Build branch main with version main (e6627ec)

Build pipeline: viash-hub.biobox.main-v4lxs Source commit: e6627ec728 Source message: FastQC (#92) * Starting Component * Creating Files * update on config file * Update on test.sh * Update on config * Update script.sh * Update on script.sh * trying to figure multiple: true * Update on script.sh * Update on script * Adding some tests * More tests * Update on script.sh * Added more tests * Small Changes * Update test.sh * Update on Script and Test - change the --zip and --html to take wild card '*' * Added one more test * Removed test_data dir * More description * Update CHANGELOG.md * Update on config and script - meta_cpus - meta_tmp_dir * Bug Fixed * unset_if_false * Updating Tests * Update script.sh * debugging * Minor changes * Update config.vsh.yaml * Update config.vsh.yaml * Required Changes - large changes on script.sh * Update config.vsh.yaml * Adding extra links * tmpdir bug * Updating tests * minor changes * Adding extra output options --summary --data * minor change * Update script.sh * small change in config
2024-09-03 09:13:58 +00:00
parent f066ef0ffa
commit ddad38b4a3
211 changed files with 7517 additions and 250 deletions
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -43,6 +43,8 @@
 * `bcftools`:
  - `bcftools/bcftools_sort`: Sorts BCF/VCF files by position and other criteria (PR #141).

+* `fastqc`: High throughput sequence quality control analysis tool (PR #92).
+
 ## MINOR CHANGES

 * `busco` components: update BUSCO to `5.7.1` (PR #72).
--- a/src/fastqc/config.vsh.yaml
+++ b/src/fastqc/config.vsh.yaml
@@ -0,0 +1,209 @@
+name: fastqc
+description: FastQC - A high throughput sequence QC analysis tool.
+keywords: [Quality control, BAM, SAM, FASTQ]
+links:
+  homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
+  documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
+  repository: https://github.com/s-andrews/FastQC
+  issue_tracker: https://github.com/s-andrews/FastQC/issues
+license: GPL-3.0, Apache-2.0
+authors:
+  - __merge__: /src/_authors/theodoro_gasperin.yaml
+    roles: [ author, maintainer ]
+
+argument_groups:
+  - name: Inputs
+    arguments:
+      - name: --input
+        type: file
+        direction: input
+        multiple: true
+        description: | 
+          FASTQ file(s) to be analyzed.
+        required: true
+        example: input.fq
+        
+  - name: Outputs
+    description: |
+      At least one of the output options (--html, --zip, --summary, --data) must be used.
+    arguments:
+
+      - name: --html
+        type: file
+        direction: output
+        multiple: true
+        description: |
+          Create the HTML report of the results. 
+          '*' wild card must be provided in the output file name. 
+          Wild card will be replaced by the input file basename.
+          e.g. 
+            --input "sample_1.fq"
+            --html "*.html"
+            would create an output html file named sample_1.html
+        example: "*.html"
+      
+      - name: --zip
+        type: file
+        direction: output
+        multiple: true
+        description: |
+          Create the zip file(s) containing: html report, data, images, icons, summary, etc.
+          '*' wild card must be provided in the output file name.
+          Wild card will be replaced by the input basename.
+          e.g. 
+            --input "sample_1.fq"
+            --html "*.zip"
+            would create an output zip file named sample_1.zip
+        example: "*.zip"   
+
+      - name: --summary
+        type: file
+        direction: output
+        multiple: true
+        description: |
+          Create the summary file(s).
+          '*' wild card must be provided in the output file name.
+          Wild card will be replaced by the input basename.
+          e.g. 
+            --input "sample_1.fq"
+            --summary "*_summary.txt"
+            would create an output summary.txt file named sample_1_summary.txt
+        example: "*_summary.txt"
+
+      - name: --data
+        type: file
+        direction: output
+        multiple: true
+        description: |
+          Create the data file(s).
+          '*' wild card must be provided in the output file name.
+          Wild card will be replaced by the input basename.
+          e.g. 
+            --input "sample_1.fq"
+            --summary "*_data.txt"
+            would create an output data.txt file named sample_1_data.txt
+        example: "*_data.txt"
+
+  - name: Options
+    arguments:  
+      - name: --casava
+        type: boolean_true
+        description: | 
+          Files come from raw casava output. Files in the same sample
+          group (differing only by the group number) will be analysed
+          as a set rather than individually. Sequences with the filter
+          flag set in the header will be excluded from the analysis.
+          Files must have the same names given to them by casava
+          (including being gzipped and ending with .gz) otherwise they
+          won't be grouped together correctly.
+      
+      - name: --nano
+        type: boolean_true
+        description: |
+          Files come from nanopore sequences and are in fast5 format. In
+          this mode you can pass in directories to process and the program
+          will take in all fast5 files within those directories and produce
+          a single output file from the sequences found in all files.
+      
+      - name: --nofilter
+        type: boolean_true
+        description: |
+          If running with --casava then don't remove read flagged by
+          casava as poor quality when performing the QC analysis.
+
+      - name: --nogroup
+        type: boolean_true
+        description: |
+          Disable grouping of bases for reads >50bp. 
+          All reports will show data for every base in the read. 
+          WARNING: Using this option will cause fastqc to crash 
+          and burn if you use it on really long reads, and your 
+          plots may end up a ridiculous size. You have been warned!
