
+    if (parent == null) {
+      return null
+    } else {
+      return _findBuildYamlFile(parent)
+    }
+  }
+}
+
+// get the root of the target folder
+def getRootDir() {
+  def dir = _findBuildYamlFile(meta.resources_dir)
+  assert dir != null: "Could not find .build.yaml in the folder structure"
+  dir.getParent()
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/functions/iterateMap.nf'
+/**
+  * Recursively apply a function over the leaves of an object.
+  * @param obj The object to iterate over.
+  * @param fun The function to apply to each value.
+  * @return The object with the function applied to each value.
+  */
+def iterateMap(obj, fun) {
+  if (obj instanceof List && obj !instanceof String) {
+    return obj.collect{item ->
+      iterateMap(item, fun)
+    }
+  } else if (obj instanceof Map) {
+    return obj.collectEntries{key, item ->
+      [key.toString(), iterateMap(item, fun)]
+    }
+  } else {
+    return fun(obj)
+  }
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/functions/niceView.nf'
+/**
+  * A view for printing the event of each channel as a YAML blob.
+  * This is useful for debugging.
+  */
+def niceView() {
+  workflow niceViewWf {
+    take: input
+    main:
+      output = input
+        | view{toYamlBlob(it)}
+    emit: output
+  }
+  return niceViewWf
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/readwrite/readCsv.nf'
+
+def readCsv(file_path) {
+  def output = []
+  def inputFile = file_path !instanceof Path ? file(file_path, hidden: true) : file_path
+
+  // todo: allow escaped quotes in string
+  // todo: allow single quotes?
+  def splitRegex = java.util.regex.Pattern.compile(''',(?=(?:[^"]*"[^"]*")*[^"]*$)''')
+  def removeQuote = java.util.regex.Pattern.compile('''"(.*)"''')
+
+  def br = java.nio.file.Files.newBufferedReader(inputFile)
+
+  def row = -1
+  def header = null
+  while (br.ready() && header == null) {
+    def line = br.readLine()
+    row++
+    if (!line.startsWith("#")) {
+      header = splitRegex.split(line, -1).collect{field ->
+        m = removeQuote.matcher(field)
+        m.find() ? m.replaceFirst('$1') : field
+      }
+    }
+  }
+  assert header != null: "CSV file should contain a header"
+
+  while (br.ready()) {
+    def line = br.readLine()
+    row++
+    if (line == null) {
+      br.close()
+      break
+    }
+
+    if (!line.startsWith("#")) {
+      def predata = splitRegex.split(line, -1)
+      def data = predata.collect{field ->
+        if (field == "") {
+          return null
+        }
+        def m = removeQuote.matcher(field)
+        if (m.find()) {
+          return m.replaceFirst('$1')
+        } else {
+          return field
+        }
+      }
+      assert header.size() == data.size(): "Row $row should contain the same number as fields as the header"
+      
+      def dataMap = [header, data].transpose().collectEntries().findAll{it.value != null}
+      output.add(dataMap)
+    }
+  }
+
+  output
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/readwrite/readJson.nf'
+def readJson(file_path) {
+  def inputFile = file_path !instanceof Path ? file(file_path, hidden: true) : file_path
+  def jsonSlurper = new groovy.json.JsonSlurper()
+  jsonSlurper.parse(inputFile)
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/readwrite/readJsonBlob.nf'
+def readJsonBlob(str) {
+  def jsonSlurper = new groovy.json.JsonSlurper()
+  jsonSlurper.parseText(str)
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/readwrite/readTaggedYaml.nf'
+// Custom constructor to modify how certain objects are parsed from YAML
+class CustomConstructor extends org.yaml.snakeyaml.constructor.Constructor {
+  Path root
+
+  class ConstructPath extends org.yaml.snakeyaml.constructor.AbstractConstruct {
+    public Object construct(org.yaml.snakeyaml.nodes.Node node) {
+      String filename = (String) constructScalar(node);
+      if (root != null) {
+        return root.resolve(filename);
+      }
+      return java.nio.file.Paths.get(filename);
+    }
+  }
+
+  CustomConstructor(org.yaml.snakeyaml.LoaderOptions options, Path root) {
+    super(options)
+    this.root = root
+    // Handling !file tag and parse it back to a File type
+    this.yamlConstructors.put(new org.yaml.snakeyaml.nodes.Tag("!file"), new ConstructPath())
+  }
+}
+
+def readTaggedYaml(Path path) {
+  def options = new org.yaml.snakeyaml.LoaderOptions()
+  def constructor = new CustomConstructor(options, path.getParent())
+  def yaml = new org.yaml.snakeyaml.Yaml(constructor)
+  return yaml.load(path.text)
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/readwrite/readYaml.nf'
+def readYaml(file_path) {
+  def inputFile = file_path !instanceof Path ? file(file_path, hidden: true) : file_path
+  def yamlSlurper = new org.yaml.snakeyaml.Yaml()
+  yamlSlurper.load(inputFile)
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/readwrite/readYamlBlob.nf'
+def readYamlBlob(str) {
+  def yamlSlurper = new org.yaml.snakeyaml.Yaml()
+  yamlSlurper.load(str)
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/readwrite/toJsonBlob.nf'
+String toJsonBlob(data) {
+  return groovy.json.JsonOutput.toJson(data)
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/readwrite/toTaggedYamlBlob.nf'
+// Custom representer to modify how certain objects are represented in YAML
+class CustomRepresenter extends org.yaml.snakeyaml.representer.Representer {
+  Path relativizer
+
+  class RepresentPath implements org.yaml.snakeyaml.representer.Represent {
+    public String getFileName(Object obj) {
+      if (obj instanceof File) {
+        obj = ((File) obj).toPath();
+      }
+      if (obj !instanceof Path) {
+        throw new IllegalArgumentException("Object: " + obj + " is not a Path or File");
+      }
+      def path = (Path) obj;
+
+      if (relativizer != null) {
+        return relativizer.relativize(path).toString()
+      } else {
+        return path.toString()
+      }
+    }
+
+    public org.yaml.snakeyaml.nodes.Node representData(Object data) {
+      String filename = getFileName(data);
+      def tag = new org.yaml.snakeyaml.nodes.Tag("!file");
+      return representScalar(tag, filename);
+    }
+  }
+  CustomRepresenter(org.yaml.snakeyaml.DumperOptions options, Path relativizer) {
+    super(options)
+    this.relativizer = relativizer
+    this.representers.put(sun.nio.fs.UnixPath, new RepresentPath())
+    this.representers.put(Path, new RepresentPath())
+    this.representers.put(File, new RepresentPath())
+  }
+}
+
+String toTaggedYamlBlob(data) {
+  return toRelativeTaggedYamlBlob(data, null)
+}
+String toRelativeTaggedYamlBlob(data, Path relativizer) {
+  def options = new org.yaml.snakeyaml.DumperOptions()
+  options.setDefaultFlowStyle(org.yaml.snakeyaml.DumperOptions.FlowStyle.BLOCK)
+  def representer = new CustomRepresenter(options, relativizer)
+  def yaml = new org.yaml.snakeyaml.Yaml(representer, options)
+  return yaml.dump(data)
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/readwrite/toYamlBlob.nf'
+String toYamlBlob(data) {
+  def options = new org.yaml.snakeyaml.DumperOptions()
+  options.setDefaultFlowStyle(org.yaml.snakeyaml.DumperOptions.FlowStyle.BLOCK)
+  options.setPrettyFlow(true)
+  def yaml = new org.yaml.snakeyaml.Yaml(options)
+  def cleanData = iterateMap(data, { it instanceof Path ? it.toString() : it })
+  return yaml.dump(cleanData)
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/readwrite/writeJson.nf'
+void writeJson(data, file) {
+  assert data: "writeJson: data should not be null"
+  assert file: "writeJson: file should not be null"
+  file.write(toJsonBlob(data))
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/readwrite/writeYaml.nf'
+void writeYaml(data, file) {
+  assert data: "writeYaml: data should not be null"
+  assert file: "writeYaml: file should not be null"
+  file.write(toYamlBlob(data))
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/findStates.nf'
+def findStates(Map params, Map config) {
+  def auto_config = deepClone(config)
+  def auto_params = deepClone(params)
+
+  auto_config = auto_config.clone()
+  // override arguments
+  auto_config.argument_groups = []
+  auto_config.arguments = [
+    [
+      type: "string",
+      name: "--id",
+      description: "A dummy identifier",
+      required: false
+    ],
+    [
+      type: "file",
+      name: "--input_states",
+      example: "/path/to/input/directory/**/state.yaml",
+      description: "Path to input directory containing the datasets to be integrated.",
+      required: true,
+      multiple: true,
+      multiple_sep: ";"
+    ],
+    [
+      type: "string",
+      name: "--filter",
+      example: "foo/.*/state.yaml",
+      description: "Regex to filter state files by path.",
+      required: false
+    ],
+    // to do: make this a yaml blob?
+    [
+      type: "string",
+      name: "--rename_keys",
+      example: ["newKey1:oldKey1", "newKey2:oldKey2"],
+      description: "Rename keys in the detected input files. This is useful if the input files do not match the set of input arguments of the workflow.",
+      required: false,
+      multiple: true,
+      multiple_sep: ";"
+    ],
+    [
+      type: "string",
+      name: "--settings",
+      example: '{"output_dataset": "dataset.h5ad", "k": 10}',
+      description: "Global arguments as a JSON glob to be passed to all components.",
+      required: false
+    ]
+  ]
+  if (!(auto_params.containsKey("id"))) {
+    auto_params["id"] = "auto"
+  }
+
+  // run auto config through processConfig once more
+  auto_config = processConfig(auto_config)
+
+  workflow findStatesWf {
+    helpMessage(auto_config)
+
+    output_ch = 
+      channelFromParams(auto_params, auto_config)
+        | flatMap { autoId, args ->
+
+          def globalSettings = args.settings ? readYamlBlob(args.settings) : [:]
+
+          // look for state files in input dir
+          def stateFiles = args.input_states
+
+          // filter state files by regex
+          if (args.filter) {
+            stateFiles = stateFiles.findAll{ stateFile ->
+              def stateFileStr = stateFile.toString()
+              def matcher = stateFileStr =~ args.filter
+              matcher.matches()}
+          }
+
+          // read in states
+          def states = stateFiles.collect { stateFile ->
+            def state_ = readTaggedYaml(stateFile)
+            [state_.id, state_]
+          }
+
+          // construct renameMap
+          if (args.rename_keys) {
+            def renameMap = args.rename_keys.collectEntries{renameString ->
+              def split = renameString.split(";")
+              assert split.size() == 2: "Argument 'rename_keys' should be of the form 'newKey:oldKey,newKey:oldKey'"
+              split
+            }
+
+            // rename keys in state, only let states through which have all keys
+            // also add global settings
+            states = states.collectMany{id, state ->
+              def newState = [:]
+
+              for (key in renameMap.keySet()) {
+                def origKey = renameMap[key]
+                if (!(state.containsKey(origKey))) {
+                  return []
+                }
+                newState[key] = state[origKey]
+              }
+
+              [[id, globalSettings + newState]]
+            }
+          }
+
+          states
+        }
+    emit:
+    output_ch
+  }
+
+  return findStatesWf
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/joinStates.nf'
+def joinStates(Closure apply_) {
+  workflow joinStatesWf {
+    take: input_ch
+    main:
+    output_ch = input_ch
+      | toSortedList
+      | filter{ it.size() > 0 }
+      | map{ tups ->
+        def ids = tups.collect{it[0]}
+        def states = tups.collect{it[1]}
+        apply_(ids, states)
+      }
+
+    emit: output_ch
+  }
+  return joinStatesWf
+}
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf'
+def collectFiles(obj) {
+  if (obj instanceof java.io.File || obj instanceof Path)  {
+    return [obj]
+  } else if (obj instanceof List && obj !instanceof String) {
+    return obj.collectMany{item ->
+      collectFiles(item)
+    }
+  } else if (obj instanceof Map) {
+    return obj.collectMany{key, item ->
+      collectFiles(item)
+    }
+  } else {
+    return []
+  }
+}
+
+/**
+ * Recurse through a state and collect all input files and their target output filenames.
+ * @param obj The state to recurse through.
+ * @param prefix The prefix to prepend to the output filenames.
+ */
+def collectInputOutputPaths(obj, prefix) {
+  if (obj instanceof File || obj instanceof Path)  {
+    def path = obj instanceof Path ? obj : obj.toPath()
+    def ext = path.getFileName().toString().find("\\.[^\\.]+\$") ?: ""
+    def newFilename = prefix + ext
+    return [[obj, newFilename]]
+  } else if (obj instanceof List && obj !instanceof String) {
+    return obj.withIndex().collectMany{item, ix ->
+      collectInputOutputPaths(item, prefix + "_" + ix)
+    }
+  } else if (obj instanceof Map) {
+    return obj.collectMany{key, item ->
+      collectInputOutputPaths(item, prefix + "." + key)
+    }
+  } else {
+    return []
+  }
+}
+
+def publishStates(Map args) {
+  def key_ = args.get("key")
+  def yamlTemplate_ = args.get("output_state", args.get("outputState", '$id.$key.state.yaml'))
+
+  assert key_ != null : "publishStates: key must be specified"
+  
+  workflow publishStatesWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1]
+
+          // the input files and the target output filenames
+          def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose()
+          def inputFiles_ = inputoutputFilenames_[0]
+          def outputFilenames_ = inputoutputFilenames_[1]
+
+          def yamlFilename = yamlTemplate_
+            .replaceAll('\\$id', id_)
+            .replaceAll('\\$key', key_)
+
+            // TODO: do the pathnames in state_ match up with the outputFilenames_?
+
+          // convert state to yaml blob
+          def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename))
+
+          [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_]
+        }
+        | publishStatesProc
+    emit: input_ch
+  }
+  return publishStatesWf
+}
+process publishStatesProc {
+  // todo: check publishpath?
