Build branch main with version main (7fb67a9)

Build pipeline: viash-hub.biobox.main-zbkpz Source commit: 7fb67a9853 Source message: Add bbmap_bbsplit (#138) * initial commit dedup * Revert "initial commit dedup" This reverts commit 38f586bec0ac9e4312b016e29c3aa0bd53f292b2. * initial commit, complete config file, add test data * complete config file, adjusted script and tests, not functional * update changelog, hep.txt, functional test, large test data * smaller test data * remove test resource from config * modify paths in test script * Arguments closer to original tool's * Extra arg to allow use of bbmap args
2024-10-18 11:59:11 +00:00
parent 55de3a494d
commit 0cdbd262c7
275 changed files with 8020 additions and 726 deletions
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -184,6 +184,9 @@
 * `bedtools`:
    - `bedtools_getfasta`: extract sequences from a FASTA file for each of the
                           intervals defined in a BED/GFF/VCF file (PR #59).
+                           
+* `bbmap`:
+    - `bbmap_bbsplit`: Split sequencing reads by mapping them to multiple references simultaneously (PR #138).



--- a/src/bbmap_bbsplit/config.vsh.yaml
+++ b/src/bbmap_bbsplit/config.vsh.yaml
@@ -0,0 +1,162 @@
+namespace: "bbmap"
+name: "bbmap_bbsplit"
+description: Split sequencing reads by mapping them to multiple references simultaneously.
+links:
+  homepage: https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/
+  documentation: https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbmap-guide/
+  repository: https://github.com/BioInfoTools/BBMap/blob/master/sh/bbsplit.sh
+
+license: BBTools Copyright (c) 2014
+
+argument_groups:
+- name: "Input"
+  arguments:
+  - name: "--id"
+    type: string
+    description: Sample ID
+  - name: "--paired"
+    type: boolean_true
+    description: Paired fastq files or not?
+  - name: "--input"
+    type: file
+    multiple: true
+    description: Input fastq files, either one or two (paired), separated by ";".
+    example: reads.fastq
+  - name: "--ref"
+    type: file
+    multiple: true
+    description: Reference FASTA files, separated by ";". The primary reference should be specified first.
+  - name: "--only_build_index"
+    type: boolean_true
+    description: If set, only builds the index. Otherwise, mapping is performed.
+  - name: "--build"
+    type: string
+    description: |
+      Designate index to use. Corresponds to the number specified when building the index.
+      If building the index, this will be the build's id. If multiple references are indexed
+      in the same directory, each needs a unique build ID. Default: 1.
+    example: "1"
+  - name: "--qin"
+    type: string
+    description: |
+      Set to 33 or 64 to specify input quality value ASCII offset. Automatically detected if
+      not specified.
+  - name: "--interleaved"
+    type: boolean_true
+    description: |
+      True forces paired/interleaved input; false forces single-ended mapping.
+      If not specified, interleaved status will be autodetected from read names.
+  - name: "--maxindel"
+    type: integer
+    description: |
+      Don't look for indels longer than this. Lower is faster. Set to >=100k for RNA-seq.
+    example: 20
+  - name: "--minratio"
+    type: double
+    description: |
+      Fraction of max alignment score required to keep a site. Higher is faster.
+    example: 0.56
+  - name: "--minhits"
+    type: integer
+    description: |
+      Minimum number of seed hits required for candidate sites. Higher is faster.
+    example: 1
+  - name: "--ambiguous"
+    type: string
+    description: |
+      Set behavior on ambiguously-mapped reads (with multiple top-scoring mapping locations).
+        * best    Use the first best site (Default)
+        * toss    Consider unmapped
+        * random  Select one top-scoring site randomly
+        * all     Retain all top-scoring sites.  Does not work yet with SAM output
+    choices: [best, toss, random, all]
+    example: best
+  - name: "--ambiguous2"
+    type: string
+    description: |
+      Set behavior only for reads that map ambiguously to multiple different references.