+
+      - name: --min_length
+        type: integer
+        description: |
+          Sets an artificial lower limit on the length of the 
+          sequence to be shown in the report. As long as you 
+          set this to a value greater or equal to your longest 
+          read length then this will be the sequence length used 
+          to create your read groups. This can be useful for making
+          directly comparable statistics from datasets with somewhat 
+          variable read lengths.
+        example: 0
+
+      - name: --format
+        alternatives: -f
+        type: string
+        description: |
+          Bypasses the normal sequence file format detection and 
+          forces the program to use the specified format. 
+          Valid formats are bam, sam, bam_mapped, sam_mapped, and fastq.
+        example: bam
+        
+      - name: --contaminants
+        alternatives: -c
+        type: file
+        description: |
+          Specifies a non-default file which contains the list 
+          of contaminants to screen overrepresented sequences against. 
+          The file must contain sets of named contaminants in the form
+          name[tab]sequence. Lines prefixed with a hash will be ignored.
+        example: contaminants.txt
+        
+      - name: --adapters
+        alternatives: -a
+        type: file
+        description: |
+          Specifies a non-default file which contains the list of 
+          adapter sequences which will be explicitly searched against 
+          the library. The file must contain sets of named adapters 
+          in the form name[tab]sequence. Lines prefixed with a hash will be ignored.
+        example: adapters.txt
+
+      - name: --limits
+        alternatives: -l
+        type: file
+        description: |
+          Specifies a non-default file which contains 
+          a set of criteria which will be used to determine 
+          the warn/error limits for the various modules. 
+          This file can also be used to selectively remove 
+          some modules from the output altogether. The format 
+          needs to mirror the default limits.txt file found in 
+          the Configuration folder.
+        example: limits.txt
+
+      - name: --kmers
+        alternatives: -k
+        type: integer
+        description: |
+          Specifies the length of Kmer to look for in the Kmer 
+          content module. Specified Kmer length must be between 
+          2 and 10. Default length is 7 if not specified.
+        example: 7
+        
+      - name: --quiet
+        alternatives: -q
+        type: boolean_true
+        description: |
+          Suppress all progress messages on stdout and only report errors.
+        
+resources:
+  - type: bash_script
+    path: script.sh
+test_resources:
+  - type: bash_script
+    path: test.sh
+
+engines:
+  - type: docker
+    image: biocontainers/fastqc:v0.11.9_cv8
+    setup:
+      - type: docker
+        run: |
+          echo "fastqc: $(fastqc --version | sed -n 's/^FastQC //p')" > /var/software_versions.txt
+
+runners:
+  - type: executable
+  - type: nextflow
--- a/src/fastqc/help.txt
+++ b/src/fastqc/help.txt
@@ -0,0 +1,125 @@
+```bash
+fastqc --help
+```
+
+            FastQC - A high throughput sequence QC analysis tool
+
+SYNOPSIS
+
+	fastqc seqfile1 seqfile2 .. seqfileN
+
+    fastqc [-o output dir] [--(no)extract] [-f fastq|bam|sam] 
+           [-c contaminant file] seqfile1 .. seqfileN
+
+DESCRIPTION
+
+    FastQC reads a set of sequence files and produces from each one a quality
+    control report consisting of a number of different modules, each one of 
+    which will help to identify a different potential type of problem in your
+    data.
+    
+    If no files to process are specified on the command line then the program
+    will start as an interactive graphical application.  If files are provided
+    on the command line then the program will run with no user interaction
+    required.  In this mode it is suitable for inclusion into a standardised
+    analysis pipeline.
+    
+    The options for the program as as follows:
+    
+    -h --help       Print this help file and exit
+    
+    -v --version    Print the version of the program and exit
+    
+    -o --outdir     Create all output files in the specified output directory.
+                    Please note that this directory must exist as the program
+                    will not create it.  If this option is not set then the 
+                    output file for each sequence file is created in the same
+                    directory as the sequence file which was processed.
+                    
+    --casava        Files come from raw casava output. Files in the same sample
+                    group (differing only by the group number) will be analysed
+                    as a set rather than individually. Sequences with the filter
+                    flag set in the header will be excluded from the analysis.
+                    Files must have the same names given to them by casava
+                    (including being gzipped and ending with .gz) otherwise they
+                    won't be grouped together correctly.
+                    
+    --nano          Files come from nanopore sequences and are in fast5 format. In
+                    this mode you can pass in directories to process and the program
+                    will take in all fast5 files within those directories and produce
+                    a single output file from the sequences found in all files.                    
+                    
+    --nofilter      If running with --casava then don't remove read flagged by
+                    casava as poor quality when performing the QC analysis.
+                   
+    --extract       If set then the zipped output file will be uncompressed in
+                    the same directory after it has been created.  By default
+                    this option will be set if fastqc is run in non-interactive
+                    mode.
+                    
+    -j --java       Provides the full path to the java binary you want to use to
+                    launch fastqc. If not supplied then java is assumed to be in
+                    your path.
+                   
+    --noextract     Do not uncompress the output file after creating it.  You
+                    should set this option if you do not wish to uncompress
+                    the output when running in non-interactive mode.
+                    
+    --nogroup       Disable grouping of bases for reads >50bp. All reports will
+                    show data for every base in the read.  WARNING: Using this
+                    option will cause fastqc to crash and burn if you use it on
+                    really long reads, and your plots may end up a ridiculous size.
+                    You have been warned!