+  publishDir path: "${getPublishDir()}/", mode: "copy"
+  tag "$id"
+  input:
+    tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles)
+  output:
+    tuple val(id), path{[yamlFile] + outputFiles}
+  script:
+  def copyCommands = [
+    inputFiles instanceof List ? inputFiles : [inputFiles],
+    outputFiles instanceof List ? outputFiles : [outputFiles]
+  ]
+    .transpose()
+    .collectMany{infile, outfile ->
+      if (infile.toString() != outfile.toString()) {
+        [
+          "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"",
+          "cp -r '${infile.toString()}' '${outfile.toString()}'"
+        ]
+      } else {
+        // no need to copy if infile is the same as outfile
+        []
+      }
+    }
+  """
+mkdir -p "\$(dirname '${yamlFile}')"
+echo "Storing state as yaml"
+echo '${yamlBlob}' > '${yamlFile}'
+echo "Copying output files to destination folder"
+${copyCommands.join("\n  ")}
+"""
+}
+
+
+// this assumes that the state contains no other values other than those specified in the config
+def publishStatesByConfig(Map args) {
+  def config = args.get("config")
+  assert config != null : "publishStatesByConfig: config must be specified"
+
+  def key_ = args.get("key", config.name)
+  assert key_ != null : "publishStatesByConfig: key must be specified"
+  
+  workflow publishStatesSimpleWf {
+    take: input_ch
+    main:
+      input_ch
+        | map { tup ->
+          def id_ = tup[0]
+          def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10]
+          def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad']
+
+          // TODO: allow overriding the state.yaml template
+          // TODO TODO: if auto.publish == "state", add output_state as an argument
+          def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml'
+          def yamlFilename = yamlTemplate
+            .replaceAll('\\$id', id_)
+            .replaceAll('\\$key', key_)
+          def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
+
+          // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
+          //   - key is a String
+          //   - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path)
+          //   - inputPath is a List[Path]
+          //   - outputFilename is a List[String]
+          //   - (key, value) are the tuples that will be saved to the state.yaml file
+          //   - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml)
+          def processedState =
+            config.allArguments
+              .findAll { it.direction == "output" }
+              .collectMany { par ->
+                def plainName_ = par.plainName
+                // if the state does not contain the key, it's an
+                // optional argument for which the component did 
+                // not generate any output
+                if (!state_.containsKey(plainName_)) {
+                  return []
+                }
+                def value = state_[plainName_]
+                // if the parameter is not a file, it should be stored
+                // in the state as-is, but is not something that needs 
+                // to be copied from the source path to the dest path
+                if (par.type != "file") {
+                  return [[key: plainName_, value: value, inputPath: [], outputFilename: []]]
+                }
+                // if the orig state does not contain this filename,
+                // it's an optional argument for which the user specified
+                // that it should not be returned as a state
+                if (!origState_.containsKey(plainName_)) {
+                  return []
+                }
+                def filenameTemplate = origState_[plainName_]
+                // if the pararameter is multiple: true, fetch the template
+                if (par.multiple && filenameTemplate instanceof List) {
+                  filenameTemplate = filenameTemplate[0]
+                }
+                // instantiate the template
+                def filename = filenameTemplate
+                  .replaceAll('\\$id', id_)
+                  .replaceAll('\\$key', key_)
+                if (par.multiple) {
+                  // if the parameter is multiple: true, the filename
+                  // should contain a wildcard '*' that is replaced with
+                  // the index of the file
+                  assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}"
+                  def outputPerFile = value.withIndex().collect{ val, ix ->
+                    def filename_ix = filename.replace("*", ix.toString())
+                    def value_ = java.nio.file.Paths.get(filename_ix)
+                    // if id contains a slash
+                    if (yamlDir != null) {
+                      value_ = yamlDir.relativize(value_)
+                    }
+                    def inputPath = val instanceof File ? val.toPath() : val
+                    [value: value_, inputPath: inputPath, outputFilename: filename_ix]
+                  }
+                  def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> 
+                    [key, outputPerFile.collect{dic -> dic[key]}]
+                  }
+                  return [[key: plainName_] + transposedOutputs]
+                } else {
+                  def value_ = java.nio.file.Paths.get(filename)
+                  // if id contains a slash
+                  if (yamlDir != null) {
+                    value_ = yamlDir.relativize(value_)
+                  }
+                  def inputPath = value instanceof File ? value.toPath() : value
+                  return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]]
+                }
+              }
+          
+          def updatedState_ = processedState.collectEntries{[it.key, it.value]}
+          def inputPaths = processedState.collectMany{it.inputPath}
+          def outputFilenames = processedState.collectMany{it.outputFilename}
+          
+          // convert state to yaml blob
+          def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_)
+
+          [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames]
+        }
+        | publishStatesProc
+    emit: input_ch
+  }
+  return publishStatesSimpleWf
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/states/setState.nf'
+def setState(fun) {
+  assert fun instanceof Closure || fun instanceof Map || fun instanceof List :
+    "Error in setState: Expected process argument to be a Closure, a Map, or a List. Found: class ${fun.getClass()}"
+
+  // if fun is a List, convert to map
+  if (fun instanceof List) {
+    // check whether fun is a list[string]
+    assert fun.every{it instanceof CharSequence} : "Error in setState: argument is a List, but not all elements are Strings"
+    fun = fun.collectEntries{[it, it]}
+  }
+
+  // if fun is a map, convert to closure
+  if (fun instanceof Map) {
+    // check whether fun is a map[string, string]
+    assert fun.values().every{it instanceof CharSequence} : "Error in setState: argument is a Map, but not all values are Strings"
+    assert fun.keySet().every{it instanceof CharSequence} : "Error in setState: argument is a Map, but not all keys are Strings"
+    def funMap = fun.clone()
+    // turn the map into a closure to be used later on
+    fun = { id_, state_ ->
+      assert state_ instanceof Map : "Error in setState: the state is not a Map"
+      funMap.collectMany{newkey, origkey ->
+        if (state_.containsKey(origkey)) {
+          [[newkey, state_[origkey]]]
+        } else {
+          []
+        }
+      }.collectEntries()
+    }
+  }
+
+  map { tup ->
+    def id = tup[0]
+    def state = tup[1]
+    def unfilteredState = fun(id, state)
+    def newState = unfilteredState.findAll{key, val -> val != null}
+    [id, newState] + tup.drop(2)
+  }
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/workflowFactory/processAuto.nf'
+// TODO: unit test processAuto
+def processAuto(Map auto) {
+  // remove null values
+  auto = auto.findAll{k, v -> v != null}
+
+  // check for unexpected keys
+  def expectedKeys = ["simplifyInput", "simplifyOutput", "transcript", "publish"]
+  def unexpectedKeys = auto.keySet() - expectedKeys
+  assert unexpectedKeys.isEmpty(), "unexpected keys in auto: '${unexpectedKeys.join("', '")}'"
+
+  // check auto.simplifyInput
+  assert auto.simplifyInput instanceof Boolean, "auto.simplifyInput must be a boolean"
+
+  // check auto.simplifyOutput
+  assert auto.simplifyOutput instanceof Boolean, "auto.simplifyOutput must be a boolean"
+
+  // check auto.transcript
+  assert auto.transcript instanceof Boolean, "auto.transcript must be a boolean"
+
+  // check auto.publish
+  assert auto.publish instanceof Boolean || auto.publish == "state", "auto.publish must be a boolean or 'state'"
+
+  return auto.subMap(expectedKeys)
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/workflowFactory/processDirectives.nf'
+def assertMapKeys(map, expectedKeys, requiredKeys, mapName) {
+  assert map instanceof Map : "Expected argument '$mapName' to be a Map. Found: class ${map.getClass()}"
+  map.forEach { key, val -> 
+    assert key in expectedKeys : "Unexpected key '$key' in ${mapName ? mapName + " " : ""}map"
+  }
+  requiredKeys.forEach { requiredKey -> 
+    assert map.containsKey(requiredKey) : "Missing required key '$key' in ${mapName ? mapName + " " : ""}map"
+  }
+}
+
+// TODO: unit test processDirectives
+def processDirectives(Map drctv) {
+  // remove null values
+  drctv = drctv.findAll{k, v -> v != null}
+
+  // check for unexpected keys
+  def expectedKeys = [
+    "accelerator", "afterScript", "beforeScript", "cache", "conda", "container", "containerOptions", "cpus", "disk", "echo", "errorStrategy", "executor", "machineType", "maxErrors", "maxForks", "maxRetries", "memory", "module", "penv", "pod", "publishDir", "queue", "label", "scratch", "storeDir", "stageInMode", "stageOutMode", "tag", "time"
+  ]
+  def unexpectedKeys = drctv.keySet() - expectedKeys
+  assert unexpectedKeys.isEmpty() : "Unexpected keys in process directive: '${unexpectedKeys.join("', '")}'"
+
+  /* DIRECTIVE accelerator
+    accepted examples:
+    - [ limit: 4, type: "nvidia-tesla-k80" ]
+  */
+  if (drctv.containsKey("accelerator")) {
+    assertMapKeys(drctv["accelerator"], ["type", "limit", "request", "runtime"], [], "accelerator")
+  }
+
+  /* DIRECTIVE afterScript
+    accepted examples:
+    - "source /cluster/bin/cleanup"
+  */
+  if (drctv.containsKey("afterScript")) {
+    assert drctv["afterScript"] instanceof CharSequence
+  }
+
+  /* DIRECTIVE beforeScript
+    accepted examples:
+    - "source /cluster/bin/setup"
+  */
+  if (drctv.containsKey("beforeScript")) {
+    assert drctv["beforeScript"] instanceof CharSequence
+  }
+
+  /* DIRECTIVE cache
+    accepted examples:
+    - true
+    - false
+    - "deep"
+    - "lenient"
+  */
+  if (drctv.containsKey("cache")) {
+    assert drctv["cache"] instanceof CharSequence || drctv["cache"] instanceof Boolean
+    if (drctv["cache"] instanceof CharSequence) {
+      assert drctv["cache"] in ["deep", "lenient"] : "Unexpected value for cache"
+    }
+  }
+
+  /* DIRECTIVE conda
+    accepted examples:
+    - "bwa=0.7.15"
+    - "bwa=0.7.15 fastqc=0.11.5"
+    - ["bwa=0.7.15", "fastqc=0.11.5"]
+  */
+  if (drctv.containsKey("conda")) {
+    if (drctv["conda"] instanceof List) {
+      drctv["conda"] = drctv["conda"].join(" ")
+    }
+    assert drctv["conda"] instanceof CharSequence
+  }
+
+  /* DIRECTIVE container
+    accepted examples:
+    - "foo/bar:tag"
+    - [ registry: "reg", image: "im", tag: "ta" ]
+      is transformed to "reg/im:ta"
+    - [ image: "im" ] 
+      is transformed to "im:latest"
+  */
+  if (drctv.containsKey("container")) {
+    assert drctv["container"] instanceof Map || drctv["container"] instanceof CharSequence
+    if (drctv["container"] instanceof Map) {
+      def m = drctv["container"]
+      assertMapKeys(m, [ "registry", "image", "tag" ], ["image"], "container")
+      def part1 = 
+        System.getenv('OVERRIDE_CONTAINER_REGISTRY') ? System.getenv('OVERRIDE_CONTAINER_REGISTRY') + "/" : 
+        params.containsKey("override_container_registry") ? params["override_container_registry"] + "/" : // todo: remove?
+        m.registry ? m.registry + "/" : 
+        ""
+      def part2 = m.image
+      def part3 = m.tag ? ":" + m.tag : ":latest"
+      drctv["container"] = part1 + part2 + part3
+    }
+  }
+
+  /* DIRECTIVE containerOptions
+    accepted examples:
+    - "--foo bar"
+    - ["--foo bar", "-f b"]
+  */
+  if (drctv.containsKey("containerOptions")) {
+    if (drctv["containerOptions"] instanceof List) {
+      drctv["containerOptions"] = drctv["containerOptions"].join(" ")
+    }
+    assert drctv["containerOptions"] instanceof CharSequence
+  }
+
+  /* DIRECTIVE cpus
+    accepted examples:
+    - 1
+    - 10
+  */
+  if (drctv.containsKey("cpus")) {
+    assert drctv["cpus"] instanceof Integer
+  }
+
+  /* DIRECTIVE disk
+    accepted examples:
+    - "1 GB"
+    - "2TB"
+    - "3.2KB"
+    - "10.B"
+  */
+  if (drctv.containsKey("disk")) {
+    assert drctv["disk"] instanceof CharSequence
+    // assert drctv["disk"].matches("[0-9]+(\\.[0-9]*)? *[KMGTPEZY]?B")
+    // ^ does not allow closures
+  }
+
+  /* DIRECTIVE echo
+    accepted examples:
+    - true
+    - false
+  */
+  if (drctv.containsKey("echo")) {
+    assert drctv["echo"] instanceof Boolean
+  }
+
+  /* DIRECTIVE errorStrategy
+    accepted examples:
+    - "terminate"
+    - "finish"
+  */
+  if (drctv.containsKey("errorStrategy")) {
+    assert drctv["errorStrategy"] instanceof CharSequence
+    assert drctv["errorStrategy"] in ["terminate", "finish", "ignore", "retry"] : "Unexpected value for errorStrategy"
+  }
+
+  /* DIRECTIVE executor
+    accepted examples:
+    - "local"
+    - "sge"
+  */
+  if (drctv.containsKey("executor")) {
+    assert drctv["executor"] instanceof CharSequence
+    assert drctv["executor"] in ["local", "sge", "uge", "lsf", "slurm", "pbs", "pbspro", "moab", "condor", "nqsii", "ignite", "k8s", "awsbatch", "google-pipelines"] : "Unexpected value for executor"
+  }
+
+  /* DIRECTIVE machineType
+    accepted examples:
+    - "n1-highmem-8"
+  */
+  if (drctv.containsKey("machineType")) {
+    assert drctv["machineType"] instanceof CharSequence
+  }
+
+  /* DIRECTIVE maxErrors
+    accepted examples:
+    - 1
+    - 3
+  */
+  if (drctv.containsKey("maxErrors")) {
+    assert drctv["maxErrors"] instanceof Integer
+  }
+
+  /* DIRECTIVE maxForks
+    accepted examples:
+    - 1
+    - 3
+  */
+  if (drctv.containsKey("maxForks")) {
+    assert drctv["maxForks"] instanceof Integer
+  }
+
+  /* DIRECTIVE maxRetries
+    accepted examples:
+    - 1
+    - 3
+  */
+  if (drctv.containsKey("maxRetries")) {
+    assert drctv["maxRetries"] instanceof Integer
+  }
+
+  /* DIRECTIVE memory
+    accepted examples:
+    - "1 GB"
+    - "2TB"
+    - "3.2KB"
+    - "10.B"
+  */
+  if (drctv.containsKey("memory")) {
+    assert drctv["memory"] instanceof CharSequence
+    // assert drctv["memory"].matches("[0-9]+(\\.[0-9]*)? *[KMGTPEZY]?B")
+    // ^ does not allow closures
+  }
+
+  /* DIRECTIVE module
+    accepted examples:
+    - "ncbi-blast/2.2.27"
+    - "ncbi-blast/2.2.27:t_coffee/10.0"
+    - ["ncbi-blast/2.2.27", "t_coffee/10.0"]
+  */
+  if (drctv.containsKey("module")) {
+    if (drctv["module"] instanceof List) {
+      drctv["module"] = drctv["module"].join(":")
+    }
+    assert drctv["module"] instanceof CharSequence
+  }
+
+  /* DIRECTIVE penv
+    accepted examples:
+    - "smp"
+  */
+  if (drctv.containsKey("penv")) {
+    assert drctv["penv"] instanceof CharSequence
+  }
+
+  /* DIRECTIVE pod
+    accepted examples:
+    - [ label: "key", value: "val" ]
+    - [ annotation: "key", value: "val" ]
+    - [ env: "key", value: "val" ]
+    - [ [label: "l", value: "v"], [env: "e", value: "v"]]
+  */
+  if (drctv.containsKey("pod")) {
+    if (drctv["pod"] instanceof Map) {
+      drctv["pod"] = [ drctv["pod"] ]
+    }
+    assert drctv["pod"] instanceof List
+    drctv["pod"].forEach { pod ->
+      assert pod instanceof Map
+      // TODO: should more checks be added?
+      // See https://www.nextflow.io/docs/latest/process.html?highlight=directives#pod
+      // e.g. does it contain 'label' and 'value', or 'annotation' and 'value', or ...?