+      Normal 'ambiguous=' controls behavior on all ambiguous reads;
+      Ambiguous2 excludes reads that map ambiguously within a single reference.
+        * best    Use the first best site (Default)
+        * toss    Consider unmapped
+        * all     Write a copy to the output for each reference to which it maps
+        * split   Write a copy to the AMBIGUOUS_ output for each reference to which it maps
+    choices: [best, toss, all, split]
+    example: best
+  - name: "--qtrim"
+    type: string
+    description: |
+      Quality-trim ends to Q5 before mapping. Options are 'l' (left), 'r' (right), and 'lr' (both).
+    choices: [l, r, lr]
+  - name: "--untrim"
+    type: boolean_true
+    description: Undo trimming after mapping. Untrimmed bases will be soft-clipped in cigar strings.
+
+
+- name: "Output"
+  arguments:
+  - name: "--fastq_1"
+    type: file
+    description: |
+      Output file for read 1.
+    direction: output
+    example: read_out1.fastq
+  - name: "--fastq_2"
+    type: file
+    description: |
+      Output file for read 2.
+    direction: output
+    example: read_out2.fastq
+  - name: "--sam2bam"
+    alternatives: ["--bs"]
+    type: file
+    description: |
+      Write a shell script to 'file' that will turn the sam output into a sorted, indexed bam file.
+    direction: output
+    example: script.sh
+  - name: "--scafstats"
+    type: file
+    description: |
+      Write statistics on how many reads mapped to which scaffold to this file.
+    direction: output
+    example: scaffold_stats.txt
+  - name: "--refstats"
+    type: file
+    description: |
+      Write statistics on how many reads were assigned to which reference to this file.
+      Unmapped reads whose mate mapped to a reference are considered assigned and will be counted.
+    direction: output
+    example: reference_stats.txt
+  - name: "--nzo"
+    type: boolean_true
+    description: Only print lines with nonzero coverage.
+  - name: "--bbmap_args"
+    type: string
+    description: |
+      Additional arguments from BBMap to pass to BBSplit.
+    
+resources:
+  - type: bash_script
+    path: script.sh
+
+test_resources:
+  - type: bash_script
+    path: test.sh
+  
+engines:
+- type: docker
+  image: ubuntu:22.04
+  setup:
+    - type: docker
+      run: | 
+        apt-get update && \
+        apt-get install -y build-essential openjdk-17-jdk wget tar && \
+        wget --no-check-certificate https://sourceforge.net/projects/bbmap/files/BBMap_39.01.tar.gz && \
+        tar xzf BBMap_39.01.tar.gz && \
+        cp -r bbmap/* /usr/local/bin
+    - type: docker
+      run: |
+        bbsplit.sh --version 2>&1 | awk '/BBMap version/{print "BBMAP:", $NF}' > /var/software_versions.txt
+runners:
+  - type: executable
+  - type: nextflow
--- a/src/bbmap_bbsplit/help.txt
+++ b/src/bbmap_bbsplit/help.txt
@@ -0,0 +1,83 @@
+```
+bbsplit.sh
+```
+
+BBSplit
+Written by Brian Bushnell, from Dec. 2010 - present
+Last modified June 11, 2018
+
+Description:  Maps reads to multiple references simultaneously.
+Outputs reads to a file for the reference they best match, with multiple options for dealing with ambiguous mappings.
+
+To index:     bbsplit.sh build=<1> ref_x=<reference fasta> ref_y=<another reference fasta>
+To map:       bbsplit.sh build=<1> in=<reads> out_x=<output file> out_y=<another output file>
+
+To be concise, and do everything in one command:
+bbsplit.sh ref=x.fa,y.fa in=reads.fq basename=o%.fq
+
+that is equivalent to
+bbsplit.sh build=1 in=reads.fq ref_x=x.fa ref_y=y.fa out_x=ox.fq out_y=oy.fq
+
+By default paired reads will yield interleaved output, but you can use the # symbol to produce twin output files.
+For example, basename=o%_#.fq will produce ox_1.fq, ox_2.fq, oy_1.fq, and oy_2.fq.