+                    
+    --min_length    Sets an artificial lower limit on the length of the sequence
+                    to be shown in the report.  As long as you set this to a value
+                    greater or equal to your longest read length then this will be
+                    the sequence length used to create your read groups.  This can
+                    be useful for making directly comaparable statistics from 
+                    datasets with somewhat variable read lengths.
+                    
+    -f --format     Bypasses the normal sequence file format detection and
+                    forces the program to use the specified format.  Valid
+                    formats are bam,sam,bam_mapped,sam_mapped and fastq
+                    
+    -t --threads    Specifies the number of files which can be processed
+                    simultaneously.  Each thread will be allocated 250MB of
+                    memory so you shouldn't run more threads than your
+                    available memory will cope with, and not more than
+                    6 threads on a 32 bit machine
+                  
+    -c              Specifies a non-default file which contains the list of
+    --contaminants  contaminants to screen overrepresented sequences against.
+                    The file must contain sets of named contaminants in the
+                    form name[tab]sequence.  Lines prefixed with a hash will
+                    be ignored.
+
+    -a              Specifies a non-default file which contains the list of
+    --adapters      adapter sequences which will be explicity searched against
+                    the library. The file must contain sets of named adapters
+                    in the form name[tab]sequence.  Lines prefixed with a hash
+                    will be ignored.
+                    
+    -l              Specifies a non-default file which contains a set of criteria
+    --limits        which will be used to determine the warn/error limits for the
+                    various modules.  This file can also be used to selectively 
+                    remove some modules from the output all together.  The format
+                    needs to mirror the default limits.txt file found in the
+                    Configuration folder.
+                    
+   -k --kmers       Specifies the length of Kmer to look for in the Kmer content
+                    module. Specified Kmer length must be between 2 and 10. Default
+                    length is 7 if not specified.
+                    
+   -q --quiet       Supress all progress messages on stdout and only report errors.
+   
+   -d --dir         Selects a directory to be used for temporary files written when
+                    generating report images. Defaults to system temp directory if
+                    not specified.
+                    
+BUGS
+
+    Any bugs in fastqc should be reported either to simon.andrews@babraham.ac.uk
+    or in www.bioinformatics.babraham.ac.uk/bugzilla/
+                   
+    
--- a/src/fastqc/script.sh
+++ b/src/fastqc/script.sh
@@ -0,0 +1,86 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+# exit on error
+set -eo pipefail
+
+# Check if both outputs are empty, at least one must be passed.
+if [[ -z "$par_html" ]] && [[ -z "$par_zip" ]] && [[ -z "$par_summary" ]] && [[ -z "$par_data" ]]; then
+  echo "Error: At least one of the output arguments (--html, --zip, --summary, and --data) must be passed."
+  exit 1
+fi
+
+# unset flags
+unset_if_false=(
+  par_casava
+  par_nano
+  par_nofilter
+  par_extract
+  par_noextract
+  par_nogroup
+  par_quiet
+)
+
+for par in ${unset_if_false[@]}; do
+    test_val="${!par}"
+    [[ "$test_val" == "false" ]] && unset $par
+done
+
+tmpdir=$(mktemp -d "${meta_temp_dir}/${meta_name}-XXXXXXXX")
+function clean_up {
+  rm -rf "$tmpdir"
+}
+trap clean_up EXIT
+
+# Create input array 
+IFS=";" read -ra input <<< $par_input
+
+# Run fastqc
+fastqc \
+  --extract \
+  ${par_casava:+--casava} \
+  ${par_nano:+--nano} \
+  ${par_nofilter:+--nofilter} \
+  ${par_nogroup:+--nogroup} \
+  ${par_min_length:+--min_length "$par_min_length"} \
+  ${par_format:+--format "$par_format"} \
+  ${par_contaminants:+--contaminants "$par_contaminants"} \
+  ${par_adapters:+--adapters "$par_adapters"} \
+  ${par_limits:+--limits "$par_limits"} \
+  ${par_kmers:+--kmers "$par_kmers"} \
+  ${par_quiet:+--quiet} \
+  ${meta_cpus:+--threads "$meta_cpus"} \
+  ${meta_temp_dir:+--dir "$meta_temp_dir"} \
+  --outdir "${tmpdir}" \
+  "${input[@]}"
+ 
+# Move output files
+for file in "${input[@]}"; do
+  # Removes everthing after the first dot of the basename
+  sample_name=$(basename "${file}" | sed 's/\..*$//')
+  if [[ -n "$par_html" ]]; then
+    input_html="${tmpdir}/${sample_name}_fastqc.html"
+    html_file="${par_html//\*/$sample_name}"
+    mv "$input_html" "$html_file"
+  fi
+  if [[ -n "$par_zip" ]]; then
+    input_zip="${tmpdir}/${sample_name}_fastqc.zip"
+    zip_file="${par_zip//\*/$sample_name}"
+    mv "$input_zip" "$zip_file"
+  fi
+  if [[ -n "$par_summary" ]]; then
+    summary_file="${tmpdir}/${sample_name}_fastqc/summary.txt"
+    new_summary="${par_summary//\*/$sample_name}"
+    mv "$summary_file" "$new_summary"
+  fi
+  if [[ -n "$par_data" ]]; then
+    data_file="${tmpdir}/${sample_name}_fastqc/fastqc_data.txt"
+    new_data="${par_data//\*/$sample_name}"
+    mv "$data_file" "$new_data"
+  fi
+  # Remove the extracted directory
+  rm -r "${tmpdir}/${sample_name}_fastqc"
+done
+
--- a/src/fastqc/test.sh
+++ b/src/fastqc/test.sh
@@ -0,0 +1,235 @@
+#!/bin/bash
+
+# exit on error
+set -eo pipefail
+
+## VIASH START
+# meta_executable="target/executable/fastqc"
+# meta_resources_dir="src/fastqc"
+## VIASH END
+
+#############################################
+# helper functions
+assert_file_exists() {
+  [ -f "$1" ] || { echo "File '$1' does not exist" && 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; }
+}
+assert_identical_content() {
+  diff -a "$2" "$1" \
+    || (echo "Files are not identical!" && exit 1)
+}
+#############################################
+
+# Create directories for tests
+echo "Creating Test Data..."