+    }
+  }
+
+  /* DIRECTIVE publishDir
+    accepted examples:
+    - []
+    - [ [ path: "foo", enabled: true ], [ path: "bar", enabled: false ] ]
+    - "/path/to/dir" 
+      is transformed to [[ path: "/path/to/dir" ]]
+    - [ path: "/path/to/dir", mode: "cache" ]
+      is transformed to [[ path: "/path/to/dir", mode: "cache" ]]
+  */
+  // TODO: should we also look at params["publishDir"]?
+  if (drctv.containsKey("publishDir")) {
+    def pblsh = drctv["publishDir"]
+    
+    // check different options
+    assert pblsh instanceof List || pblsh instanceof Map || pblsh instanceof CharSequence
+    
+    // turn into list if not already so
+    // for some reason, 'if (!pblsh instanceof List) pblsh = [ pblsh ]' doesn't work.
+    pblsh = pblsh instanceof List ? pblsh : [ pblsh ]
+
+    // check elements of publishDir
+    pblsh = pblsh.collect{ elem ->
+      // turn into map if not already so
+      elem = elem instanceof CharSequence ? [ path: elem ] : elem
+
+      // check types and keys
+      assert elem instanceof Map : "Expected publish argument '$elem' to be a String or a Map. Found: class ${elem.getClass()}"
+      assertMapKeys(elem, [ "path", "mode", "overwrite", "pattern", "saveAs", "enabled" ], ["path"], "publishDir")
+
+      // check elements in map
+      assert elem.containsKey("path")
+      assert elem["path"] instanceof CharSequence
+      if (elem.containsKey("mode")) {
+        assert elem["mode"] instanceof CharSequence
+        assert elem["mode"] in [ "symlink", "rellink", "link", "copy", "copyNoFollow", "move" ]
+      }
+      if (elem.containsKey("overwrite")) {
+        assert elem["overwrite"] instanceof Boolean
+      }
+      if (elem.containsKey("pattern")) {
+        assert elem["pattern"] instanceof CharSequence
+      }
+      if (elem.containsKey("saveAs")) {
+        assert elem["saveAs"] instanceof CharSequence //: "saveAs as a Closure is currently not supported. Surround your closure with single quotes to get the desired effect. Example: '\{ foo \}'"
+      }
+      if (elem.containsKey("enabled")) {
+        assert elem["enabled"] instanceof Boolean
+      }
+
+      // return final result
+      elem
+    }
+    // store final directive
+    drctv["publishDir"] = pblsh
+  }
+
+  /* DIRECTIVE queue
+    accepted examples:
+    - "long"
+    - "short,long"
+    - ["short", "long"]
+  */
+  if (drctv.containsKey("queue")) {
+    if (drctv["queue"] instanceof List) {
+      drctv["queue"] = drctv["queue"].join(",")
+    }
+    assert drctv["queue"] instanceof CharSequence
+  }
+
+  /* DIRECTIVE label
+    accepted examples:
+    - "big_mem"
+    - "big_cpu"
+    - ["big_mem", "big_cpu"]
+  */
+  if (drctv.containsKey("label")) {
+    if (drctv["label"] instanceof CharSequence) {
+      drctv["label"] = [ drctv["label"] ]
+    }
+    assert drctv["label"] instanceof List
+    drctv["label"].forEach { label ->
+      assert label instanceof CharSequence
+      // assert label.matches("[a-zA-Z0-9]([a-zA-Z0-9_]*[a-zA-Z0-9])?")
+      // ^ does not allow closures
+    }
+  }
+
+  /* DIRECTIVE scratch
+    accepted examples:
+    - true
+    - "/path/to/scratch"
+    - '$MY_PATH_TO_SCRATCH'
+    - "ram-disk"
+  */
+  if (drctv.containsKey("scratch")) {
+    assert drctv["scratch"] == true || drctv["scratch"] instanceof CharSequence
+  }
+
+  /* DIRECTIVE storeDir
+    accepted examples:
+    - "/path/to/storeDir"
+  */
+  if (drctv.containsKey("storeDir")) {
+    assert drctv["storeDir"] instanceof CharSequence
+  }
+
+  /* DIRECTIVE stageInMode
+    accepted examples:
+    - "copy"
+    - "link"
+  */
+  if (drctv.containsKey("stageInMode")) {
+    assert drctv["stageInMode"] instanceof CharSequence
+    assert drctv["stageInMode"] in ["copy", "link", "symlink", "rellink"]
+  }
+
+  /* DIRECTIVE stageOutMode
+    accepted examples:
+    - "copy"
+    - "link"
+  */
+  if (drctv.containsKey("stageOutMode")) {
+    assert drctv["stageOutMode"] instanceof CharSequence
+    assert drctv["stageOutMode"] in ["copy", "move", "rsync"]
+  }
+
+  /* DIRECTIVE tag
+    accepted examples:
+    - "foo"
+    - '$id'
+  */
+  if (drctv.containsKey("tag")) {
+    assert drctv["tag"] instanceof CharSequence
+  }
+
+  /* DIRECTIVE time
+    accepted examples:
+    - "1h"
+    - "2days"
+    - "1day 6hours 3minutes 30seconds"
+  */
+  if (drctv.containsKey("time")) {
+    assert drctv["time"] instanceof CharSequence
+    // todo: validation regex?
+  }
+
+  return drctv
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/workflowFactory/processWorkflowArgs.nf'
+def processWorkflowArgs(Map args, Map defaultWfArgs, Map meta) {
+  // override defaults with args
+  def workflowArgs = defaultWfArgs + args
+
+  // check whether 'key' exists
+  assert workflowArgs.containsKey("key") : "Error in module '${meta.config.name}': key is a required argument"
+
+  // if 'key' is a closure, apply it to the original key
+  if (workflowArgs["key"] instanceof Closure) {
+    workflowArgs["key"] = workflowArgs["key"](meta.config.name)
+  }
+  def key = workflowArgs["key"]
+  assert key instanceof CharSequence : "Expected process argument 'key' to be a String. Found: class ${key.getClass()}"
+  assert key ==~ /^[a-zA-Z_]\w*$/ : "Error in module '$key': Expected process argument 'key' to consist of only letters, digits or underscores. Found: ${key}"
+
+  // check for any unexpected keys
+  def expectedKeys = ["key", "directives", "auto", "map", "mapId", "mapData", "mapPassthrough", "filter", "runIf", "fromState", "toState", "args", "renameKeys", "debug"]
+  def unexpectedKeys = workflowArgs.keySet() - expectedKeys
+  assert unexpectedKeys.isEmpty() : "Error in module '$key': unexpected arguments to the '.run()' function: '${unexpectedKeys.join("', '")}'"
+
+  // check whether directives exists and apply defaults
+  assert workflowArgs.containsKey("directives") : "Error in module '$key': directives is a required argument"
+  assert workflowArgs["directives"] instanceof Map : "Error in module '$key': Expected process argument 'directives' to be a Map. Found: class ${workflowArgs['directives'].getClass()}"
+  workflowArgs["directives"] = processDirectives(defaultWfArgs.directives + workflowArgs["directives"])
+
+  // check whether directives exists and apply defaults
+  assert workflowArgs.containsKey("auto") : "Error in module '$key': auto is a required argument"
+  assert workflowArgs["auto"] instanceof Map : "Error in module '$key': Expected process argument 'auto' to be a Map. Found: class ${workflowArgs['auto'].getClass()}"
+  workflowArgs["auto"] = processAuto(defaultWfArgs.auto + workflowArgs["auto"])
+
+  // auto define publish, if so desired
+  if (workflowArgs.auto.publish == true && (workflowArgs.directives.publishDir != null ? workflowArgs.directives.publishDir : [:]).isEmpty()) {
+    // can't assert at this level thanks to the no_publish profile
+    // assert params.containsKey("publishDir") || params.containsKey("publish_dir") : 
+    //   "Error in module '${workflowArgs['key']}': if auto.publish is true, params.publish_dir needs to be defined.\n" +
+    //   "  Example: params.publish_dir = \"./output/\""
+    def publishDir = getPublishDir()
+    
+    if (publishDir != null) {
+      workflowArgs.directives.publishDir = [[ 
+        path: publishDir, 
+        saveAs: "{ it.startsWith('.') ? null : it }", // don't publish hidden files, by default
+        mode: "copy"
+      ]]
+    }
+  }
+
+  // auto define transcript, if so desired
+  if (workflowArgs.auto.transcript == true) {
+    // can't assert at this level thanks to the no_publish profile
+    // assert params.containsKey("transcriptsDir") || params.containsKey("transcripts_dir") || params.containsKey("publishDir") || params.containsKey("publish_dir") : 
+    //   "Error in module '${workflowArgs['key']}': if auto.transcript is true, either params.transcripts_dir or params.publish_dir needs to be defined.\n" +
+    //   "  Example: params.transcripts_dir = \"./transcripts/\""
+    def transcriptsDir = 
+      params.containsKey("transcripts_dir") ? params.transcripts_dir : 
+      params.containsKey("transcriptsDir") ? params.transcriptsDir : 
+      params.containsKey("publish_dir") ? params.publish_dir + "/_transcripts" :
+      params.containsKey("publishDir") ? params.publishDir + "/_transcripts" : 
+      null
+    if (transcriptsDir != null) {
+      def timestamp = nextflow.Nextflow.getSession().getWorkflowMetadata().start.format('yyyy-MM-dd_HH-mm-ss')
+      def transcriptsPublishDir = [ 
+        path: "$transcriptsDir/$timestamp/\${task.process.replaceAll(':', '-')}/\${id}/",
+        saveAs: "{ it.startsWith('.') ? it.replaceAll('^.', '') : null }", 
+        mode: "copy"
+      ]
+      def publishDirs = workflowArgs.directives.publishDir != null ? workflowArgs.directives.publishDir : null ? workflowArgs.directives.publishDir : []
+      workflowArgs.directives.publishDir = publishDirs + transcriptsPublishDir
+    }
+  }
+
+  // if this is a stubrun, remove certain directives?
+  if (workflow.stubRun) {
+    workflowArgs.directives.keySet().removeAll(["publishDir", "cpus", "memory", "label"])
+  }
+
+  for (nam in ["map", "mapId", "mapData", "mapPassthrough", "filter", "runIf"]) {
+    if (workflowArgs.containsKey(nam) && workflowArgs[nam]) {
+      assert workflowArgs[nam] instanceof Closure : "Error in module '$key': Expected process argument '$nam' to be null or a Closure. Found: class ${workflowArgs[nam].getClass()}"
+    }
+  }
+
+  // TODO: should functions like 'map', 'mapId', 'mapData', 'mapPassthrough' be deprecated as well?
+  for (nam in ["map", "mapData", "mapPassthrough", "renameKeys"]) {
+    if (workflowArgs.containsKey(nam) && workflowArgs[nam] != null) {
+      log.warn "module '$key': workflow argument '$nam' is deprecated and will be removed in Viash 0.9.0. Please use 'fromState' and 'toState' instead."
+    }
+  }
+
+  // check fromState
+  workflowArgs["fromState"] = _processFromState(workflowArgs.get("fromState"), key, meta.config)
+
+  // check toState
+  workflowArgs["toState"] = _processToState(workflowArgs.get("toState"), key, meta.config)
+
+  // return output
+  return workflowArgs
+}
+
+def _processFromState(fromState, key_, config_) {
+  assert fromState == null || fromState instanceof Closure || fromState instanceof Map || fromState instanceof List :
+    "Error in module '$key_': Expected process argument 'fromState' to be null, a Closure, a Map, or a List. Found: class ${fromState.getClass()}"
+  if (fromState == null) {
+    return null
+  }
+  
+  // if fromState is a List, convert to map
+  if (fromState instanceof List) {
+    // check whether fromstate is a list[string]
+    assert fromState.every{it instanceof CharSequence} : "Error in module '$key_': fromState is a List, but not all elements are Strings"
+    fromState = fromState.collectEntries{[it, it]}
+  }
+
+  // if fromState is a map, convert to closure
+  if (fromState instanceof Map) {
+    // check whether fromstate is a map[string, string]
+    assert fromState.values().every{it instanceof CharSequence} : "Error in module '$key_': fromState is a Map, but not all values are Strings"
+    assert fromState.keySet().every{it instanceof CharSequence} : "Error in module '$key_': fromState is a Map, but not all keys are Strings"
+    def fromStateMap = fromState.clone()
+    def requiredInputNames = meta.config.allArguments.findAll{it.required && it.direction == "Input"}.collect{it.plainName}
+    // turn the map into a closure to be used later on
+    fromState = { it ->
+      def state = it[1]
+      assert state instanceof Map : "Error in module '$key_': the state is not a Map"
+      def data = fromStateMap.collectMany{newkey, origkey ->
+        // check whether newkey corresponds to a required argument
+        if (state.containsKey(origkey)) {
+          [[newkey, state[origkey]]]
+        } else if (!requiredInputNames.contains(origkey)) {
+          []
+        } else {
+          throw new Exception("Error in module '$key_': fromState key '$origkey' not found in current state")
+        }
+      }.collectEntries()
+      data
+    }
+  }
+  
+  return fromState
+}
+
+def _processToState(toState, key_, config_) {
+  if (toState == null) {
+    toState = { tup -> tup[1] }
+  }
+
+  // toState should be a closure, map[string, string], or list[string]
+  assert toState instanceof Closure || toState instanceof Map || toState instanceof List :
+    "Error in module '$key_': Expected process argument 'toState' to be a Closure, a Map, or a List. Found: class ${toState.getClass()}"
+
+  // if toState is a List, convert to map
+  if (toState instanceof List) {
+    // check whether toState is a list[string]
+    assert toState.every{it instanceof CharSequence} : "Error in module '$key_': toState is a List, but not all elements are Strings"
+    toState = toState.collectEntries{[it, it]}
+  }
+
+  // if toState is a map, convert to closure
+  if (toState instanceof Map) {
+    // check whether toState is a map[string, string]
+    assert toState.values().every{it instanceof CharSequence} : "Error in module '$key_': toState is a Map, but not all values are Strings"
+    assert toState.keySet().every{it instanceof CharSequence} : "Error in module '$key_': toState is a Map, but not all keys are Strings"
+    def toStateMap = toState.clone()
+    def requiredOutputNames = config_.allArguments.findAll{it.required && it.direction == "Output"}.collect{it.plainName}
+    // turn the map into a closure to be used later on
+    toState = { it ->
+      def output = it[1]
+      def state = it[2]
+      assert output instanceof Map : "Error in module '$key_': the output is not a Map"
+      assert state instanceof Map : "Error in module '$key_': the state is not a Map"
+      def extraEntries = toStateMap.collectMany{newkey, origkey ->
+        // check whether newkey corresponds to a required argument
+        if (output.containsKey(origkey)) {
+          [[newkey, output[origkey]]]
+        } else if (!requiredOutputNames.contains(origkey)) {
+          []
+        } else {
+          throw new Exception("Error in module '$key_': toState key '$origkey' not found in current output")
+        }
+      }.collectEntries()
+      state + extraEntries
+    }
+  }
+
+  return toState
+}
+
+// helper file: 'src/main/resources/io/viash/runners/nextflow/workflowFactory/workflowFactory.nf'
+def _debug(workflowArgs, debugKey) {
+  if (workflowArgs.debug) {
+    view { "process '${workflowArgs.key}' $debugKey tuple: $it"  }
+  } else {
+    map { it }
+  }
+}
+
+// depends on: innerWorkflowFactory
+def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
+  def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta)
+  def key_ = workflowArgs["key"]
+  
+  workflow workflowInstance {
+    take: input_
+
+    main:
+    def chModified = input_
+      | checkUniqueIds([:])
+      | _debug(workflowArgs, "input")
+      | map { tuple ->
+        tuple = deepClone(tuple)
+        
+        if (workflowArgs.map) {
+          tuple = workflowArgs.map(tuple)
+        }
+        if (workflowArgs.mapId) {
+          tuple[0] = workflowArgs.mapId(tuple[0])
+        }
+        if (workflowArgs.mapData) {
+          tuple[1] = workflowArgs.mapData(tuple[1])
+        }
+        if (workflowArgs.mapPassthrough) {
+          tuple = tuple.take(2) + workflowArgs.mapPassthrough(tuple.drop(2))
+        }
+
+        // check tuple
+        assert tuple instanceof List : 
+          "Error in module '${key_}': element in channel should be a tuple [id, data, ...otherargs...]\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}"
+        assert tuple.size() >= 2 : 
+          "Error in module '${key_}': expected length of tuple in input channel to be two or greater.\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Found: tuple.size() == ${tuple.size()}"
+        
+        // check id field
+        if (tuple[0] instanceof GString) {
+          tuple[0] = tuple[0].toString()
+        }
+        assert tuple[0] instanceof CharSequence : 
+          "Error in module '${key_}': first element of tuple in channel should be a String\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Found: ${tuple[0]}"
+        
+        // match file to input file
+        if (workflowArgs.auto.simplifyInput && (tuple[1] instanceof Path || tuple[1] instanceof List)) {
+          def inputFiles = meta.config.allArguments
+            .findAll { it.type == "file" && it.direction == "input" }
+          
+          assert inputFiles.size() == 1 : 
+              "Error in module '${key_}' id '${tuple[0]}'.\n" +
+              "  Anonymous file inputs are only allowed when the process has exactly one file input.\n" +
+              "  Expected: inputFiles.size() == 1. Found: inputFiles.size() is ${inputFiles.size()}"
+
+          tuple[1] = [[ inputFiles[0].plainName, tuple[1] ]].collectEntries()
+        }
+
+        // check data field
+        assert tuple[1] instanceof Map : 
+          "Error in module '${key_}' id '${tuple[0]}': second element of tuple in channel should be a Map\n" +
+          "  Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" +
+          "  Expected class: Map. Found: tuple[1].getClass() is ${tuple[1].getClass()}"
+
+        // rename keys of data field in tuple
+        if (workflowArgs.renameKeys) {
+          assert workflowArgs.renameKeys instanceof Map : 
+              "Error renaming data keys in module '${key_}' id '${tuple[0]}'.\n" +
+              "  Example: renameKeys: ['new_key': 'old_key'].\n" +
+              "  Expected class: Map. Found: renameKeys.getClass() is ${workflowArgs.renameKeys.getClass()}"
+          assert tuple[1] instanceof Map : 
+              "Error renaming data keys in module '${key_}' id '${tuple[0]}'.\n" +
+              "  Expected class: Map. Found: tuple[1].getClass() is ${tuple[1].getClass()}"
+
+          // TODO: allow renameKeys to be a function?