+
+     
+Indexing Parameters (required when building the index):
+ref=<file,file>     A list of references, or directories containing fasta files.
+ref_<name>=<ref.fa> Alternate, longer way to specify references. e.g., ref_ecoli=ecoli.fa
+                    These can also be comma-delimited lists of files; e.g., ref_a=a1.fa,a2.fa,a3.fa
+build=<1>           If multiple references are indexed in the same directory, each needs a unique build ID.
+path=<.>            Specify the location to write the index, if you don't want it in the current working directory.
+
+Input Parameters:
+build=<1>           Designate index to use.  Corresponds to the number specified when building the index.
+in=<reads.fq>       Primary reads input; required parameter.
+in2=<reads2.fq>     For paired reads in two files.
+qin=<auto>          Set to 33 or 64 to specify input quality value ASCII offset.
+interleaved=<auto>  True forces paired/interleaved input; false forces single-ended mapping.
+                    If not specified, interleaved status will be autodetected from read names.
+
+Mapping Parameters:
+maxindel=<20>       Don't look for indels longer than this.  Lower is faster.  Set to >=100k for RNA-seq.
+minratio=<0.56>     Fraction of max alignment score required to keep a site.  Higher is faster.
+minhits=<1>         Minimum number of seed hits required for candidate sites.  Higher is faster.
+ambiguous=<best>    Set behavior on ambiguously-mapped reads (with multiple top-scoring mapping locations).
+                       best   (use the first best site)
+                       toss   (consider unmapped)
+                       random   (select one top-scoring site randomly)
+                       all   (retain all top-scoring sites.  Does not work yet with SAM output)
+ambiguous2=<best>   Set behavior only for reads that map ambiguously to multiple different references.
+                    Normal 'ambiguous=' controls behavior on all ambiguous reads;
+                    Ambiguous2 excludes reads that map ambiguously within a single reference.
+                       best   (use the first best site)
+                       toss   (consider unmapped)
+                       all   (write a copy to the output for each reference to which it maps)
+                       split   (write a copy to the AMBIGUOUS_ output for each reference to which it maps)
+qtrim=<true>        Quality-trim ends to Q5 before mapping.  Options are 'l' (left), 'r' (right), and 'lr' (both).
+untrim=<true>       Undo trimming after mapping.  Untrimmed bases will be soft-clipped in cigar strings.
+
+Output Parameters:
+out_<name>=<file>   Output reads that map to the reference <name> to <file>.
+basename=prefix%suffix     Equivalent to multiple out_%=prefix%suffix expressions, in which each % is replaced by the name of a reference file.
+bs=<file>           Write a shell script to 'file' that will turn the sam output into a sorted, indexed bam file.
+scafstats=<file>    Write statistics on how many reads mapped to which scaffold to this file.
+refstats=<file>     Write statistics on how many reads were assigned to which reference to this file.
+                    Unmapped reads whose mate mapped to a reference are considered assigned and will be counted.
+nzo=t               Only print lines with nonzero coverage.
+
+***** Notes *****
+Almost all BBMap parameters can be used; run bbmap.sh for more details.
+Exceptions include the 'nodisk' flag, which BBSplit does not support.
+BBSplit is recommended for fastq and fasta output, not for sam/bam output.
+When the reference sequences are shorter than read length, use Seal instead of BBSplit.
+
+Java Parameters:
+-Xmx                This will set Java's memory usage, overriding autodetection.
+                    -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.
+                    The max is typically 85% of physical memory.
+-eoom               This flag will cause the process to exit if an
+                    out-of-memory exception occurs.  Requires Java 8u92+.
+-da                 Disable assertions.