+TMPDIR=$(mktemp -d "$meta_temp_dir/XXXXXX")
+function clean_up {
+  [[ -d "$TMPDIR" ]] && rm -r "$TMPDIR"
+}
+trap clean_up EXIT
+
+# Create and populate input.fasta
+cat > "$TMPDIR/input_1.fq" <<EOL
+@HWI-ST330:304:H045HADXX:1:1101:1111:61397
+CACTTGTAAGGGCAGGCCCCCTTCACCCTCCCGCTCCTGGGGGANNNNNNNNNNANNNCGAGGCCCTGGGGTAGAGGGNNNNNNNNNNNNNNGATCTTGG
+
+@?@DDDDDDHHH?GH:?FCBGGB@C?DBEGIIIIAEF;FCGGI#########################################################
+EOL
+
+cat > "$TMPDIR/input_2.fq" <<EOL
+@HWI-ST330:304:H045HADXX:1:1101:1111:61397
+CACTTGTAAGGGCAGGCCCCCTTCACCCTCCCGCTCCTGGGGGANNNNNNNNNNANNNCGAGGCCCTGGGGTAGAGGGNNNNNNNNNNNNNNGATCTTGG
+
+@?@DDDDDDHHH?GH:?FCBGGB@C?DBEGIIIIAEF;FCGGI#########################################################
+EOL
+
+# Create and populate contaminants.txt
+printf "contaminant_sequence1\tCACTTGTAAGGGCAGGCCCCCTTCACCCTCCCGCTCCTGGGGGA\n" > "$TMPDIR/contaminants.txt"
+printf "contaminant_sequence2\tGATCTTGG\n" >> "$TMPDIR/contaminants.txt"
+
+# Create and populate SAM file 
+printf "@HD\tVN:1.0\tSO:unsorted\n" > "$TMPDIR/example.sam"
+printf "@SQ\tSN:chr1\tLN:248956422\n" >> "$TMPDIR/example.sam"
+printf "@SQ\tSN:chr2\tLN:242193529\n" >> "$TMPDIR/example.sam"
+printf "@PG\tID:bowtie2\tPN:bowtie2\tVN:2.3.4.1\tCL:\"/usr/bin/bowtie2-align-s --wrapper basic-0 -x genome -U reads.fq -S output.sam\"\n" >> "$TMPDIR/example.sam"
+printf "read1\t0\tchr1\t100\t255\t50M\t*\t0\t0\tACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:-10\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:50\tYT:Z:UU\n" >> "$TMPDIR/example.sam"
+printf "read2\t0\tchr2\t150\t255\t50M\t*\t0\t0\tTGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:-8\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:50\tYT:Z:UU\n" >> "$TMPDIR/example.sam"
+printf "read3\t16\tchr1\t200\t255\t50M\t*\t0\t0\tGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTA\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\tAS:i:-12\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:50\tYT:Z:UU" >> "$TMPDIR/example.sam"
+
+cat > "$TMPDIR/expected_summary.txt" <<EOL
+PASS	Basic Statistics	input_1.fq
+PASS	Per base sequence quality	input_1.fq
+FAIL	Per sequence quality scores	input_1.fq
+FAIL	Per base sequence content	input_1.fq
+FAIL	Per sequence GC content	input_1.fq
+FAIL	Per base N content	input_1.fq
+PASS	Sequence Length Distribution	input_1.fq
+PASS	Sequence Duplication Levels	input_1.fq
+FAIL	Overrepresented sequences	input_1.fq
+PASS	Adapter Content	input_1.fq
+EOL
+
+cat > "$TMPDIR/expected_summary2.txt" <<EOL
+PASS	Basic Statistics	input_2.fq
+PASS	Per base sequence quality	input_2.fq
+FAIL	Per sequence quality scores	input_2.fq
+FAIL	Per base sequence content	input_2.fq
+FAIL	Per sequence GC content	input_2.fq
+FAIL	Per base N content	input_2.fq
+PASS	Sequence Length Distribution	input_2.fq
+PASS	Sequence Duplication Levels	input_2.fq
+FAIL	Overrepresented sequences	input_2.fq
+PASS	Adapter Content	input_2.fq
+EOL
+
+cat > "$TMPDIR/expected_summary_sam.txt" <<EOL
+PASS	Basic Statistics	example.sam
+PASS	Per base sequence quality	example.sam
+FAIL	Per sequence quality scores	example.sam
+FAIL	Per base sequence content	example.sam
+WARN	Per sequence GC content	example.sam
+PASS	Per base N content	example.sam
+WARN	Sequence Length Distribution	example.sam
+PASS	Sequence Duplication Levels	example.sam
+FAIL	Overrepresented sequences	example.sam
+PASS	Adapter Content	example.sam
+EOL
+
+# Test 1: Run fastqc with default parameters
+mkdir "$TMPDIR/test1" && pushd "$TMPDIR/test1" > /dev/null
+
+echo "-> Run Test1: one input"
+"$meta_executable" \
+  --input "../input_1.fq" \
+  --html "*_fastqc.html" \
+  --zip "*_fastqc.zip" \