+          workflowArgs.renameKeys.each { newKey, oldKey ->
+            assert newKey instanceof CharSequence : 
+              "Error renaming data keys in module '${key_}' id '${tuple[0]}'.\n" +
+              "  Example: renameKeys: ['new_key': 'old_key'].\n" +
+              "  Expected class of newKey: String. Found: newKey.getClass() is ${newKey.getClass()}"
+            assert oldKey instanceof CharSequence : 
+              "Error renaming data keys in module '${key_}' id '${tuple[0]}'.\n" +
+              "  Example: renameKeys: ['new_key': 'old_key'].\n" +
+              "  Expected class of oldKey: String. Found: oldKey.getClass() is ${oldKey.getClass()}"
+            assert tuple[1].containsKey(oldKey) : 
+              "Error renaming data keys in module '${key}' id '${tuple[0]}'.\n" +
+              "  Key '$oldKey' is missing in the data map. tuple[1].keySet() is '${tuple[1].keySet()}'"
+            tuple[1].put(newKey, tuple[1][oldKey])
+          }
+          tuple[1].keySet().removeAll(workflowArgs.renameKeys.collect{ newKey, oldKey -> oldKey })
+        }
+        tuple
+      }
+
+    def chModifiedFiltered = workflowArgs.filter ?
+      chModified | filter{workflowArgs.filter(it)} :
+      chModified
+
+    def chRun = null
+    def chPassthrough = null
+    if (workflowArgs.runIf) {
+      def runIfBranch = chModifiedFiltered.branch{ tup ->
+        run: workflowArgs.runIf(tup[0], tup[1])
+        passthrough: true
+      }
+      chRun = runIfBranch.run
+      chPassthrough = runIfBranch.passthrough
+    } else {
+      chRun = chModifiedFiltered
+      chPassthrough = Channel.empty()
+    }
+
+    def chArgs = workflowArgs.fromState ? 
+      chRun | map{
+        def new_data = workflowArgs.fromState(it.take(2))
+        [it[0], new_data]
+      } :
+      chRun | map {tup -> tup.take(2)}
+
+    // fill in defaults
+    def chArgsWithDefaults = chArgs
+      | map { tuple ->
+        def id_ = tuple[0]
+        def data_ = tuple[1]
+
+        // TODO: could move fromState to here
+
+        // fetch default params from functionality
+        def defaultArgs = meta.config.allArguments
+          .findAll { it.containsKey("default") }
+          .collectEntries { [ it.plainName, it.default ] }
+
+        // fetch overrides in params
+        def paramArgs = meta.config.allArguments
+          .findAll { par ->
+            def argKey = key_ + "__" + par.plainName
+            params.containsKey(argKey)
+          }
+          .collectEntries { [ it.plainName, params[key_ + "__" + it.plainName] ] }
+        
+        // fetch overrides in data
+        def dataArgs = meta.config.allArguments
+          .findAll { data_.containsKey(it.plainName) }
+          .collectEntries { [ it.plainName, data_[it.plainName] ] }
+        
+        // combine params
+        def combinedArgs = defaultArgs + paramArgs + workflowArgs.args + dataArgs
+
+        // remove arguments with explicit null values
+        combinedArgs
+          .removeAll{_, val -> val == null || val == "viash_no_value" || val == "force_null"}
+
+        combinedArgs = _processInputValues(combinedArgs, meta.config, id_, key_)
+
+        [id_, combinedArgs] + tuple.drop(2)
+      }
+
+    // TODO: move some of the _meta.join_id wrangling to the safeJoin() function.
+    def chInitialOutput = chArgsWithDefaults
+      | _debug(workflowArgs, "processed")
+      // run workflow
+      | innerWorkflowFactory(workflowArgs)
+      // check output tuple
+      | map { id_, output_ ->
+
+        // see if output map contains metadata
+        def meta_ =
+          output_ instanceof Map && output_.containsKey("_meta") ? 
+          output_["_meta"] :
+          [:]
+        def join_id = meta_.join_id ?: id_
+        
+        // remove metadata
+        output_ = output_.findAll{k, v -> k != "_meta"}
+
+        // check value types
+        output_ = _processOutputValues(output_, meta.config, id_, key_)
+
+        // simplify output if need be
+        if (workflowArgs.auto.simplifyOutput && output_.size() == 1) {
+          output_ = output_.values()[0]
+        }
+
+        [join_id, id_, output_]
+      }
+      // | view{"chInitialOutput: ${it.take(3)}"}
+
+    // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
+    def chNewState = safeJoin(chInitialOutput, chModifiedFiltered, key_)
+      // input tuple format: [join_id, id, output, prev_state, ...]
+      // output tuple format: [join_id, id, new_state, ...]
+      | map{ tup ->
+        def new_state = workflowArgs.toState(tup.drop(1).take(3))
+        tup.take(2) + [new_state] + tup.drop(4)
+      }
+
+    if (workflowArgs.auto.publish == "state") {
+      def chPublish = chNewState
+        // input tuple format: [join_id, id, new_state, ...]
+        // output tuple format: [join_id, id, new_state]
+        | map{ tup ->
+          tup.take(3)
+        }
+
+      safeJoin(chPublish, chArgsWithDefaults, key_)
+        // input tuple format: [join_id, id, new_state, orig_state, ...]
+        // output tuple format: [id, new_state, orig_state]
+        | map { tup ->
+          tup.drop(1).take(3)
+      }
+        | publishStatesByConfig(key: key_, config: meta.config)
+    }
+
+    // remove join_id and meta
+    chReturn = chNewState
+      | map { tup ->
+        // input tuple format: [join_id, id, new_state, ...]
+        // output tuple format: [id, new_state, ...]
+        tup.drop(1)
+      }
+      | _debug(workflowArgs, "output")
+      | concat(chPassthrough)
+
+    emit: chReturn
+  }
+
+  def wf = workflowInstance.cloneWithName(key_)
+
+  // add factory function
+  wf.metaClass.run = { runArgs ->
+    workflowFactory(runArgs, workflowArgs, meta)
+  }
+  // add config to module for later introspection
+  wf.metaClass.config = meta.config
+
+  return wf
+}
+
+nextflow.enable.dsl=2
+
+// START COMPONENT-SPECIFIC CODE
+
+// create meta object
+meta = [
+  "resources_dir": moduleDir.toRealPath().normalize(),
+  "config": processConfig(readJsonBlob('''{
+  "name" : "qualimap_rnaseq",
+  "namespace" : "qualimap",
+  "version" : "main",
+  "authors" : [
+    {
+      "name" : "Dorien Roosen",
+      "roles" : [
+        "author",
+        "maintainer"
+      ],
+      "info" : {
+        "links" : {
+          "email" : "dorien@data-intuitive.com",
+          "github" : "dorien-er",
+          "linkedin" : "dorien-roosen"
+        },
+        "organizations" : [
+          {
+            "name" : "Data Intuitive",
+            "href" : "https://www.data-intuitive.com",
+            "role" : "Data Scientist"
+          }
+        ]
+      }
+    }
+  ],
+  "argument_groups" : [
+    {
+      "name" : "Input",
+      "arguments" : [
+        {
+          "type" : "file",
+          "name" : "--bam",
+          "description" : "Path to the sequence alignment file in BAM format, produced by a splicing-aware aligner.",
+          "example" : [
+            "alignment.bam"
+          ],
+          "must_exist" : true,
+          "create_parent" : true,
+          "required" : true,
+          "direction" : "input",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        },
+        {
+          "type" : "file",
+          "name" : "--gtf",
+          "description" : "Path to genomic annotations in Ensembl GTF format.",
+          "example" : [
+            "annotations.gtf"
+          ],
+          "must_exist" : true,
+          "create_parent" : true,
+          "required" : true,
+          "direction" : "input",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        }
+      ]
+    },
+    {
+      "name" : "Output",
+      "arguments" : [
+        {
+          "type" : "file",
+          "name" : "--qc_results",
+          "description" : "Text file containing the RNAseq QC results.",
+          "example" : [
+            "rnaseq_qc_results.txt"
+          ],
+          "must_exist" : true,
+          "create_parent" : true,
+          "required" : true,
+          "direction" : "output",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        },
+        {
+          "type" : "file",
+          "name" : "--counts",
+          "description" : "Output file for computed counts.",
+          "must_exist" : true,
+          "create_parent" : true,
+          "required" : false,
+          "direction" : "output",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        },
+        {
+          "type" : "file",
+          "name" : "--report",
+          "description" : "Report output file. Supported formats are PDF or HTML.",
+          "example" : [
+            "report.html"
+          ],
+          "must_exist" : true,
+          "create_parent" : true,
+          "required" : false,
+          "direction" : "output",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        }
+      ]
+    },
+    {
+      "name" : "Optional",
+      "arguments" : [
+        {
+          "type" : "integer",
+          "name" : "--num_pr_bases",
+          "description" : "Number of upstream/downstream nucleotide bases to compute 5'-3' bias (default = 100).",
+          "required" : false,
+          "min" : 1,
+          "direction" : "input",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        },
+        {
+          "type" : "integer",
+          "name" : "--num_tr_bias",
+          "description" : "Number of top highly expressed transcripts to compute 5'-3' bias (default = 1000).",
+          "required" : false,
+          "min" : 1,
+          "direction" : "input",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        },
+        {
+          "type" : "string",
+          "name" : "--algorithm",
+          "description" : "Counting algorithm (uniquely-mapped-reads (default) or proportional).",
+          "required" : false,
+          "choices" : [
+            "uniquely-mapped-reads",
+            "proportional"
+          ],
+          "direction" : "input",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        },
+        {
+          "type" : "string",
+          "name" : "--sequencing_protocol",
+          "description" : "Sequencing library protocol (strand-specific-forward, strand-specific-reverse or non-strand-specific (default)).",
+          "required" : false,
+          "choices" : [
+            "non-strand-specific",
+            "strand-specific-reverse",
+            "strand-specific-forward"
+          ],
+          "direction" : "input",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        },
+        {
+          "type" : "boolean_true",
+          "name" : "--paired",
+          "description" : "Setting this flag for paired-end experiments will result in counting fragments instead of reads.",
+          "direction" : "input"
+        },
+        {
+          "type" : "boolean_true",
+          "name" : "--sorted",
+          "description" : "Setting this flag indicates that the input file is already sorted by name. If flag is not set, additional sorting by name will be performed. Only requiredfor paired-end analysis.",
+          "direction" : "input"
+        },
+        {
+          "type" : "string",
+          "name" : "--java_memory_size",
+          "description" : "maximum Java heap memory size, default = 4G.",
+          "required" : false,
+          "direction" : "input",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        }
+      ]
+    }
+  ],
+  "resources" : [
+    {
+      "type" : "bash_script",
+      "path" : "script.sh",
+      "is_executable" : true
+    }
+  ],
+  "description" : "Qualimap RNA-seq QC reports quality control metrics and bias estimations \nwhich are specific for whole transcriptome sequencing, including reads genomic \norigin, junction analysis, transcript coverage and 5’-3’ bias computation.\n",
+  "test_resources" : [
+    {
+      "type" : "bash_script",
+      "path" : "test.sh",
+      "is_executable" : true
+    },
+    {
+      "type" : "file",
+      "path" : "test_data/"
+    }
+  ],
+  "status" : "enabled",
+  "requirements" : {
+    "commands" : [
+      "ps"
+    ]
+  },
+  "keywords" : [
+    "RNA-seq",
+    "quality control",
+    "QC Report"
+  ],