+
+This list is not complete.  For more information, please consult /readme.txt
+Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
--- a/src/bbmap_bbsplit/script.sh
+++ b/src/bbmap_bbsplit/script.sh
@@ -0,0 +1,91 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+set -eo pipefail
+
+function clean_up {
+    rm -rf "$tmpdir"
+}
+trap clean_up EXIT 
+
+unset_if_false=( par_paired par_only_build_index par_interleaved par_untrim par_nzo)
+
+for var in "${unset_if_false[@]}"; do
+    if [ -z "${!var}" ]; then
+        unset $var
+    fi
+done
+
+if [ ! -d "$par_build" ]; then
+    IFS=";" read -ra ref_files <<< "$par_ref"
+    primary_ref="${ref_files[0]}"
+    refs=()
+    for file in "${ref_files[@]:1}"
+    do
+        name=$(basename "$file" | sed 's/\.[^.]*$//')
+        refs+=("ref_$name=$file")
+    done
+fi
+
+if $par_only_build_index; then
+    if [ ${#refs[@]} -gt 1 ]; then
+        bbsplit.sh \
+            --ref_primary="$primary_ref" \
+            "${refs[@]}" \
+            path=$par_build
+    else
+        echo "ERROR: Please specify at least two reference fasta files."
+    fi
+else
+    IFS=";" read -ra input <<< "$par_input"
+    tmpdir=$(mktemp -d "$meta_temp_dir/$meta_functionality_name-XXXXXXXX")
+    index_files=''
+    if [ -d "$par_build" ]; then
+        index_files="path=$par_build"
+    elif [ ${#refs[@]} -gt 0 ]; then
+        index_files="--ref_primary=$primary_ref ${refs[*]}"
+    else
+        echo "ERROR: Please either specify a BBSplit index as input or at least two reference fasta files."
+    fi
+
+    extra_args=""
+    if [ -n "$par_refstats" ]; then extra_args+=" --refstats $par_refstats"; fi
+    if [ -n "$par_ambiguous" ]; then extra_args+=" --ambiguous $par_ambiguous"; fi
+    if [ -n "$par_ambiguous2" ]; then extra_args+=" --ambiguous2 $par_ambiguous2"; fi
+    if [ -n "$par_minratio" ]; then extra_args+=" --minratio $par_minratio"; fi
+    if [ -n "$par_minhits" ]; then extra_args+=" --minhits $par_minhits"; fi
+    if [ -n "$par_maxindel" ]; then extra_args+=" --maxindel $par_maxindel"; fi
+    if [ -n "$par_qin" ]; then extra_args+=" --qin $par_qin"; fi
+    if [ -n "$par_qtrim" ]; then extra_args+=" --qtrim $par_qtrim"; fi
+    if [ "$par_interleaved" = true ]; then extra_args+=" --interleaved"; fi
+    if [ "$par_untrim" = true ]; then extra_args+=" --untrim"; fi
+    if [ "$par_nzo" = true ]; then extra_args+=" --nzo"; fi
+
+    if [ -n "$par_bbmap_args" ]; then extra_args+=" $par_bbmap_args"; fi
+
+    
+    if $par_paired; then
+        bbsplit.sh \
+            $index_files \
+            in=${input[0]} \
+            in2=${input[1]} \
+            basename=${tmpdir}/%_#.fastq \
+            $extra_args
+        read1=$(find $tmpdir/ -iname primary_1*)
+        read2=$(find $tmpdir/ -iname primary_2*)
+        cp $read1 $par_fastq_1
+        cp $read2 $par_fastq_2
+    else
+        bbsplit.sh \
+            $index_files \
+            in=${input[0]} \
+            basename=${tmpdir}/%.fastq \
+            $extra_args
+        read1=$(find $tmpdir/ -iname primary*)
+        cp $read1 $par_fastq_1
+    fi
+fi
+
+exit 0
--- a/src/bbmap_bbsplit/test.sh
+++ b/src/bbmap_bbsplit/test.sh
@@ -0,0 +1,145 @@
+#!/bin/bash
+
+echo ">>> Test $meta_functionality_name"
+
+echo "> Prepare test data"
+
+cat > reads_R1.fastq <<'EOF'
+@SEQ_ID1
+ACAGGGTTTCACCATGTTGGCCAGG
+
+IIIIIIIIIIIIIIIIIIIIIIIII
+@SEQ_ID2
+TCCCAGGTAACAAACCAACCAACTT
+
+!!!!!!!!!!!!!!!!!!!!!!!!!