+  --summary "*_summary.txt" \
+  --data "*_data.txt" \
+  --quiet \
+
+assert_file_exists "input_1_fastqc.html"
+assert_file_exists "input_1_fastqc.zip"
+assert_file_exists "input_1_summary.txt"
+assert_file_not_empty "input_1_fastqc.html"
+assert_file_not_empty "input_1_fastqc.zip"
+assert_identical_content "input_1_summary.txt" "../expected_summary.txt"
+echo "- test succeeded -"
+
+popd > /dev/null
+
+
+# Test 2: Run fastqc with multiple inputs
+mkdir "$TMPDIR/test2" && pushd "$TMPDIR/test2" > /dev/null
+
+echo "-> Run Test2: two inputs"
+"$meta_executable" \
+  --input "../input_1.fq" \
+  --input "../input_2.fq" \
+  --html "*_fastqc.html" \
+  --zip "*_fastqc.zip" \
+  --summary "*_summary.txt" \
+  --data "*_data.txt" \
+  --quiet \
+
+# File 1
+assert_file_exists "input_1_fastqc.html"
+assert_file_exists "input_1_fastqc.zip"
+assert_file_exists "input_1_summary.txt"
+assert_file_not_empty "input_1_fastqc.html"
+assert_file_not_empty "input_1_fastqc.zip"
+assert_identical_content "input_1_summary.txt" "../expected_summary.txt"
+# File 2
+assert_file_exists "input_2_fastqc.html"
+assert_file_exists "input_2_fastqc.zip"
+assert_file_exists "input_2_summary.txt"
+assert_file_not_empty "input_2_fastqc.html"
+assert_file_not_empty "input_2_fastqc.zip"
+assert_identical_content "input_2_summary.txt" "../expected_summary2.txt"
+echo "- test succeeded -"
+
+popd > /dev/null
+
+# Test 3: Run fastqc with contaminants
+mkdir "$TMPDIR/test3" && pushd "$TMPDIR/test3" > /dev/null
+
+echo "-> Run Test3: contaminants"
+"$meta_executable" \
+  --input "../input_1.fq" \
+  --contaminants "../contaminants.txt" \
+  --html "*_fastqc.html" \
+  --zip "*_fastqc.zip" \
+  --summary "*_summary.txt" \
+  --data "*_data.txt" \
+  --quiet \
+
+assert_file_exists "input_1_fastqc.html"
+assert_file_exists "input_1_fastqc.zip"
+assert_file_exists "input_1_summary.txt"
+assert_file_not_empty "input_1_fastqc.html"
+assert_file_not_empty "input_1_fastqc.zip"
+assert_identical_content "input_1_summary.txt" "../expected_summary.txt"
+assert_file_contains "input_1_data.txt" "contaminant"
+echo "- test succeeded -"
+
+popd > /dev/null
+
+# Test 4: Run fastqc with sam file
+mkdir "$TMPDIR/test4" && pushd "$TMPDIR/test4" > /dev/null
+
+echo "-> Run Test4: sam file"
+"$meta_executable" \
+  --input "../example.sam" \
+  --format "sam" \
+  --html "*_fastqc.html" \
+  --zip "*_fastqc.zip" \
+  --summary "*_summary.txt" \
+  --data "*_data.txt" \
+  --quiet \
+
+assert_file_exists "example_fastqc.html"
+assert_file_exists "example_fastqc.zip"
+assert_file_exists "example_summary.txt"
+assert_file_not_empty "example_fastqc.html"
+assert_file_not_empty "example_fastqc.zip"
+assert_identical_content "example_summary.txt" "../expected_summary_sam.txt"
+echo "- test succeeded -"
+
+popd > /dev/null
+
+# Test 5: Run fastqc with multiple options
+mkdir "$TMPDIR/test5" && pushd "$TMPDIR/test5" > /dev/null
+
+echo "-> Run Test5: multiple options"
+"$meta_executable" \
+  --input "../input_1.fq" \
+  --contaminants "../contaminants.txt" \
+  --format "fastq" \
+  --nofilter \
+  --nogroup \
+  --min_length 10 \
+  --kmers 5 \
+  --html "*_fastqc.html" \
+  --zip "*_fastqc.zip" \
+  --summary "*_summary.txt" \
+  --data "*_data.txt" \
+  --quiet \
+# --casava \
+
+assert_file_exists "input_1_fastqc.html"
+assert_file_exists "input_1_fastqc.zip"
+assert_file_exists "input_1_summary.txt"
+assert_file_not_empty "input_1_fastqc.html"
+assert_file_not_empty "input_1_fastqc.zip"
+assert_identical_content "input_1_summary.txt" "../expected_summary.txt"
+assert_file_contains "input_1_data.txt" "contaminant"
+echo "- test succeeded -"
+
+popd > /dev/null
+
+echo "All tests succeeded!"