+  "license" : "GPL-2.0",
+  "references" : {
+    "doi" : [
+      "10.1093/bioinformatics/btv566"
+    ]
+  },
+  "links" : {
+    "repository" : "https://bitbucket.org/kokonech/qualimap/commits/branch/master",
+    "homepage" : "http://qualimap.conesalab.org/",
+    "documentation" : "http://qualimap.conesalab.org/doc_html/analysis.html#rna-seq-qc",
+    "issue_tracker" : "https://bitbucket.org/kokonech/qualimap/issues?status=new&status=open"
+  },
+  "runners" : [
+    {
+      "type" : "executable",
+      "id" : "executable",
+      "docker_setup_strategy" : "ifneedbepullelsecachedbuild"
+    },
+    {
+      "type" : "nextflow",
+      "id" : "nextflow",
+      "directives" : {
+        "tag" : "$id"
+      },
+      "auto" : {
+        "simplifyInput" : true,
+        "simplifyOutput" : false,
+        "transcript" : false,
+        "publish" : false
+      },
+      "config" : {
+        "labels" : {
+          "mem1gb" : "memory = 1000000000.B",
+          "mem2gb" : "memory = 2000000000.B",
+          "mem5gb" : "memory = 5000000000.B",
+          "mem10gb" : "memory = 10000000000.B",
+          "mem20gb" : "memory = 20000000000.B",
+          "mem50gb" : "memory = 50000000000.B",
+          "mem100gb" : "memory = 100000000000.B",
+          "mem200gb" : "memory = 200000000000.B",
+          "mem500gb" : "memory = 500000000000.B",
+          "mem1tb" : "memory = 1000000000000.B",
+          "mem2tb" : "memory = 2000000000000.B",
+          "mem5tb" : "memory = 5000000000000.B",
+          "mem10tb" : "memory = 10000000000000.B",
+          "mem20tb" : "memory = 20000000000000.B",
+          "mem50tb" : "memory = 50000000000000.B",
+          "mem100tb" : "memory = 100000000000000.B",
+          "mem200tb" : "memory = 200000000000000.B",
+          "mem500tb" : "memory = 500000000000000.B",
+          "mem1gib" : "memory = 1073741824.B",
+          "mem2gib" : "memory = 2147483648.B",
+          "mem4gib" : "memory = 4294967296.B",
+          "mem8gib" : "memory = 8589934592.B",
+          "mem16gib" : "memory = 17179869184.B",
+          "mem32gib" : "memory = 34359738368.B",
+          "mem64gib" : "memory = 68719476736.B",
+          "mem128gib" : "memory = 137438953472.B",
+          "mem256gib" : "memory = 274877906944.B",
+          "mem512gib" : "memory = 549755813888.B",
+          "mem1tib" : "memory = 1099511627776.B",
+          "mem2tib" : "memory = 2199023255552.B",
+          "mem4tib" : "memory = 4398046511104.B",
+          "mem8tib" : "memory = 8796093022208.B",
+          "mem16tib" : "memory = 17592186044416.B",
+          "mem32tib" : "memory = 35184372088832.B",
+          "mem64tib" : "memory = 70368744177664.B",
+          "mem128tib" : "memory = 140737488355328.B",
+          "mem256tib" : "memory = 281474976710656.B",
+          "mem512tib" : "memory = 562949953421312.B",
+          "cpu1" : "cpus = 1",
+          "cpu2" : "cpus = 2",
+          "cpu5" : "cpus = 5",
+          "cpu10" : "cpus = 10",
+          "cpu20" : "cpus = 20",
+          "cpu50" : "cpus = 50",
+          "cpu100" : "cpus = 100",
+          "cpu200" : "cpus = 200",
+          "cpu500" : "cpus = 500",
+          "cpu1000" : "cpus = 1000"
+        }
+      },
+      "debug" : false,
+      "container" : "docker"
+    }
+  ],
+  "engines" : [
+    {
+      "type" : "docker",
+      "id" : "docker",
+      "image" : "quay.io/biocontainers/qualimap:2.3--hdfd78af_0",
+      "target_registry" : "images.viash-hub.com",
+      "target_tag" : "main",
+      "namespace_separator" : "/",
+      "setup" : [
+        {
+          "type" : "docker",
+          "run" : [
+            "echo QualiMap: $(qualimap 2>&1 | grep QualiMap | sed 's/^.*QualiMap//') > /var/software_versions.txt\n"
+          ]
+        }
+      ]
+    },
+    {
+      "type" : "native",
+      "id" : "native"
+    }
+  ],
+  "build_info" : {
+    "config" : "/workdir/root/repo/src/qualimap/qualimap_rnaseq/config.vsh.yaml",
+    "runner" : "nextflow",
+    "engine" : "docker|native",
+    "output" : "target/nextflow/qualimap/qualimap_rnaseq",
+    "viash_version" : "0.9.0-RC6",
+    "git_commit" : "766ab6c9c3059004c7c3f205621909b2d8b0b26d",
+    "git_remote" : "https://github.com/viash-hub/biobox"
+  },
+  "package_config" : {
+    "name" : "biobox",
+    "version" : "main",
+    "description" : "A collection of bioinformatics tools for working with sequence data.\n",
+    "viash_version" : "0.9.0-RC6",
+    "source" : "src",
+    "target" : "target",
+    "config_mods" : [
+      ".requirements.commands := ['ps']\n",
+      ".engines += { type: \\"native\\" }",
+      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
+      ".engines[.type == 'docker'].target_tag := 'main'"
+    ],
+    "keywords" : [
+      "bioinformatics",
+      "modules",
+      "sequencing"
+    ],
+    "license" : "MIT",
+    "organization" : "vsh",
+    "links" : {
+      "repository" : "https://github.com/viash-hub/biobox",
+      "issue_tracker" : "https://github.com/viash-hub/biobox/issues"
+    }
+  }
+}'''))
+]
+
+// resolve dependencies dependencies (if any)
+
+
+// inner workflow
+// inner workflow hook
+def innerWorkflowFactory(args) {
+  def rawScript = '''set -e
+tempscript=".viash_script.sh"
+cat > "$tempscript" << VIASHMAIN
+## VIASH START
+# The following code has been auto-generated by Viash.
+$( if [ ! -z ${VIASH_PAR_BAM+x} ]; then echo "${VIASH_PAR_BAM}" | sed "s#'#'\\"'\\"'#g;s#.*#par_bam='&'#" ; else echo "# par_bam="; fi )
+$( if [ ! -z ${VIASH_PAR_GTF+x} ]; then echo "${VIASH_PAR_GTF}" | sed "s#'#'\\"'\\"'#g;s#.*#par_gtf='&'#" ; else echo "# par_gtf="; fi )
+$( if [ ! -z ${VIASH_PAR_QC_RESULTS+x} ]; then echo "${VIASH_PAR_QC_RESULTS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_qc_results='&'#" ; else echo "# par_qc_results="; fi )
+$( if [ ! -z ${VIASH_PAR_COUNTS+x} ]; then echo "${VIASH_PAR_COUNTS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_counts='&'#" ; else echo "# par_counts="; fi )
+$( if [ ! -z ${VIASH_PAR_REPORT+x} ]; then echo "${VIASH_PAR_REPORT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_report='&'#" ; else echo "# par_report="; fi )
+$( if [ ! -z ${VIASH_PAR_NUM_PR_BASES+x} ]; then echo "${VIASH_PAR_NUM_PR_BASES}" | sed "s#'#'\\"'\\"'#g;s#.*#par_num_pr_bases='&'#" ; else echo "# par_num_pr_bases="; fi )
+$( if [ ! -z ${VIASH_PAR_NUM_TR_BIAS+x} ]; then echo "${VIASH_PAR_NUM_TR_BIAS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_num_tr_bias='&'#" ; else echo "# par_num_tr_bias="; fi )
+$( if [ ! -z ${VIASH_PAR_ALGORITHM+x} ]; then echo "${VIASH_PAR_ALGORITHM}" | sed "s#'#'\\"'\\"'#g;s#.*#par_algorithm='&'#" ; else echo "# par_algorithm="; fi )
+$( if [ ! -z ${VIASH_PAR_SEQUENCING_PROTOCOL+x} ]; then echo "${VIASH_PAR_SEQUENCING_PROTOCOL}" | sed "s#'#'\\"'\\"'#g;s#.*#par_sequencing_protocol='&'#" ; else echo "# par_sequencing_protocol="; fi )
+$( if [ ! -z ${VIASH_PAR_PAIRED+x} ]; then echo "${VIASH_PAR_PAIRED}" | sed "s#'#'\\"'\\"'#g;s#.*#par_paired='&'#" ; else echo "# par_paired="; fi )
+$( if [ ! -z ${VIASH_PAR_SORTED+x} ]; then echo "${VIASH_PAR_SORTED}" | sed "s#'#'\\"'\\"'#g;s#.*#par_sorted='&'#" ; else echo "# par_sorted="; fi )
+$( if [ ! -z ${VIASH_PAR_JAVA_MEMORY_SIZE+x} ]; then echo "${VIASH_PAR_JAVA_MEMORY_SIZE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_java_memory_size='&'#" ; else echo "# par_java_memory_size="; 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 )
+$( if [ ! -z ${VIASH_META_EXECUTABLE+x} ]; then echo "${VIASH_META_EXECUTABLE}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_executable='&'#" ; else echo "# meta_executable="; fi )
+$( if [ ! -z ${VIASH_META_CONFIG+x} ]; then echo "${VIASH_META_CONFIG}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_config='&'#" ; else echo "# meta_config="; fi )
+$( if [ ! -z ${VIASH_META_TEMP_DIR+x} ]; then echo "${VIASH_META_TEMP_DIR}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_temp_dir='&'#" ; else echo "# meta_temp_dir="; fi )
+$( if [ ! -z ${VIASH_META_CPUS+x} ]; then echo "${VIASH_META_CPUS}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_cpus='&'#" ; else echo "# meta_cpus="; fi )
+$( if [ ! -z ${VIASH_META_MEMORY_B+x} ]; then echo "${VIASH_META_MEMORY_B}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_memory_b='&'#" ; else echo "# meta_memory_b="; fi )
+$( if [ ! -z ${VIASH_META_MEMORY_KB+x} ]; then echo "${VIASH_META_MEMORY_KB}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_memory_kb='&'#" ; else echo "# meta_memory_kb="; fi )
+$( if [ ! -z ${VIASH_META_MEMORY_MB+x} ]; then echo "${VIASH_META_MEMORY_MB}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_memory_mb='&'#" ; else echo "# meta_memory_mb="; fi )
+$( if [ ! -z ${VIASH_META_MEMORY_GB+x} ]; then echo "${VIASH_META_MEMORY_GB}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_memory_gb='&'#" ; else echo "# meta_memory_gb="; fi )
+$( if [ ! -z ${VIASH_META_MEMORY_TB+x} ]; then echo "${VIASH_META_MEMORY_TB}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_memory_tb='&'#" ; else echo "# meta_memory_tb="; fi )
+$( if [ ! -z ${VIASH_META_MEMORY_PB+x} ]; then echo "${VIASH_META_MEMORY_PB}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_memory_pb='&'#" ; else echo "# meta_memory_pb="; fi )
+$( if [ ! -z ${VIASH_META_MEMORY_KIB+x} ]; then echo "${VIASH_META_MEMORY_KIB}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_memory_kib='&'#" ; else echo "# meta_memory_kib="; fi )
+$( if [ ! -z ${VIASH_META_MEMORY_MIB+x} ]; then echo "${VIASH_META_MEMORY_MIB}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_memory_mib='&'#" ; else echo "# meta_memory_mib="; fi )
+$( if [ ! -z ${VIASH_META_MEMORY_GIB+x} ]; then echo "${VIASH_META_MEMORY_GIB}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_memory_gib='&'#" ; else echo "# meta_memory_gib="; fi )
+$( if [ ! -z ${VIASH_META_MEMORY_TIB+x} ]; then echo "${VIASH_META_MEMORY_TIB}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_memory_tib='&'#" ; else echo "# meta_memory_tib="; fi )
+$( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_memory_pib='&'#" ; else echo "# meta_memory_pib="; fi )
+
+## VIASH END
+#!/bin/bash
+
+set -eo pipefail
+
+tmp_dir=\\$(mktemp -d -p "\\$meta_temp_dir" qualimap_XXXXXXXXX)
+
+# Handle output parameters
+if [ -n "\\$par_report" ]; then
+    outfile=\\$(basename "\\$par_report")
+    report_extension="\\${outfile##*.}"
+fi
+
+if [ -n "\\$par_counts" ]; then
+    counts=\\$(basename "\\$par_counts")
+fi
+
+# disable flags
+[[ "\\$par_paired" == "false" ]] && unset par_paired
+[[ "\\$par_sorted" == "false" ]] && unset par_sorted
+
+# Run qualimap
+qualimap rnaseq \\\\
+    \\${meta_memory_mb:+--java-mem-size=\\${meta_memory_mb}M} \\\\
+    \\${par_algorithm:+--algorithm \\$par_algorithm} \\\\
+    \\${par_sequencing_protocol:+--sequencing-protocol \\$par_sequencing_protocol} \\\\
+    -bam \\$par_bam \\\\
+    -gtf \\$par_gtf \\\\
+    -outdir "\\$tmp_dir" \\\\
+    \\${par_num_pr_bases:+--num-pr-bases \\$par_num_pr_bases} \\\\
+    \\${par_num_tr_bias:+--num-tr-bias \\$par_num_tr_bias} \\\\
+    \\${par_report:+-outformat \\$report_extension} \\\\
+    \\${par_paired:+--paired} \\\\
+    \\${par_sorted:+--sorted} \\\\
+    \\${par_report:+-outfile "\\$outfile"} \\\\
+    \\${par_counts:+-oc "\\$counts"}
+
+# Move output files
+mv "\\$tmp_dir/rnaseq_qc_results.txt" "\\$par_qc_results"
+
+if [ -n "\\$par_report" ] && [ \\$report_extension = "html" ]; then
+    mv "\\$tmp_dir/qualimapReport.html" "\\$par_report"
+fi
+
+if [ -n "\\$par_report" ] && [ \\$report_extension = "pdf" ]; then
+    mv "\\$tmp_dir/\\$outfile" "\\$par_report"
+fi
+
+if [ -n "\\$par_counts" ]; then
+    mv "\\$tmp_dir/\\$counts" "\\$par_counts"
+fi
+VIASHMAIN
+bash "$tempscript"
+'''
+  
+  return vdsl3WorkflowFactory(args, meta, rawScript)
+}
+
+
+
+/**
+  * Generate a workflow for VDSL3 modules.
+  * 
+  * This function is called by the workflowFactory() function.
+  * 
+  * Input channel: [id, input_map]
+  * Output channel: [id, output_map]
+  * 
+  * Internally, this workflow will convert the input channel
+  * to a format which the Nextflow module will be able to handle.