+EOF
+
+cat > reads_R2.fastq <<'EOF'
+@SEQ_ID1
+TACCATTACCCTACCATCCACCATG
+
+IIIIIIIIIIIIIIIIIIIIIIIII
+@SEQ_ID2
+CACTCGGCTGCATGCTTAGTGCACT
+
+!!!!!!!!!!!!!!!!!!!!!!!!!
+EOF
+
+cat > genome.fasta <<'EOF'
+>I
+AGTATTTTTAGTAGAGACAGGGTTTCACCATGTTGGCCAGGCTGGTCTTGATCTCCTGACCTCAGGTGATCCATCCGCCT
+TGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCACCTGGCCTGGTTTCGAACTCTTGACCTCAGGTGGTCTG
+CCCATCTTGACCTTCCAAAGTGCTGGAGCTACAGGCATGAGCCACTGCACCTGGTGCTTTTGGTAAAAGCAACCTGGAAT
+CAAATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTT
+TAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGAC
+EOF
+
+cat > human.fa <<'EOF'
+>human
+AGTATTTTTAGTAGAGACAGGGTTTCACCATGTTGGCCAGGCTGGTCTTGATCTCCTGACCTCAGGTGATCCATCCGCCT
+TGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCACCTGGCCTGGTTTCGAACTCTTGACCTCAGGTGGTCTG
+CCCATCTTGACCTTCCAAAGTGCTGGAGCTACAGGCATGAGCCACTGCACCTGGTGCTTTTGGTAAAAGCAACCTGGAAT
+EOF
+
+cat > sarscov2.fa <<'EOF'
+>sarscov2
+ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAA
+AATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGG
+ACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTT
+EOF
+
+####################################################################################################
+
+echo ">>> Building BBSplit index"
+"${meta_executable}" \
+  --ref "genome.fasta;human.fa;sarscov2.fa" \
+  --only_build_index \
+  --build "BBSplit_index" 
+
+echo ">>> Check whether output exists"
+[ ! -d "BBSplit_index" ] && echo "BBSplit index does not exist!" && exit 1
+[ -z "$(ls -A 'BBSplit_index')" ] && echo "BBSplit index is empty!" && exit 1
+
+####################################################################################################
+
+
+echo ">>> Testing with single-end reads and primary/non-primary FASTA files"
+"${meta_executable}" \
+  --input "reads_R1.fastq" \
+  --ref "genome.fasta;human.fa;sarscov2.fa" \
+  --fastq_1 "filtered_reads_R1.fastq"
+
+echo ">>> Check whether output exists"
+[ ! -f "filtered_reads_R1.fastq" ] && echo "Filtered reads file does not exist!" && exit 1
+[ ! -s "filtered_reads_R1.fastq" ] && echo "Filtered reads file is empty!" && exit 1
+
+echo ">>> Check whether output is correct"
+grep -q "ACAGGGTTTCACCATGTTGGCCAGG" filtered_reads_R1.fastq || { echo "Filtered reads file does not contain expected sequence!"; exit 1; }
+
+rm filtered_reads_R1.fastq
+
+####################################################################################################
+
+echo ">>> Testing with paired-end reads and primary/non-primary FASTA files"
+"${meta_executable}" \
+  --paired \
+  --input "reads_R1.fastq;reads_R2.fastq" \
+  --ref "genome.fasta;human.fa;sarscov2.fa" \
+  --fastq_1 "filtered_reads_R1.fastq" \
+  --fastq_2 "filtered_reads_R2.fastq"
+
+echo ">>> Check whether output exists"
+[ ! -f "filtered_reads_R1.fastq" ] && echo "Filtered read 1 file does not exist!" && exit 1
+[ ! -s "filtered_reads_R1.fastq" ] && echo "Filtered read 1 file is empty!" && exit 1
+[ ! -f "filtered_reads_R2.fastq" ] && echo "Filtered read 2 file does not exist!" && exit 1
+[ ! -s "filtered_reads_R2.fastq" ] && echo "Filtered read 2 file is empty!" && exit 1
+
+echo ">>> Check whether output is correct"
+grep -q "ACAGGGTTTCACCATGTTGGCCAGG" filtered_reads_R1.fastq || { echo "Filtered read 1 file does not contain expected sequence!"; exit 1; }
+grep -q "TACCATTACCCTACCATCCACCATG" filtered_reads_R2.fastq || { echo "Filtered read 2 file does not contain expected sequence!"; exit 1; }
+
+rm filtered_reads_R1.fastq filtered_reads_R2.fastq
+
+####################################################################################################
+
+echo ">>> Testing with single-end reads and BBSplit index"
+"${meta_executable}" \
+  --input "reads_R1.fastq" \
+  --build "BBSplit_index" \
+  --fastq_1 "filtered_reads_R1.fastq"
+
+echo ">>> Check whether output exists"
+[ ! -f "filtered_reads_R1.fastq" ] && echo "Filtered reads file does not exist!" && exit 1
