Build branch main with version main (766ab6c)

Build pipeline: viash-hub.biobox.main-lpdjj Source commit: 766ab6c9c3 Source message: Qualimap rnaseq (#74) * first version * complete script for qualimap * add escaping character before leading hashtag (#50) * add escaping character before leading hashtag * update changelog * Update CHANGELOG.md Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com> * replace escaping \ by \\ --------- Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com> * Samtools collate (#49) * initial commit dedup * Revert "initial commit dedup" This reverts commit 38f586bec0ac9e4312b016e29c3aa0bd53f292b2. * Initial commit, whole component is functional * Update viash (#51) * update viash * update readme * update changelog * update changelog * fix incorrect heading detection * update again * clean up readme * Samtools view (#48) * initial commit dedup * Revert "initial commit dedup" This reverts commit 38f586bec0ac9e4312b016e29c3aa0bd53f292b2. * initial version with a few tests, script, and config file * update changelog, add one test * add a 4th test, fix option names in the script * Fix name of component in config * remove option named with a number * add must_exist to input file argument * removed "default: null" from one of the arguments in config * remove utf8 characters from config * Update CHANGELOG.md --------- Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com> * Samtools fastq (#52) * initial commit dedup * Revert "initial commit dedup" This reverts commit 38f586bec0ac9e4312b016e29c3aa0bd53f292b2. * Initial commit, config, script, help and test_data * Update changelog, add tests, fix argument naming errors, add test data * update changelog, remove gffread namespace field --------- Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com> * format URL in the description (#55) * format URL in the description * update changelog * Change name in _viash.yaml (#60) * Update operational code (#63) * update readme * switch ci to toolbox * update to viash 0.9.0-RC6 * edit keywords * fix version * update biobox * cutadapt (#7) * First commit, clone of cutadapt in htrnaseq + help.txt * Add config * Don't allow multiple: true when providing a FASTA file with adapters * First version of script * Updates and fixes - se/pe * Add tests and fix --json argument * Add software version * Better consistency in using snake_case * Update src/cutadapt/config.vsh.yaml Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com> * Update src/cutadapt/config.vsh.yaml Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com> * Update src/cutadapt/config.vsh.yaml Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com> * Specify --input and --input_r2 as separate arguments * Avoid specifying default arg values * Add more information to `--minimum_length` and `maximum_length` * Add --cpus by means of $meta_cpus and set proper default * Allow multiple for adapters/fasta and add test * change multiple_sep to ';' * add example * simplify code with a helper function * create directories in test * use a different output extension if --fasta is provided * decrease code duplication by separating optional outputs from paired/unpaired output arguments * write custom tests for cutadapt * fix _r2 arguments * add debug flag as not to always print the cli command * remove comment * Update to Viash 0.9.0-RC4 * Ability to specify output globbing patterns * Avoid the need for both output_dir and output * Move fields from `info` to `links` Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com> * Move references back to the info field * apologies, I proposed a wrong syntax --------- Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com> * update changelog * update readme * Update salmon quant arguments (#57) * Make index an optional argument * FIx argument type and add optional argument * FEAT: add bedtools getfasta. (#59) * FEAT: add bedtools getfasta. * Add PR number to CHANGELOG * Add star genomegenerate component (#58) * Add star genomegenerate component * Update changelog * Rename component * Update test * Update CHANGELOG.md --------- Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com> * fix package config (#65) * Delete src/bgzip directory (#64) It was moved to toolbox * Output alignments to the transcriptome (#56) * Output alignments to the transcriptome * Change argument name * BUG: pear component failure is ignored (#70) * FEAT + BUG: cutadapt; allowing disabling demultiplexing and fix par_quality_cutoff_r2 (#69) * FEAT: Disable cutadapt demultiplexing by default * Cutadapt: fix --par_quality_cutoff_r2 * FEAT: update busco to 5.7.1 (#72) * FEAT: update busco to 5.7.1 * Typo * Samtools fasta (#53) * initial commit dedup * Revert "initial commit dedup" This reverts commit 38f586bec0ac9e4312b016e29c3aa0bd53f292b2. * Fasta component * change script resource to samtools_fastq script, with dummy argument to specify the command * add dummy argument to samtools_fastq to share the script with samtools_fasta * fix path to script in config * Update src/samtools/samtools_fastq/script.sh Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com> * Change default fields to examples * Two more default fields changed to examples * Minor formatting changes * Markdown formatting changes in configs --------- Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com> * Umi tools dedup (#54) * initial commit dedup * Revert "initial commit dedup" This reverts commit 38f586bec0ac9e4312b016e29c3aa0bd53f292b2. * inital commit dedup * Working component with one test * Update test 1 and test data, fix some arg types in config and script * test data files and changes to script * Add third test and test data * Fix typo in script * remove utf8 characters in config * Add choices fields and change default fields to exampels * Minor formatting changes * md formatting changes in config * Fix typo (#79) * add vscode to gitignore * update multiple separator (#81) * update multiple separator * update changelog * Update src/multiqc/config.vsh.yaml Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com> * Update src/multiqc/config.vsh.yaml Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com> * Update src/multiqc/config.vsh.yaml Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com> * Update src/multiqc/config.vsh.yaml Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com> * update ifs --------- Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com> * add test data * add tests * update changelog * remove unrequired test data * update descriptions * update changelog * update help text * Update src/qualimap/qualimap_rnaseq/script.sh Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com> * update unit tests * update unit tests * addres pr changes request * add version * remove whitespace multiqc * Apply suggestions from code review Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com> * address pr comments * Update CHANGELOG.md * fix doi * Fix name * update version and container image * write software version to file --------- Co-authored-by: dorien-er <roosen.dorien@gmail.com> Co-authored-by: Leila011 <leilapaquay@gmail.com> Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com> Co-authored-by: emmarousseau <emmarou1@icloud.com> Co-authored-by: Sai Nirmayi Yasa <92786623+sainirmayi@users.noreply.github.com> Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com> Co-authored-by: Dorien <41797896+dorien-er@users.noreply.github.com>
2024-08-21 11:54:23 +00:00
parent b833613f7c
commit b17c19f92e
188 changed files with 6832 additions and 215 deletions
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -32,6 +32,8 @@
  - `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

 * `busco` components: update BUSCO to `5.7.1` (PR #72).
--- a/src/qualimap/qualimap_rnaseq/config.vsh.yaml
+++ 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
--- a/src/qualimap/qualimap_rnaseq/help.txt
+++ 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.
--- a/src/qualimap/qualimap_rnaseq/script.sh
+++ 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
--- a/src/qualimap/qualimap_rnaseq/test.sh
+++ 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
--- a/src/qualimap/qualimap_rnaseq/test_data/a.bam
+++ b/src/qualimap/qualimap_rnaseq/test_data/a.bam
--- a/src/qualimap/qualimap_rnaseq/test_data/annotation.gtf
+++ 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";
--- a/src/qualimap/qualimap_rnaseq/test_data/script.sh
+++ 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
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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
--- a/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml
+++ 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"
--- a/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq
+++ b/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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" : {
--- 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"
--- 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" : {
--- a/Show More
+++ b/Show More