+  */
+def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) {
+  def key = args["key"]
+  def processObj = null
+
+  workflow processWf {
+    take: input_
+    main:
+
+    if (processObj == null) {
+      processObj = _vdsl3ProcessFactory(args, meta, rawScript)
+    }
+    
+    output_ = input_
+      | map { tuple ->
+        def id = tuple[0]
+        def data_ = tuple[1]
+
+        if (workflow.stubRun) {
+          // add id if missing
+          data_ = [id: 'stub'] + data_
+        }
+
+        // process input files separately
+        def inputPaths = meta.config.allArguments
+          .findAll { it.type == "file" && it.direction == "input" }
+          .collect { par ->
+            def val = data_.containsKey(par.plainName) ? data_[par.plainName] : []
+            def inputFiles = []
+            if (val == null) {
+              inputFiles = []
+            } else if (val instanceof List) {
+              inputFiles = val
+            } else if (val instanceof Path) {
+              inputFiles = [ val ]
+            } else {
+              inputFiles = []
+            }
+            if (!workflow.stubRun) {
+              // throw error when an input file doesn't exist
+              inputFiles.each{ file -> 
+                assert file.exists() :
+                  "Error in module '${key}' id '${id}' argument '${par.plainName}'.\n" +
+                  "  Required input file does not exist.\n" +
+                  "  Path: '$file'.\n" +
+                  "  Expected input file to exist"
+              }
+            }
+            inputFiles 
+          } 
+
+        // remove input files
+        def argsExclInputFiles = meta.config.allArguments
+          .findAll { (it.type != "file" || it.direction != "input") && data_.containsKey(it.plainName) }
+          .collectEntries { par ->
+            def parName = par.plainName
+            def val = data_[parName]
+            if (par.multiple && val instanceof Collection) {
+              val = val.join(par.multiple_sep)
+            }
+            if (par.direction == "output" && par.type == "file") {
+              val = val.replaceAll('\\$id', id).replaceAll('\\$key', key)
+            }
+            [parName, val]
+          }
+
+        [ id ] + inputPaths + [ argsExclInputFiles, meta.resources_dir ]
+      }
+      | processObj
+      | map { output ->
+        def outputFiles = meta.config.allArguments
+          .findAll { it.type == "file" && it.direction == "output" }
+          .indexed()
+          .collectEntries{ index, par ->
+            def out = output[index + 1]
+            // strip dummy '.exitcode' file from output (see nextflow-io/nextflow#2678)
+            if (!out instanceof List || out.size() <= 1) {
+              if (par.multiple) {
+                out = []
+              } else {
+                assert !par.required :
+                    "Error in module '${key}' id '${output[0]}' argument '${par.plainName}'.\n" +
+                    "  Required output file is missing"
+                out = null
+              }
+            } else if (out.size() == 2 && !par.multiple) {
+              out = out[1]
+            } else {
+              out = out.drop(1)
+            }
+            [ par.plainName, out ]
+          }
+        
+        // drop null outputs
+        outputFiles.removeAll{it.value == null}
+
+        [ output[0], outputFiles ]
+      }
+    emit: output_
+  }
+
+  return processWf
+}
+
+// depends on: session?
+def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
+  // autodetect process key
+  def wfKey = workflowArgs["key"]
+  def procKeyPrefix = "${wfKey}_process"
+  def scriptMeta = nextflow.script.ScriptMeta.current()
+  def existing = scriptMeta.getProcessNames().findAll{it.startsWith(procKeyPrefix)}
+  def numbers = existing.collect{it.replace(procKeyPrefix, "0").toInteger()}
+  def newNumber = (numbers + [-1]).max() + 1
+
+  def procKey = newNumber == 0 ? procKeyPrefix : "$procKeyPrefix$newNumber"
+
+  if (newNumber > 0) {
+    log.warn "Key for module '${wfKey}' is duplicated.\n",
+      "If you run a component multiple times in the same workflow,\n" +
+      "it's recommended you set a unique key for every call,\n" +
+      "for example: ${wfKey}.run(key: \"foo\")."
+  }
+
+  // subset directives and convert to list of tuples
+  def drctv = workflowArgs.directives
+
+  // TODO: unit test the two commands below
+  // convert publish array into tags
+  def valueToStr = { val ->
+    // ignore closures
+    if (val instanceof CharSequence) {
+      if (!val.matches('^[{].*[}]$')) {
+        '"' + val + '"'
+      } else {
+        val
+      }
+    } else if (val instanceof List) {
+      "[" + val.collect{valueToStr(it)}.join(", ") + "]"
+    } else if (val instanceof Map) {
+      "[" + val.collect{k, v -> k + ": " + valueToStr(v)}.join(", ") + "]"
+    } else {
+      val.inspect()
+    }
+  }
+
+  // multiple entries allowed: label, publishdir
+  def drctvStrs = drctv.collect { key, value ->
+    if (key in ["label", "publishDir"]) {
+      value.collect{ val ->
+        if (val instanceof Map) {
+          "\n$key " + val.collect{ k, v -> k + ": " + valueToStr(v) }.join(", ")
+        } else if (val == null) {
+          ""
+        } else {
+          "\n$key " + valueToStr(val)
+        }
+      }.join()
+    } else if (value instanceof Map) {
+      "\n$key " + value.collect{ k, v -> k + ": " + valueToStr(v) }.join(", ")
+    } else {
+      "\n$key " + valueToStr(value)
+    }
+  }.join()
+
+  def inputPaths = meta.config.allArguments
+    .findAll { it.type == "file" && it.direction == "input" }
+    .collect { ', path(viash_par_' + it.plainName + ', stageAs: "_viash_par/' + it.plainName + '_?/*")' }
+    .join()
+
+  def outputPaths = meta.config.allArguments
+    .findAll { it.type == "file" && it.direction == "output" }
+    .collect { par ->
+      // insert dummy into every output (see nextflow-io/nextflow#2678)
+      if (!par.multiple) {
+        ', path{[".exitcode", args.' + par.plainName + ']}'
+      } else {
+        ', path{[".exitcode"] + args.' + par.plainName + '}'
+      }
+    }
+    .join()
+
+  // TODO: move this functionality somewhere else?
+  if (workflowArgs.auto.transcript) {
+    outputPaths = outputPaths + ', path{[".exitcode", ".command*"]}'
+  } else {
+    outputPaths = outputPaths + ', path{[".exitcode"]}'
+  }
+
+  // create dirs for output files (based on BashWrapper.createParentFiles)
+  def createParentStr = meta.config.allArguments
+    .findAll { it.type == "file" && it.direction == "output" && it.create_parent }
+    .collect { par -> 
+      "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }"
+    }
+    .join("\n")
+
+  // construct inputFileExports
+  def inputFileExports = meta.config.allArguments
+    .findAll { it.type == "file" && it.direction.toLowerCase() == "input" }
+    .collect { par ->
+      def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})"
+      "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}"
+    }
+
+  // NOTE: if using docker, use /tmp instead of tmpDir!
+  def tmpDir = java.nio.file.Paths.get(
+    System.getenv('NXF_TEMP') ?: 
+    System.getenv('VIASH_TEMP') ?: 
+    System.getenv('VIASH_TMPDIR') ?: 
+    System.getenv('VIASH_TEMPDIR') ?: 
+    System.getenv('VIASH_TMP') ?: 
+    System.getenv('TEMP') ?: 
+    System.getenv('TMPDIR') ?: 
+    System.getenv('TEMPDIR') ?:
+    System.getenv('TMP') ?: 
+    '/tmp'
+  ).toAbsolutePath()
+
+  // construct stub
+  def stub = meta.config.allArguments
+    .findAll { it.type == "file" && it.direction == "output" }
+    .collect { par -> 
+      "\${ args.containsKey(\"${par.plainName}\") ? \"touch2 \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"].replace(\"_*\", \"_0\") : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }"
+    }
+    .join("\n")
+
+  // escape script
+  def escapedScript = rawScript.replace('\\', '\\\\').replace('$', '\\$').replace('"""', '\\"\\"\\"')
+
+  // publishdir assert
+  def assertStr = (workflowArgs.auto.publish == true) || workflowArgs.auto.transcript ? 
+    """\nassert task.publishDir.size() > 0: "if auto.publish is true, params.publish_dir needs to be defined.\\n  Example: --publish_dir './output/'" """ :
+    ""
+
+  // generate process string
+  def procStr = 
+  """nextflow.enable.dsl=2
+  |
+  |process $procKey {$drctvStrs
+  |input:
+  |  tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources")
+  |output:
+  |  tuple val("\$id")$outputPaths, optional: true
+  |stub:
+  |\"\"\"
+  |touch2() { mkdir -p "\\\$(dirname "\\\$1")" && touch "\\\$1" ; }
+  |$stub
+  |\"\"\"
+  |script:$assertStr
+  |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') }
+  |def parInject = args
+  |  .findAll{key, value -> value != null}
+  |  .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""}
+  |  .join("\\n")
+  |\"\"\"
+  |# meta exports
+  |export VIASH_META_RESOURCES_DIR="\${resourcesDir}"
+  |export VIASH_META_TEMP_DIR="${['docker', 'podman', 'charliecloud'].any{ it == workflow.containerEngine } ? '/tmp' : tmpDir}"
+  |export VIASH_META_NAME="${meta.config.name}"
+  |# export VIASH_META_EXECUTABLE="\\\$VIASH_META_RESOURCES_DIR/\\\$VIASH_META_NAME"
+  |export VIASH_META_CONFIG="\\\$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
+  |\${task.cpus ? "export VIASH_META_CPUS=\$task.cpus" : "" }
+  |\${task.memory?.bytes != null ? "export VIASH_META_MEMORY_B=\$task.memory.bytes" : "" }
+  |if [ ! -z \\\${VIASH_META_MEMORY_B+x} ]; then
+  |  export VIASH_META_MEMORY_KB=\\\$(( (\\\$VIASH_META_MEMORY_B+999) / 1000 ))
+  |  export VIASH_META_MEMORY_MB=\\\$(( (\\\$VIASH_META_MEMORY_KB+999) / 1000 ))
+  |  export VIASH_META_MEMORY_GB=\\\$(( (\\\$VIASH_META_MEMORY_MB+999) / 1000 ))
+  |  export VIASH_META_MEMORY_TB=\\\$(( (\\\$VIASH_META_MEMORY_GB+999) / 1000 ))
+  |  export VIASH_META_MEMORY_PB=\\\$(( (\\\$VIASH_META_MEMORY_TB+999) / 1000 ))
+  |  export VIASH_META_MEMORY_KIB=\\\$(( (\\\$VIASH_META_MEMORY_B+1023) / 1024 ))
+  |  export VIASH_META_MEMORY_MIB=\\\$(( (\\\$VIASH_META_MEMORY_KIB+1023) / 1024 ))
+  |  export VIASH_META_MEMORY_GIB=\\\$(( (\\\$VIASH_META_MEMORY_MIB+1023) / 1024 ))
+  |  export VIASH_META_MEMORY_TIB=\\\$(( (\\\$VIASH_META_MEMORY_GIB+1023) / 1024 ))
+  |  export VIASH_META_MEMORY_PIB=\\\$(( (\\\$VIASH_META_MEMORY_TIB+1023) / 1024 ))
+  |fi
+  |
+  |# meta synonyms
+  |export VIASH_TEMP="\\\$VIASH_META_TEMP_DIR"
+  |export TEMP_DIR="\\\$VIASH_META_TEMP_DIR"
+  |
+  |# create output dirs if need be
+  |function mkdir_parent {
+  |  for file in "\\\$@"; do 
+  |    mkdir -p "\\\$(dirname "\\\$file")"
+  |  done
+  |}
+  |$createParentStr
+  |
+  |# argument exports${inputFileExports.join()}
+  |\$parInject
+  |
+  |# process script
+  |${escapedScript}
+  |\"\"\"
+  |}
+  |""".stripMargin()
+
+  // TODO: print on debug
+  // if (workflowArgs.debug == true) {
+  //   println("######################\n$procStr\n######################")
+  // }
+
+  // write process to temp file
+  def tempFile = java.nio.file.Files.createTempFile("viash-process-${procKey}-", ".nf")
+  addShutdownHook { java.nio.file.Files.deleteIfExists(tempFile) }
+  tempFile.text = procStr
+
+  // create process from temp file
+  def binding = new nextflow.script.ScriptBinding([:])
+  def session = nextflow.Nextflow.getSession()
+  def parser = new nextflow.script.ScriptParser(session)
+    .setModule(true)
+    .setBinding(binding)
+  def moduleScript = parser.runScript(tempFile)
+    .getScript()
+
+  // register module in meta
+  def module = new nextflow.script.IncludeDef.Module(name: procKey)
+  scriptMeta.addModule(moduleScript, module.name, module.alias)
+
+  // retrieve and return process from meta
+  return scriptMeta.getProcess(procKey)
+}
+
+// defaults
+meta["defaults"] = [
+  // key to be used to trace the process and determine output names
+  key: null,
+
+  // fixed arguments to be passed to script
+  args: [:],
+
+  // default directives
+  directives: readJsonBlob('''{
+  "container" : {
+    "registry" : "images.viash-hub.com",
+    "image" : "vsh/biobox/qualimap/qualimap_rnaseq",
+    "tag" : "main"
+  },
+  "tag" : "$id"
+}'''),
+
+  // auto settings
+  auto: readJsonBlob('''{
+  "simplifyInput" : true,
+  "simplifyOutput" : false,
+  "transcript" : false,
+  "publish" : false
+}'''),
+
+  // Apply a map over the incoming tuple
+  // Example: `{ tup -> [ tup[0], [input: tup[1].output] ] + tup.drop(2) }`
+  map: null,
+
+  // Apply a map over the ID element of a tuple (i.e. the first element)
+  // Example: `{ id -> id + "_foo" }`
+  mapId: null,
+
+  // Apply a map over the data element of a tuple (i.e. the second element)
+  // Example: `{ data -> [ input: data.output ] }`
+  mapData: null,
+
+  // Apply a map over the passthrough elements of a tuple (i.e. the tuple excl. the first two elements)
+  // Example: `{ pt -> pt.drop(1) }`
+  mapPassthrough: null,
+
+  // Filter the channel
+  // Example: `{ tup -> tup[0] == "foo" }`
+  filter: null,
+
+  // Choose whether or not to run the component on the tuple if the condition is true.
+  // Otherwise, the tuple will be passed through.
+  // Example: `{ tup -> tup[0] != "skip_this" }`
+  runIf: null,
+
+  // Rename keys in the data field of the tuple (i.e. the second element)
+  // Will likely be deprecated in favour of `fromState`.
+  // Example: `[ "new_key": "old_key" ]`
+  renameKeys: null,
+
+  // Fetch data from the state and pass it to the module without altering the current state.
+  // 
+  // `fromState` should be `null`, `List[String]`, `Map[String, String]` or a function. 
+  // 
+  // - If it is `null`, the state will be passed to the module as is.
+  // - If it is a `List[String]`, the data will be the values of the state at the given keys.
+  // - If it is a `Map[String, String]`, the data will be the values of the state at the given keys, with the keys renamed according to the map.
+  // - If it is a function, the tuple (`[id, state]`) in the channel will be passed to the function, and the result will be used as the data.
+  // 
+  // Example: `{ id, state -> [input: state.fastq_file] }`
+  // Default: `null`
+  fromState: null,
+
+  // Determine how the state should be updated after the module has been run.
+  // 
+  // `toState` should be `null`, `List[String]`, `Map[String, String]` or a function.
+  // 
+  // - If it is `null`, the state will be replaced with the output of the module.
+  // - If it is a `List[String]`, the state will be updated with the values of the data at the given keys.
+  // - If it is a `Map[String, String]`, the state will be updated with the values of the data at the given keys, with the keys renamed according to the map.