+[ ! -s "filtered_reads_R1.fastq" ] && echo "Filtered reads file is empty!" && exit 1
+
+echo ">>> Check whether output is correct"
+grep -q "ACAGGGTTTCACCATGTTGGCCAGG" filtered_reads_R1.fastq || { echo "Filtered reads file does not contain expected sequence!"; exit 1; }
+
+rm filtered_reads_R1.fastq
+
+####################################################################################################
+
+echo ">>> Testing with paired-end reads and BBSplit index"
+"${meta_executable}" \
+  --paired \
+  --input "reads_R1.fastq;reads_R2.fastq" \
+  --build "BBSplit_index" \
+  --fastq_1 "filtered_reads_R1.fastq" \
+  --fastq_2 "filtered_reads_R2.fastq"
+
+echo ">>> Check whether output exists"
+[ ! -f "filtered_reads_R1.fastq" ] && echo "Filtered read 1 file does not exist!" && exit 1
+[ ! -s "filtered_reads_R1.fastq" ] && echo "Filtered read 1 file is empty!" && exit 1
+[ ! -f "filtered_reads_R2.fastq" ] && echo "Filtered read 2 file does not exist!" && exit 1
+[ ! -s "filtered_reads_R2.fastq" ] && echo "Filtered read 2 file is empty!" && exit 1
+
+
+echo ">>> Check whether output is correct"
+grep -q "ACAGGGTTTCACCATGTTGGCCAGG" filtered_reads_R1.fastq || { echo "Filtered read 1 file does not contain expected sequence!"; exit 1; }
+grep -q "TACCATTACCCTACCATCCACCATG" filtered_reads_R2.fastq || { echo "Filtered read 2 file does not contain expected sequence!"; exit 1; }
+
+rm filtered_reads_R1.fastq filtered_reads_R2.fastq
+
+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
@@ -235,9 +235,9 @@ build_info:
  output: "target/executable/agat/agat_convert_bed2gff"
  executable: "target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff"
  viash_version: "0.9.0"
-  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
-  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-10-g86333c1"
+  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
+  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-11-g7fb67a9"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-10-16T08:57:44Z"
+LABEL org.opencontainers.image.created="2024-10-18T09:18:56Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
+LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7"
 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
@@ -225,9 +225,9 @@ build_info:
  output: "target/executable/agat/agat_convert_embl2gff"
  executable: "target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff"
  viash_version: "0.9.0"
-  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
-  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-10-g86333c1"
+  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
+  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-11-g7fb67a9"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-10-16T08:57:46Z"
+LABEL org.opencontainers.image.created="2024-10-18T09:18:55Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
+LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/agat/agat_convert_genscan2gff/.config.vsh.yaml
+++ b/target/executable/agat/agat_convert_genscan2gff/.config.vsh.yaml
@@ -230,9 +230,9 @@ build_info:
  output: "target/executable/agat/agat_convert_genscan2gff"
  executable: "target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff"
  viash_version: "0.9.0"
-  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
-  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-10-g86333c1"
+  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
+  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-11-g7fb67a9"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff
+++ b/target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff
@@ -514,9 +514,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t

 LABEL org.opencontainers.image.authors="Leïla Paquay"
 LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_genscan2gff"
-LABEL org.opencontainers.image.created="2024-10-16T08:57:46Z"