+exit 0
--- 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-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  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
@@ -515,9 +515,9 @@ 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="2024-09-02T13:28:20Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:45Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 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-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  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
@@ -505,9 +505,9 @@ 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="2024-09-02T13:28:19Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:45Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 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-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  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
@@ -519,9 +519,9 @@ 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="2024-09-02T13:28:20Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:45Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 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-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  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
@@ -484,9 +484,9 @@ 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="2024-09-02T13:28:19Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:45Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 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-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  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
@@ -493,9 +493,9 @@ 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="2024-09-02T13:28:19Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:44Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 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-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/arriba/arriba
+++ b/target/executable/arriba/arriba
@@ -754,9 +754,9 @@ 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="2024-09-02T13:28:21Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:47Z"
 LABEL org.opencontainers.image.source="https://github.com/suhrig/arriba"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bcftools/bcftools_sort/.config.vsh.yaml
+++ b/target/executable/bcftools/bcftools_sort/.config.vsh.yaml
@@ -185,7 +185,7 @@ build_info:
  output: "target/executable/bcftools/bcftools_sort"
  executable: "target/executable/bcftools/bcftools_sort/bcftools_sort"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/bcftools/bcftools_sort/bcftools_sort
+++ b/target/executable/bcftools/bcftools_sort/bcftools_sort
@@ -483,9 +483,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_sort"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:15Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:40Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 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-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  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
@@ -599,9 +599,9 @@ 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="2024-09-02T13:28:21Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:46Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 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-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  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
@@ -549,9 +549,9 @@ 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="2024-09-02T13:28:24Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:49Z"
 LABEL org.opencontainers.image.source="https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1/Extra_Utilities/"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 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-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  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
@@ -483,9 +483,9 @@ 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="2024-09-02T13:28:09Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:33Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml
@@ -176,7 +176,7 @@ build_info:
  output: "target/executable/bedtools/bedtools_bed12tobed6"
  executable: "target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6
+++ b/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6
@@ -480,9 +480,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bed12tobed6"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:07Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:32Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 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-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  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
@@ -496,9 +496,9 @@ 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="2024-09-02T13:28:10Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:34Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 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-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  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
@@ -526,9 +526,9 @@ 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="2024-09-02T13:28:08Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:32Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml
@@ -273,7 +273,7 @@ build_info:
  output: "target/executable/bedtools/bedtools_groupby"
  executable: "target/executable/bedtools/bedtools_groupby/bedtools_groupby"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/bedtools/bedtools_groupby/bedtools_groupby
+++ b/target/executable/bedtools/bedtools_groupby/bedtools_groupby
@@ -552,9 +552,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_groupby"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:09Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:34Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 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-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  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
@@ -633,9 +633,9 @@ 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="2024-09-02T13:28:08Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:33Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_links/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_links/.config.vsh.yaml
@@ -210,7 +210,7 @@ build_info:
  output: "target/executable/bedtools/bedtools_links"
  executable: "target/executable/bedtools/bedtools_links/bedtools_links"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/bedtools/bedtools_links/bedtools_links
+++ b/target/executable/bedtools/bedtools_links/bedtools_links
@@ -500,9 +500,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_links"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:08Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:33Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_merge/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_merge/.config.vsh.yaml
@@ -279,7 +279,7 @@ build_info:
  output: "target/executable/bedtools/bedtools_merge"
  executable: "target/executable/bedtools/bedtools_merge/bedtools_merge"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/bedtools/bedtools_merge/bedtools_merge
+++ b/target/executable/bedtools/bedtools_merge/bedtools_merge
@@ -558,9 +558,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_merge"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:07Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:32Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 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-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  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
@@ -509,9 +509,9 @@ 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="2024-09-02T13:28:09Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:34Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 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-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  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
@@ -475,9 +475,9 @@ 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="2024-09-02T13:28:17Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:43Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 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-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  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
@@ -465,9 +465,9 @@ 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="2024-09-02T13:28:18Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:43Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 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-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  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