+  // - If it is a function, a tuple (`[id, output, state]`) will be passed to the function, and the result will be used as the new state.
+  //
+  // Example: `{ id, output, state -> state + [counts: state.output] }`
+  // Default: `{ id, output, state -> output }`
+  toState: null,
+
+  // Whether or not to print debug messages
+  // Default: `false`
+  debug: false
+]
+
+// initialise default workflow
+meta["workflow"] = workflowFactory([key: meta.config.name], meta.defaults, meta)
+
+// add workflow to environment
+nextflow.script.ScriptMeta.current().addDefinition(meta.workflow)
+
+// anonymous workflow for running this module as a standalone
+workflow {
+  // add id argument if it's not already in the config
+  // TODO: deep copy
+  def newConfig = deepClone(meta.config)
+  def newParams = deepClone(params)
+
+  def argsContainsId = newConfig.allArguments.any{it.plainName == "id"}
+  if (!argsContainsId) {
+    def idArg = [
+      'name': '--id',
+      'required': false,
+      'type': 'string',
+      'description': 'A unique id for every entry.',
+      'multiple': false
+    ]
+    newConfig.arguments.add(0, idArg)
+    newConfig = processConfig(newConfig)
+  }
+  if (!newParams.containsKey("id")) {
+    newParams.id = "run"
+  }
+
+  helpMessage(newConfig)
+
+  channelFromParams(newParams, newConfig)
+    // make sure id is not in the state if id is not in the args
+    | map {id, state ->
+      if (!argsContainsId) {
+        [id, state.findAll{k, v -> k != "id"}]
+      } else {
+        [id, state]
+      }
+    }
+    | meta.workflow.run(
+      auto: [ publish: "state" ]
+    )
+}
+
+// END COMPONENT-SPECIFIC CODE
diff --git a/target/nextflow/qualimap/qualimap_rnaseq/nextflow.config b/target/nextflow/qualimap/qualimap_rnaseq/nextflow.config
new file mode 100644
index 00000000..d3ec32b2
--- /dev/null
+++ b/target/nextflow/qualimap/qualimap_rnaseq/nextflow.config
@@ -0,0 +1,126 @@
+manifest {
+  name = 'qualimap/qualimap_rnaseq'
+  mainScript = 'main.nf'
+  nextflowVersion = '!>=20.12.1-edge'
+  version = 'main'
+  description = 'Qualimap RNA-seq QC reports quality control metrics and bias estimations \nwhich are specific for whole transcriptome sequencing, including reads genomic \norigin, junction analysis, transcript coverage and 5’-3’ bias computation.\n'
+  author = 'Dorien Roosen'
+}
+
+process.container = 'nextflow/bash:latest'
+
+// detect tempdir
+tempDir = java.nio.file.Paths.get(
+  System.getenv('NXF_TEMP') ?:
+    System.getenv('VIASH_TEMP') ?: 
+    System.getenv('TEMPDIR') ?: 
+    System.getenv('TMPDIR') ?: 
+    '/tmp'
+).toAbsolutePath()
+
+profiles {
+  no_publish {
+    process {
+      withName: '.*' {
+        publishDir = [
+          enabled: false
+        ]
+      }
+    }
+  }
+  mount_temp {
+    docker.temp            = tempDir
+    podman.temp            = tempDir
+    charliecloud.temp      = tempDir
+  }
+  docker {
+    docker.enabled         = true
+    // docker.userEmulation   = true
+    singularity.enabled    = false
+    podman.enabled         = false
+    shifter.enabled        = false
+    charliecloud.enabled   = false
+  }
+  singularity {
+    singularity.enabled    = true
+    singularity.autoMounts = true
+    docker.enabled         = false
+    podman.enabled         = false
+    shifter.enabled        = false
+    charliecloud.enabled   = false
+  }
+  podman {
+    podman.enabled         = true
+    docker.enabled         = false
+    singularity.enabled    = false
+    shifter.enabled        = false
+    charliecloud.enabled   = false
+  }
+  shifter {
+    shifter.enabled        = true
+    docker.enabled         = false
+    singularity.enabled    = false
+    podman.enabled         = false
+    charliecloud.enabled   = false
+  }
+  charliecloud {
+    charliecloud.enabled   = true
+    docker.enabled         = false
+    singularity.enabled    = false
+    podman.enabled         = false
+    shifter.enabled        = false
+  }
+}
+
+process{
+  withLabel: mem1gb { memory = 1000000000.B }
+  withLabel: mem2gb { memory = 2000000000.B }
+  withLabel: mem5gb { memory = 5000000000.B }
+  withLabel: mem10gb { memory = 10000000000.B }
+  withLabel: mem20gb { memory = 20000000000.B }
+  withLabel: mem50gb { memory = 50000000000.B }
+  withLabel: mem100gb { memory = 100000000000.B }
+  withLabel: mem200gb { memory = 200000000000.B }
+  withLabel: mem500gb { memory = 500000000000.B }
+  withLabel: mem1tb { memory = 1000000000000.B }
+  withLabel: mem2tb { memory = 2000000000000.B }
+  withLabel: mem5tb { memory = 5000000000000.B }
+  withLabel: mem10tb { memory = 10000000000000.B }
+  withLabel: mem20tb { memory = 20000000000000.B }
+  withLabel: mem50tb { memory = 50000000000000.B }
+  withLabel: mem100tb { memory = 100000000000000.B }
+  withLabel: mem200tb { memory = 200000000000000.B }
+  withLabel: mem500tb { memory = 500000000000000.B }
+  withLabel: mem1gib { memory = 1073741824.B }
+  withLabel: mem2gib { memory = 2147483648.B }
+  withLabel: mem4gib { memory = 4294967296.B }
+  withLabel: mem8gib { memory = 8589934592.B }
+  withLabel: mem16gib { memory = 17179869184.B }
+  withLabel: mem32gib { memory = 34359738368.B }
+  withLabel: mem64gib { memory = 68719476736.B }
+  withLabel: mem128gib { memory = 137438953472.B }
+  withLabel: mem256gib { memory = 274877906944.B }
+  withLabel: mem512gib { memory = 549755813888.B }
+  withLabel: mem1tib { memory = 1099511627776.B }
+  withLabel: mem2tib { memory = 2199023255552.B }
+  withLabel: mem4tib { memory = 4398046511104.B }
+  withLabel: mem8tib { memory = 8796093022208.B }
+  withLabel: mem16tib { memory = 17592186044416.B }
+  withLabel: mem32tib { memory = 35184372088832.B }
+  withLabel: mem64tib { memory = 70368744177664.B }
+  withLabel: mem128tib { memory = 140737488355328.B }
+  withLabel: mem256tib { memory = 281474976710656.B }
+  withLabel: mem512tib { memory = 562949953421312.B }
+  withLabel: cpu1 { cpus = 1 }
+  withLabel: cpu2 { cpus = 2 }
+  withLabel: cpu5 { cpus = 5 }
+  withLabel: cpu10 { cpus = 10 }
+  withLabel: cpu20 { cpus = 20 }
+  withLabel: cpu50 { cpus = 50 }
+  withLabel: cpu100 { cpus = 100 }
+  withLabel: cpu200 { cpus = 200 }
+  withLabel: cpu500 { cpus = 500 }
+  withLabel: cpu1000 { cpus = 1000 }
+}
+
+
diff --git a/target/nextflow/qualimap/qualimap_rnaseq/nextflow_schema.json b/target/nextflow/qualimap/qualimap_rnaseq/nextflow_schema.json
new file mode 100644
index 00000000..aaf2e054
--- /dev/null
+++ b/target/nextflow/qualimap/qualimap_rnaseq/nextflow_schema.json
@@ -0,0 +1,217 @@
+{
+"$schema": "http://json-schema.org/draft-07/schema",
+"title": "qualimap_rnaseq",
+"description": "Qualimap RNA-seq QC reports quality control metrics and bias estimations \nwhich are specific for whole transcriptome sequencing, including reads genomic \norigin, junction analysis, transcript coverage and 5\u2019-3\u2019 bias computation.\n",
+"type": "object",
+"definitions": {
+
+    
+    
+    "input" : {
+    "title": "Input",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "bam": {
+                "type":
+                "string",
+                "description": "Type: `file`, required, example: `alignment.bam`. Path to the sequence alignment file in BAM format, produced by a splicing-aware aligner",
+                "help_text": "Type: `file`, required, example: `alignment.bam`. Path to the sequence alignment file in BAM format, produced by a splicing-aware aligner."
+            
+            }
+    
+
+        ,
+                "gtf": {
+                "type":
+                "string",
+                "description": "Type: `file`, required, example: `annotations.gtf`. Path to genomic annotations in Ensembl GTF format",
+                "help_text": "Type: `file`, required, example: `annotations.gtf`. Path to genomic annotations in Ensembl GTF format."
+            
+            }
+    
+
+}
+},
+    
+    
+    "output" : {
+    "title": "Output",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "qc_results": {
+                "type":
+                "string",
+                "description": "Type: `file`, required, default: `$id.$key.qc_results.txt`, example: `rnaseq_qc_results.txt`. Text file containing the RNAseq QC results",
+                "help_text": "Type: `file`, required, default: `$id.$key.qc_results.txt`, example: `rnaseq_qc_results.txt`. Text file containing the RNAseq QC results."
+            ,
+                "default": "$id.$key.qc_results.txt"
+            }
+    
+
+        ,
+                "counts": {
+                "type":
+                "string",
+                "description": "Type: `file`, default: `$id.$key.counts.counts`. Output file for computed counts",
+                "help_text": "Type: `file`, default: `$id.$key.counts.counts`. Output file for computed counts."
+            ,
+                "default": "$id.$key.counts.counts"
+            }
+    
+
+        ,
+                "report": {
+                "type":
+                "string",
+                "description": "Type: `file`, default: `$id.$key.report.html`, example: `report.html`. Report output file",
+                "help_text": "Type: `file`, default: `$id.$key.report.html`, example: `report.html`. Report output file. Supported formats are PDF or HTML."
+            ,
+                "default": "$id.$key.report.html"
+            }
+    
+
+}
+},
+    
+    
+    "optional" : {
+    "title": "Optional",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "num_pr_bases": {
+                "type":
+                "integer",
+                "description": "Type: `integer`. Number of upstream/downstream nucleotide bases to compute 5\u0027-3\u0027 bias (default = 100)",
+                "help_text": "Type: `integer`. Number of upstream/downstream nucleotide bases to compute 5\u0027-3\u0027 bias (default = 100)."
+            
+            }
+    
+
+        ,
+                "num_tr_bias": {
+                "type":
+                "integer",
+                "description": "Type: `integer`. Number of top highly expressed transcripts to compute 5\u0027-3\u0027 bias (default = 1000)",
+                "help_text": "Type: `integer`. Number of top highly expressed transcripts to compute 5\u0027-3\u0027 bias (default = 1000)."
+            
+            }
+    
+
+        ,
+                "algorithm": {
+                "type":
+                "string",
+                "description": "Type: `string`, choices: ``uniquely-mapped-reads`, `proportional``. Counting algorithm (uniquely-mapped-reads (default) or proportional)",
+                "help_text": "Type: `string`, choices: ``uniquely-mapped-reads`, `proportional``. Counting algorithm (uniquely-mapped-reads (default) or proportional).",
+                "enum": ["uniquely-mapped-reads", "proportional"]
+            
+            
+            }
+    
+
+        ,
+                "sequencing_protocol": {
+                "type":
+                "string",
+                "description": "Type: `string`, choices: ``non-strand-specific`, `strand-specific-reverse`, `strand-specific-forward``. Sequencing library protocol (strand-specific-forward, strand-specific-reverse or non-strand-specific (default))",
+                "help_text": "Type: `string`, choices: ``non-strand-specific`, `strand-specific-reverse`, `strand-specific-forward``. Sequencing library protocol (strand-specific-forward, strand-specific-reverse or non-strand-specific (default)).",
+                "enum": ["non-strand-specific", "strand-specific-reverse", "strand-specific-forward"]
+            
+            
+            }
+    
+
+        ,
+                "paired": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Setting this flag for paired-end experiments will result in counting fragments instead of reads",
+                "help_text": "Type: `boolean_true`, default: `false`. Setting this flag for paired-end experiments will result in counting fragments instead of reads."
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "sorted": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Setting this flag indicates that the input file is already sorted by name",
+                "help_text": "Type: `boolean_true`, default: `false`. Setting this flag indicates that the input file is already sorted by name. If flag is not set, additional sorting by name will be performed. Only requiredfor paired-end analysis."
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "java_memory_size": {
+                "type":
+                "string",
+                "description": "Type: `string`. maximum Java heap memory size, default = 4G",
+                "help_text": "Type: `string`. maximum Java heap memory size, default = 4G."