+LABEL org.opencontainers.image.created="2024-10-18T09:18:55Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
+LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7"
 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
@@ -228,9 +228,9 @@ 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"
-  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
-  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-10-g86333c1"
+  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
+  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-11-g7fb67a9"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-10-16T08:57:46Z"
+LABEL org.opencontainers.image.created="2024-10-18T09:18:56Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
+LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7"
 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
@@ -188,9 +188,9 @@ 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"
-  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
-  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-10-g86333c1"
+  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
+  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-11-g7fb67a9"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-10-16T08:57:46Z"
+LABEL org.opencontainers.image.created="2024-10-18T09:18:55Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
+LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7"
 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
@@ -195,9 +195,9 @@ 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"
-  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
-  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-10-g86333c1"
+  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
+  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-11-g7fb67a9"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-10-16T08:57:45Z"
+LABEL org.opencontainers.image.created="2024-10-18T09:18:54Z"
 LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
-LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
+LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/arriba/.config.vsh.yaml
+++ b/target/executable/arriba/.config.vsh.yaml
@@ -706,9 +706,9 @@ build_info:
  output: "target/executable/arriba"
  executable: "target/executable/arriba/arriba"
  viash_version: "0.9.0"
-  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
-  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-10-g86333c1"
+  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
+  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-11-g7fb67a9"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-10-16T08:57:44Z"
+LABEL org.opencontainers.image.created="2024-10-18T09:18:56Z"
 LABEL org.opencontainers.image.source="https://github.com/suhrig/arriba"
-LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
+LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bbmap/bbmap_bbsplit/.config.vsh.yaml
+++ b/target/executable/bbmap/bbmap_bbsplit/.config.vsh.yaml
@@ -0,0 +1,386 @@
+name: "bbmap_bbsplit"
+namespace: "bbmap"
+version: "main"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "string"
+    name: "--id"
+    description: "Sample ID"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--paired"
+    description: "Paired fastq files or not?"
+    info: null
+    direction: "input"
+  - type: "file"
+    name: "--input"
+    description: "Input fastq files, either one or two (paired), separated by \";\"\
+      ."
+    info: null
+    example:
+    - "reads.fastq"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+  - type: "file"
+    name: "--ref"
+    description: "Reference FASTA files, separated by \";\". The primary reference\
+      \ should be specified first."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--only_build_index"
+    description: "If set, only builds the index. Otherwise, mapping is performed."