@@ -632,9 +632,9 @@ 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="2024-09-02T13:28:18Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:43Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 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-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/cutadapt/cutadapt
+++ b/target/executable/cutadapt/cutadapt
@@ -831,9 +831,9 @@ 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="2024-09-02T13:28:22Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:48Z"
 LABEL org.opencontainers.image.source="https://github.com/marcelm/cutadapt"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 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-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/falco/falco
+++ b/target/executable/falco/falco
@@ -589,9 +589,9 @@ 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="2024-09-02T13:28:23Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:49Z"
 LABEL org.opencontainers.image.source="https://github.com/smithlabcode/falco"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 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-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/fastp/fastp
+++ b/target/executable/fastp/fastp
@@ -1028,9 +1028,9 @@ 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="2024-09-02T13:28:20Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:46Z"
 LABEL org.opencontainers.image.source="https://github.com/OpenGene/fastp"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/fastqc/.config.vsh.yaml
+++ b/target/executable/fastqc/.config.vsh.yaml
@@ -0,0 +1,366 @@
+name: "fastqc"
+version: "main"
+authors:
+- name: "Theodoro Gasperin Terra Camargo"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      email: "theodorogtc@gmail.com"
+      github: "tgaspe"
+      linkedin: "theodoro-gasperin-terra-camargo"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Bioinformatician"
+argument_groups:
+- name: "Inputs"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "FASTQ file(s) to be analyzed.\n"
+    info: null
+    example:
+    - "input.fq"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+- name: "Outputs"
+  description: "At least one of the output options (--html, --zip, --summary, --data)\
+    \ must be used.\n"
+  arguments:
+  - type: "file"
+    name: "--html"
+    description: "Create the HTML report of the results. \n'*' wild card must be provided\
+      \ in the output file name. \nWild card will be replaced by the input file basename.\n\
+      e.g. \n  --input \"sample_1.fq\"\n  --html \"*.html\"\n  would create an output\
+      \ html file named sample_1.html\n"
+    info: null
+    example:
+    - "*.html"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: true
+    multiple_sep: ";"
+  - type: "file"
+    name: "--zip"
+    description: "Create the zip file(s) containing: html report, data, images, icons,\
+      \ summary, etc.\n'*' wild card must be provided in the output file name.\nWild\
+      \ card will be replaced by the input basename.\ne.g. \n  --input \"sample_1.fq\"\
+      \n  --html \"*.zip\"\n  would create an output zip file named sample_1.zip\n"
+    info: null
+    example:
+    - "*.zip"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: true
+    multiple_sep: ";"
+  - type: "file"
+    name: "--summary"
+    description: "Create the summary file(s).\n'*' wild card must be provided in the\
+      \ output file name.\nWild card will be replaced by the input basename.\ne.g.\
+      \ \n  --input \"sample_1.fq\"\n  --summary \"*_summary.txt\"\n  would create\
+      \ an output summary.txt file named sample_1_summary.txt\n"
+    info: null
+    example:
+    - "*_summary.txt"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: true
+    multiple_sep: ";"
+  - type: "file"
+    name: "--data"
+    description: "Create the data file(s).\n'*' wild card must be provided in the\
+      \ output file name.\nWild card will be replaced by the input basename.\ne.g.\
+      \ \n  --input \"sample_1.fq\"\n  --summary \"*_data.txt\"\n  would create an\
+      \ output data.txt file named sample_1_data.txt\n"
+    info: null
+    example:
+    - "*_data.txt"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: true
+    multiple_sep: ";"
+- name: "Options"
+  arguments:
+  - type: "boolean_true"
+    name: "--casava"
+    description: "Files come from raw casava output. Files in the same sample\ngroup\
+      \ (differing only by the group number) will be analysed\nas a set rather than\
+      \ individually. Sequences with the filter\nflag set in the header will be excluded\
+      \ from the analysis.\nFiles must have the same names given to them by casava\n\
+      (including being gzipped and ending with .gz) otherwise they\nwon't be grouped\
+      \ together correctly.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--nano"
+    description: "Files come from nanopore sequences and are in fast5 format. In\n\
+      this mode you can pass in directories to process and the program\nwill take\
+      \ in all fast5 files within those directories and produce\na single output file\
+      \ from the sequences found in all files.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--nofilter"
+    description: "If running with --casava then don't remove read flagged by\ncasava\
+      \ as poor quality when performing the QC analysis.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--nogroup"
+    description: "Disable grouping of bases for reads >50bp. \nAll reports will show\
+      \ data for every base in the read. \nWARNING: Using this option will cause fastqc\
+      \ to crash \nand burn if you use it on really long reads, and your \nplots may\
+      \ end up a ridiculous size. You have been warned!\n"
+    info: null
+    direction: "input"
+  - type: "integer"
+    name: "--min_length"
+    description: "Sets an artificial lower limit on the length of the \nsequence to\
+      \ be shown in the report. As long as you \nset this to a value greater or equal\
+      \ to your longest \nread length then this will be the sequence length used \n\
+      to create your read groups. This can be useful for making\ndirectly comparable\
+      \ statistics from datasets with somewhat \nvariable read lengths.\n"
+    info: null
+    example:
+    - 0
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--format"
+    alternatives:
+    - "-f"
+    description: "Bypasses the normal sequence file format detection and \nforces\
+      \ the program to use the specified format. \nValid formats are bam, sam, bam_mapped,\
+      \ sam_mapped, and fastq.\n"
+    info: null
+    example:
+    - "bam"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--contaminants"
+    alternatives:
+    - "-c"
+    description: "Specifies a non-default file which contains the list \nof contaminants\
+      \ to screen overrepresented sequences against. \nThe file must contain sets\
+      \ of named contaminants in the form\nname[tab]sequence. Lines prefixed with\
+      \ a hash will be ignored.\n"
+    info: null
+    example:
+    - "contaminants.txt"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--adapters"
+    alternatives:
+    - "-a"
+    description: "Specifies a non-default file which contains the list of \nadapter\
+      \ sequences which will be explicitly searched against \nthe library. The file\
+      \ must contain sets of named adapters \nin the form name[tab]sequence. Lines\
+      \ prefixed with a hash will be ignored.\n"
+    info: null
+    example:
+    - "adapters.txt"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--limits"
+    alternatives:
+    - "-l"
+    description: "Specifies a non-default file which contains \na set of criteria\
+      \ which will be used to determine \nthe warn/error limits for the various modules.\
+      \ \nThis file can also be used to selectively remove \nsome modules from the\
+      \ output altogether. The format \nneeds to mirror the default limits.txt file\
+      \ found in \nthe Configuration folder.\n"
+    info: null
+    example:
+    - "limits.txt"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--kmers"
+    alternatives:
+    - "-k"
+    description: "Specifies the length of Kmer to look for in the Kmer \ncontent module.\
+      \ Specified Kmer length must be between \n2 and 10. Default length is 7 if not\
+      \ specified.\n"
+    info: null
+    example:
+    - 7
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--quiet"
+    alternatives:
+    - "-q"
+    description: "Suppress all progress messages on stdout and only report errors.\n"
+    info: null
+    direction: "input"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "FastQC - A high throughput sequence QC analysis tool."