+            
+            }
+    
+
+}
+},
+    
+    
+    "nextflow input-output arguments" : {
+    "title": "Nextflow input-output arguments",
+    "type": "object",
+    "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
+    "properties": {
+    
+        
+                "publish_dir": {
+                "type":
+                "string",
+                "description": "Type: `string`, required, example: `output/`. Path to an output directory",
+                "help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
+            
+            }
+    
+
+        ,
+                "param_list": {
+                "type":
+                "string",
+                "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
+                "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.",
+                "hidden": true
+            
+            }
+    
+
+}
+}
+},
+"allOf": [
+
+    {
+    "$ref": "#/definitions/input"
+    },
+
+    {
+    "$ref": "#/definitions/output"
+    },
+
+    {
+    "$ref": "#/definitions/optional"
+    },
+
+    {
+    "$ref": "#/definitions/nextflow input-output arguments"
+    }
+]
+}
diff --git a/target/nextflow/salmon/salmon_index/.config.vsh.yaml b/target/nextflow/salmon/salmon_index/.config.vsh.yaml
index c3c40390..7f9b4ff5 100644
--- a/target/nextflow/salmon/salmon_index/.config.vsh.yaml
+++ b/target/nextflow/salmon/salmon_index/.config.vsh.yaml
@@ -277,7 +277,7 @@ build_info:
   output: "target/nextflow/salmon/salmon_index"
   executable: "target/nextflow/salmon/salmon_index/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/salmon/salmon_index/main.nf b/target/nextflow/salmon/salmon_index/main.nf
index da9c2453..258d4cb5 100644
--- a/target/nextflow/salmon/salmon_index/main.nf
+++ b/target/nextflow/salmon/salmon_index/main.nf
@@ -3103,7 +3103,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/salmon/salmon_index",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "923a6da3898a832df96a0e17c8a3b74c2806d939",
+    "git_commit" : "766ab6c9c3059004c7c3f205621909b2d8b0b26d",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/salmon/salmon_quant/.config.vsh.yaml b/target/nextflow/salmon/salmon_quant/.config.vsh.yaml
index c4bd21d0..55af9657 100644
--- a/target/nextflow/salmon/salmon_quant/.config.vsh.yaml
+++ b/target/nextflow/salmon/salmon_quant/.config.vsh.yaml
@@ -1173,7 +1173,7 @@ build_info:
   output: "target/nextflow/salmon/salmon_quant"
   executable: "target/nextflow/salmon/salmon_quant/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/salmon/salmon_quant/main.nf b/target/nextflow/salmon/salmon_quant/main.nf
index a6fe62da..804e441f 100644
--- a/target/nextflow/salmon/salmon_quant/main.nf
+++ b/target/nextflow/salmon/salmon_quant/main.nf
@@ -3938,7 +3938,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/salmon/salmon_quant",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "923a6da3898a832df96a0e17c8a3b74c2806d939",
+    "git_commit" : "766ab6c9c3059004c7c3f205621909b2d8b0b26d",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/samtools/samtools_collate/.config.vsh.yaml b/target/nextflow/samtools/samtools_collate/.config.vsh.yaml
index b8a18346..d1b99575 100644
--- a/target/nextflow/samtools/samtools_collate/.config.vsh.yaml
+++ b/target/nextflow/samtools/samtools_collate/.config.vsh.yaml
@@ -264,7 +264,7 @@ build_info:
   output: "target/nextflow/samtools/samtools_collate"
   executable: "target/nextflow/samtools/samtools_collate/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/samtools/samtools_collate/main.nf b/target/nextflow/samtools/samtools_collate/main.nf
index faedab07..f44604c5 100644
--- a/target/nextflow/samtools/samtools_collate/main.nf
+++ b/target/nextflow/samtools/samtools_collate/main.nf
@@ -3114,7 +3114,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_collate",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "923a6da3898a832df96a0e17c8a3b74c2806d939",
+    "git_commit" : "766ab6c9c3059004c7c3f205621909b2d8b0b26d",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml b/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml
index f31dedcc..fbf79dc7 100644
--- a/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml
+++ b/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml
@@ -243,7 +243,7 @@ build_info:
   output: "target/nextflow/samtools/samtools_faidx"
   executable: "target/nextflow/samtools/samtools_faidx/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/samtools/samtools_faidx/main.nf b/target/nextflow/samtools/samtools_faidx/main.nf
index ec97ef94..ee0259f6 100644
--- a/target/nextflow/samtools/samtools_faidx/main.nf
+++ b/target/nextflow/samtools/samtools_faidx/main.nf
@@ -3086,7 +3086,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_faidx",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "923a6da3898a832df96a0e17c8a3b74c2806d939",
+    "git_commit" : "766ab6c9c3059004c7c3f205621909b2d8b0b26d",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml b/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml
index db020266..a3e5b79b 100644
--- a/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml
+++ b/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml
@@ -433,7 +433,7 @@ build_info:
   output: "target/nextflow/samtools/samtools_fasta"
   executable: "target/nextflow/samtools/samtools_fasta/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/samtools/samtools_fasta/main.nf b/target/nextflow/samtools/samtools_fasta/main.nf
index f87fbf7c..e23b0258 100644
--- a/target/nextflow/samtools/samtools_fasta/main.nf
+++ b/target/nextflow/samtools/samtools_fasta/main.nf
@@ -3278,7 +3278,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_fasta",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "923a6da3898a832df96a0e17c8a3b74c2806d939",
+    "git_commit" : "766ab6c9c3059004c7c3f205621909b2d8b0b26d",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml b/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml
index 33781464..4d1aa8fe 100644
--- a/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml
+++ b/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml
@@ -433,7 +433,7 @@ build_info:
   output: "target/nextflow/samtools/samtools_fastq"
   executable: "target/nextflow/samtools/samtools_fastq/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/samtools/samtools_fastq/main.nf b/target/nextflow/samtools/samtools_fastq/main.nf
index 6f8c00f8..77d4f129 100644
--- a/target/nextflow/samtools/samtools_fastq/main.nf
+++ b/target/nextflow/samtools/samtools_fastq/main.nf
@@ -3278,7 +3278,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_fastq",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "923a6da3898a832df96a0e17c8a3b74c2806d939",
+    "git_commit" : "766ab6c9c3059004c7c3f205621909b2d8b0b26d",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml b/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml
index 9efe148e..f0c69b30 100644
--- a/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml
+++ b/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml
@@ -173,7 +173,7 @@ build_info:
   output: "target/nextflow/samtools/samtools_flagstat"
   executable: "target/nextflow/samtools/samtools_flagstat/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/samtools/samtools_flagstat/main.nf b/target/nextflow/samtools/samtools_flagstat/main.nf
index 37621953..683f8c50 100644
--- a/target/nextflow/samtools/samtools_flagstat/main.nf
+++ b/target/nextflow/samtools/samtools_flagstat/main.nf
@@ -3002,7 +3002,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_flagstat",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "923a6da3898a832df96a0e17c8a3b74c2806d939",
+    "git_commit" : "766ab6c9c3059004c7c3f205621909b2d8b0b26d",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml b/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml
index da949b68..c7c917ef 100644
--- a/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml
+++ b/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml
@@ -183,7 +183,7 @@ build_info:
   output: "target/nextflow/samtools/samtools_idxstats"
   executable: "target/nextflow/samtools/samtools_idxstats/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/samtools/samtools_idxstats/main.nf b/target/nextflow/samtools/samtools_idxstats/main.nf
index 8bee0da7..7bfe9ea1 100644
--- a/target/nextflow/samtools/samtools_idxstats/main.nf
+++ b/target/nextflow/samtools/samtools_idxstats/main.nf
@@ -3014,7 +3014,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_idxstats",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "923a6da3898a832df96a0e17c8a3b74c2806d939",
+    "git_commit" : "766ab6c9c3059004c7c3f205621909b2d8b0b26d",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/samtools/samtools_index/.config.vsh.yaml b/target/nextflow/samtools/samtools_index/.config.vsh.yaml
index 3cae8bb3..7b3f46a5 100644
--- a/target/nextflow/samtools/samtools_index/.config.vsh.yaml
+++ b/target/nextflow/samtools/samtools_index/.config.vsh.yaml
@@ -189,7 +189,7 @@ build_info:
   output: "target/nextflow/samtools/samtools_index"
   executable: "target/nextflow/samtools/samtools_index/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/samtools/samtools_index/main.nf b/target/nextflow/samtools/samtools_index/main.nf
index b84216a2..38e42575 100644
--- a/target/nextflow/samtools/samtools_index/main.nf
+++ b/target/nextflow/samtools/samtools_index/main.nf
@@ -3027,7 +3027,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_index",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "923a6da3898a832df96a0e17c8a3b74c2806d939",
+    "git_commit" : "766ab6c9c3059004c7c3f205621909b2d8b0b26d",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/samtools/samtools_sort/.config.vsh.yaml b/target/nextflow/samtools/samtools_sort/.config.vsh.yaml
index ce1e3474..0db5d84f 100644
--- a/target/nextflow/samtools/samtools_sort/.config.vsh.yaml
+++ b/target/nextflow/samtools/samtools_sort/.config.vsh.yaml
@@ -332,7 +332,7 @@ build_info:
   output: "target/nextflow/samtools/samtools_sort"
   executable: "target/nextflow/samtools/samtools_sort/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/samtools/samtools_sort/main.nf b/target/nextflow/samtools/samtools_sort/main.nf
index 97e332b2..21332804 100644
--- a/target/nextflow/samtools/samtools_sort/main.nf
+++ b/target/nextflow/samtools/samtools_sort/main.nf
@@ -3199,7 +3199,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_sort",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "923a6da3898a832df96a0e17c8a3b74c2806d939",
+    "git_commit" : "766ab6c9c3059004c7c3f205621909b2d8b0b26d",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/samtools/samtools_stats/.config.vsh.yaml b/target/nextflow/samtools/samtools_stats/.config.vsh.yaml
index 1c9c56a3..a1dd9ffc 100644
--- a/target/nextflow/samtools/samtools_stats/.config.vsh.yaml
+++ b/target/nextflow/samtools/samtools_stats/.config.vsh.yaml
@@ -401,7 +401,7 @@ build_info:
   output: "target/nextflow/samtools/samtools_stats"
   executable: "target/nextflow/samtools/samtools_stats/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/samtools/samtools_stats/main.nf b/target/nextflow/samtools/samtools_stats/main.nf
index a35cc33c..23b8bfe5 100644
--- a/target/nextflow/samtools/samtools_stats/main.nf
+++ b/target/nextflow/samtools/samtools_stats/main.nf
@@ -3269,7 +3269,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_stats",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "923a6da3898a832df96a0e17c8a3b74c2806d939",
+    "git_commit" : "766ab6c9c3059004c7c3f205621909b2d8b0b26d",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/samtools/samtools_view/.config.vsh.yaml b/target/nextflow/samtools/samtools_view/.config.vsh.yaml
index e5ca47ac..265cd362 100644
--- a/target/nextflow/samtools/samtools_view/.config.vsh.yaml
+++ b/target/nextflow/samtools/samtools_view/.config.vsh.yaml
@@ -665,7 +665,7 @@ build_info:
   output: "target/nextflow/samtools/samtools_view"
   executable: "target/nextflow/samtools/samtools_view/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/samtools/samtools_view/main.nf b/target/nextflow/samtools/samtools_view/main.nf
index b759894c..e2fd8c6e 100644
--- a/target/nextflow/samtools/samtools_view/main.nf
+++ b/target/nextflow/samtools/samtools_view/main.nf
@@ -3450,7 +3450,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/samtools/samtools_view",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "923a6da3898a832df96a0e17c8a3b74c2806d939",
+    "git_commit" : "766ab6c9c3059004c7c3f205621909b2d8b0b26d",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml b/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml
index c4df2473..5377b3c3 100644
--- a/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml
+++ b/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml
@@ -173,7 +173,7 @@ build_info:
   output: "target/nextflow/seqtk/seqtk_sample"
   executable: "target/nextflow/seqtk/seqtk_sample/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/seqtk/seqtk_sample/main.nf b/target/nextflow/seqtk/seqtk_sample/main.nf
index 7a86d26e..c2b91505 100644
--- a/target/nextflow/seqtk/seqtk_sample/main.nf
+++ b/target/nextflow/seqtk/seqtk_sample/main.nf
@@ -3004,7 +3004,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/seqtk/seqtk_sample",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "923a6da3898a832df96a0e17c8a3b74c2806d939",
+    "git_commit" : "766ab6c9c3059004c7c3f205621909b2d8b0b26d",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml b/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml
index 7ffb233f..e6f8dd4b 100644
--- a/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml
+++ b/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml
@@ -196,7 +196,7 @@ build_info:
   output: "target/nextflow/seqtk/seqtk_subseq"
   executable: "target/nextflow/seqtk/seqtk_subseq/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/seqtk/seqtk_subseq/main.nf b/target/nextflow/seqtk/seqtk_subseq/main.nf
index 90a9d159..8d2a6a62 100644
--- a/target/nextflow/seqtk/seqtk_subseq/main.nf
+++ b/target/nextflow/seqtk/seqtk_subseq/main.nf
@@ -3034,7 +3034,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/seqtk/seqtk_subseq",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "923a6da3898a832df96a0e17c8a3b74c2806d939",
+    "git_commit" : "766ab6c9c3059004c7c3f205621909b2d8b0b26d",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/star/star_align_reads/.config.vsh.yaml b/target/nextflow/star/star_align_reads/.config.vsh.yaml
index 3fffef0c..baafcdb4 100644
--- a/target/nextflow/star/star_align_reads/.config.vsh.yaml
+++ b/target/nextflow/star/star_align_reads/.config.vsh.yaml
@@ -2663,7 +2663,7 @@ build_info:
   output: "target/nextflow/star/star_align_reads"
   executable: "target/nextflow/star/star_align_reads/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/star/star_align_reads/main.nf b/target/nextflow/star/star_align_reads/main.nf
index f2cf1f06..e3d4fd07 100644
--- a/target/nextflow/star/star_align_reads/main.nf
+++ b/target/nextflow/star/star_align_reads/main.nf
@@ -5917,7 +5917,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/star/star_align_reads",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "923a6da3898a832df96a0e17c8a3b74c2806d939",
+    "git_commit" : "766ab6c9c3059004c7c3f205621909b2d8b0b26d",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/star/star_genome_generate/.config.vsh.yaml b/target/nextflow/star/star_genome_generate/.config.vsh.yaml
index c57b3fbd..a3aab66a 100644
--- a/target/nextflow/star/star_genome_generate/.config.vsh.yaml
+++ b/target/nextflow/star/star_genome_generate/.config.vsh.yaml
@@ -333,7 +333,7 @@ build_info:
   output: "target/nextflow/star/star_genome_generate"
   executable: "target/nextflow/star/star_genome_generate/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/star/star_genome_generate/main.nf b/target/nextflow/star/star_genome_generate/main.nf
index 7b51a94a..a6445ebc 100644
--- a/target/nextflow/star/star_genome_generate/main.nf
+++ b/target/nextflow/star/star_genome_generate/main.nf
@@ -3169,7 +3169,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/star/star_genome_generate",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "923a6da3898a832df96a0e17c8a3b74c2806d939",
+    "git_commit" : "766ab6c9c3059004c7c3f205621909b2d8b0b26d",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/umi_tools/umi_tools_dedup/.config.vsh.yaml b/target/nextflow/umi_tools/umi_tools_dedup/.config.vsh.yaml
index 535e9990..f5bbbfcb 100644
--- a/target/nextflow/umi_tools/umi_tools_dedup/.config.vsh.yaml
+++ b/target/nextflow/umi_tools/umi_tools_dedup/.config.vsh.yaml
@@ -611,7 +611,7 @@ build_info:
   output: "target/nextflow/umi_tools/umi_tools_dedup"
   executable: "target/nextflow/umi_tools/umi_tools_dedup/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/umi_tools/umi_tools_dedup/main.nf b/target/nextflow/umi_tools/umi_tools_dedup/main.nf
index f5998763..6bc98626 100644
--- a/target/nextflow/umi_tools/umi_tools_dedup/main.nf
+++ b/target/nextflow/umi_tools/umi_tools_dedup/main.nf
@@ -3461,7 +3461,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/umi_tools/umi_tools_dedup",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "923a6da3898a832df96a0e17c8a3b74c2806d939",
+    "git_commit" : "766ab6c9c3059004c7c3f205621909b2d8b0b26d",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {
diff --git a/target/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml b/target/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml
index 5749c250..40e11658 100644
--- a/target/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml
+++ b/target/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml
@@ -449,7 +449,7 @@ build_info:
   output: "target/nextflow/umi_tools/umi_tools_extract"
   executable: "target/nextflow/umi_tools/umi_tools_extract/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "923a6da3898a832df96a0e17c8a3b74c2806d939"
+  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
   git_remote: "https://github.com/viash-hub/biobox"
 package_config:
   name: "biobox"
diff --git a/target/nextflow/umi_tools/umi_tools_extract/main.nf b/target/nextflow/umi_tools/umi_tools_extract/main.nf
index 1677555e..3198d42f 100644
--- a/target/nextflow/umi_tools/umi_tools_extract/main.nf
+++ b/target/nextflow/umi_tools/umi_tools_extract/main.nf
@@ -3290,7 +3290,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/umi_tools/umi_tools_extract",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "923a6da3898a832df96a0e17c8a3b74c2806d939",
+    "git_commit" : "766ab6c9c3059004c7c3f205621909b2d8b0b26d",
     "git_remote" : "https://github.com/viash-hub/biobox"
   },
   "package_config" : {