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+info: null
+status: "enabled"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "Quality control"
+- "BAM"
+- "SAM"
+- "FASTQ"
+license: "GPL-3.0, Apache-2.0"
+links:
+  repository: "https://github.com/s-andrews/FastQC"
+  homepage: "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/"
+  documentation: "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/"
+  issue_tracker: "https://github.com/s-andrews/FastQC/issues"
+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: "biocontainers/fastqc:v0.11.9_cv8"
+  target_registry: "images.viash-hub.com"
+  target_tag: "main"
+  namespace_separator: "/"
+  setup:
+  - type: "docker"
+    run:
+    - "echo \"fastqc: $(fastqc --version | sed -n 's/^FastQC //p')\" > /var/software_versions.txt\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/fastqc/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/fastqc"
+  executable: "target/executable/fastqc/fastqc"
+  viash_version: "0.9.0-RC7"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
+  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-RC7"
+  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/fastqc/fastqc
+++ b/target/executable/fastqc/fastqc
--- 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-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/featurecounts/featurecounts
+++ b/target/executable/featurecounts/featurecounts
@@ -754,9 +754,9 @@ 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="2024-09-02T13:28:16Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:41Z"
 LABEL org.opencontainers.image.source="https://github.com/ShiLab-Bioinformatics/subread"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 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-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/gffread/gffread
+++ b/target/executable/gffread/gffread
@@ -807,9 +807,9 @@ 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="2024-09-02T13:28:07Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:31Z"
 LABEL org.opencontainers.image.source="https://github.com/gpertea/gffread"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 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-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  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
@@ -656,9 +656,9 @@ 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="2024-09-02T13:28:15Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:41Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 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-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  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
@@ -501,9 +501,9 @@ 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="2024-09-02T13:28:15Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:40Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 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-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/multiqc/multiqc
+++ b/target/executable/multiqc/multiqc
@@ -637,9 +637,9 @@ 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="2024-09-02T13:28:23Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:49Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 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-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/pear/pear
+++ b/target/executable/pear/pear
@@ -597,9 +597,9 @@ 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="2024-09-02T13:28:10Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:34Z"
 LABEL org.opencontainers.image.source="https://github.com/tseemann/PEAR"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 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
@@ -264,7 +264,7 @@ build_info:
  output: "target/executable/qualimap/qualimap_rnaseq"
  executable: "target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq
+++ b/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq
@@ -527,9 +527,9 @@ RUN echo QualiMap: $(qualimap 2>&1 | grep QualiMap | sed 's/^.*QualiMap//') > /v

 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component qualimap qualimap_rnaseq"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:14Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:38Z"
 LABEL org.opencontainers.image.source="https://bitbucket.org/kokonech/qualimap/commits/branch/master"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/rsem/rsem_prepare_reference/.config.vsh.yaml
+++ b/target/executable/rsem/rsem_prepare_reference/.config.vsh.yaml
@@ -416,7 +416,7 @@ build_info:
  output: "target/executable/rsem/rsem_prepare_reference"
  executable: "target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference"
  viash_version: "0.9.0-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference
+++ b/target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference
@@ -656,9 +656,9 @@ echo "HISAT2: `hisat2 --version | grep -oP 'hisat2-align-s version \K\d+\.\d+\.\

 LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
 LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_prepare_reference"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:18Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:44Z"
 LABEL org.opencontainers.image.source="https://github.com/deweylab/RSEM"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- 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-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  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
@@ -546,9 +546,9 @@ 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="2024-09-02T13:28:21Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:47Z"
 LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 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-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  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
@@ -1168,9 +1168,9 @@ 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="2024-09-02T13:28:22Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:48Z"
 LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 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-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  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
@@ -519,9 +519,9 @@ 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="2024-09-02T13:28:12Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:37Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 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-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  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
@@ -512,9 +512,9 @@ 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="2024-09-02T13:28:12Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:37Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 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-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  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
@@ -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_fasta"
-LABEL org.opencontainers.image.created="2024-09-02T13:28:13Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:37Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 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-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  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
@@ -626,9 +626,9 @@ 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="2024-09-02T13:28:12Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:36Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 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-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  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
@@ -474,9 +474,9 @@ 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="2024-09-02T13:28:11Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:36Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 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-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  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
@@ -478,9 +478,9 @@ 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="2024-09-02T13:28:11Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:35Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 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-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  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
@@ -485,9 +485,9 @@ 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="2024-09-02T13:28:10Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:35Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 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-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  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
@@ -556,9 +556,9 @@ 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="2024-09-02T13:28:13Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:38Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 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-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  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
@@ -575,9 +575,9 @@ 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="2024-09-02T13:28:13Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:38Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 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-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  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
@@ -825,9 +825,9 @@ 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="2024-09-02T13:28:11Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:35Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 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-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  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
@@ -481,9 +481,9 @@ 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="2024-09-02T13:28:24Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:50Z"
 LABEL org.opencontainers.image.source="https://github.com/lh3/seqtk/tree/v1.4"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 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-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  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
@@ -491,9 +491,9 @@ 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="2024-09-02T13:28:24Z"
+LABEL org.opencontainers.image.created="2024-09-03T08:58:50Z"
 LABEL org.opencontainers.image.source="https://github.com/lh3/seqtk/tree/v1.4"
-LABEL org.opencontainers.image.revision="da3272d0118227ee788cd93b222201f557729397"
+LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21"
 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-RC7"
-  git_commit: "da3272d0118227ee788cd93b222201f557729397"
+  git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
--- a/Show More
+++ b/Show More