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--build"
+    description: "Designate index to use. Corresponds to the number specified when\
+      \ building the index.\nIf building the index, this will be the build's id. If\
+      \ multiple references are indexed\nin the same directory, each needs a unique\
+      \ build ID. Default: 1.\n"
+    info: null
+    example:
+    - "1"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--qin"
+    description: "Set to 33 or 64 to specify input quality value ASCII offset. Automatically\
+      \ detected if\nnot specified.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--interleaved"
+    description: "True forces paired/interleaved input; false forces single-ended\
+      \ mapping.\nIf not specified, interleaved status will be autodetected from read\
+      \ names.\n"
+    info: null
+    direction: "input"
+  - type: "integer"
+    name: "--maxindel"
+    description: "Don't look for indels longer than this. Lower is faster. Set to\
+      \ >=100k for RNA-seq.\n"
+    info: null
+    example:
+    - 20
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "double"
+    name: "--minratio"
+    description: "Fraction of max alignment score required to keep a site. Higher\
+      \ is faster.\n"
+    info: null
+    example:
+    - 0.56
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--minhits"
+    description: "Minimum number of seed hits required for candidate sites. Higher\
+      \ is faster.\n"
+    info: null
+    example:
+    - 1
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--ambiguous"
+    description: "Set behavior on ambiguously-mapped reads (with multiple top-scoring\
+      \ mapping locations).\n  * best    Use the first best site (Default)\n  * toss\
+      \    Consider unmapped\n  * random  Select one top-scoring site randomly\n \
+      \ * all     Retain all top-scoring sites.  Does not work yet with SAM output\n"
+    info: null
+    example:
+    - "best"
+    required: false
+    choices:
+    - "best"
+    - "toss"
+    - "random"
+    - "all"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--ambiguous2"
+    description: "Set behavior only for reads that map ambiguously to multiple different\
+      \ references.\nNormal 'ambiguous=' controls behavior on all ambiguous reads;\n\
+      Ambiguous2 excludes reads that map ambiguously within a single reference.\n\
+      \  * best    Use the first best site (Default)\n  * toss    Consider unmapped\n\
+      \  * all     Write a copy to the output for each reference to which it maps\n\
+      \  * split   Write a copy to the AMBIGUOUS_ output for each reference to which\
+      \ it maps\n"
+    info: null
+    example:
+    - "best"
+    required: false
+    choices:
+    - "best"
+    - "toss"
+    - "all"
+    - "split"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--qtrim"
+    description: "Quality-trim ends to Q5 before mapping. Options are 'l' (left),\
+      \ 'r' (right), and 'lr' (both).\n"
+    info: null
+    required: false
+    choices:
+    - "l"
+    - "r"
+    - "lr"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--untrim"
+    description: "Undo trimming after mapping. Untrimmed bases will be soft-clipped\
+      \ in cigar strings."
+    info: null
+    direction: "input"
+- name: "Output"
+  arguments:
+  - type: "file"
+    name: "--fastq_1"
+    description: "Output file for read 1.\n"
+    info: null
+    example:
+    - "read_out1.fastq"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--fastq_2"
+    description: "Output file for read 2.\n"
+    info: null
+    example:
+    - "read_out2.fastq"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--sam2bam"
+    alternatives:
+    - "--bs"
+    description: "Write a shell script to 'file' that will turn the sam output into\
+      \ a sorted, indexed bam file.\n"
+    info: null
+    example:
+    - "script.sh"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--scafstats"
+    description: "Write statistics on how many reads mapped to which scaffold to this\
+      \ file.\n"
+    info: null
+    example:
+    - "scaffold_stats.txt"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--refstats"
+    description: "Write statistics on how many reads were assigned to which reference\
+      \ to this file.\nUnmapped reads whose mate mapped to a reference are considered\
+      \ assigned and will be counted.\n"
+    info: null
+    example:
+    - "reference_stats.txt"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--nzo"
+    description: "Only print lines with nonzero coverage."
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--bbmap_args"
+    description: "Additional arguments from BBMap to pass to BBSplit.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Split sequencing reads by mapping them to multiple references simultaneously."
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+info: null
+status: "enabled"
+requirements:
+  commands:
+  - "ps"
+license: "BBTools Copyright (c) 2014"
+links:
+  repository: "https://github.com/BioInfoTools/BBMap/blob/master/sh/bbsplit.sh"
+  homepage: "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/"
+  documentation: "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbmap-guide/"
+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: "ubuntu:22.04"
+  target_registry: "images.viash-hub.com"
+  target_tag: "main"
+  namespace_separator: "/"
+  setup:
+  - type: "docker"
+    run:
+    - "apt-get update && \\\napt-get install -y build-essential openjdk-17-jdk wget\
+      \ tar && \\\nwget --no-check-certificate https://sourceforge.net/projects/bbmap/files/BBMap_39.01.tar.gz\
+      \ && \\\ntar xzf BBMap_39.01.tar.gz && \\\ncp -r bbmap/* /usr/local/bin\n"
+  - type: "docker"
+    run:
+    - "bbsplit.sh --version 2>&1 | awk '/BBMap version/{print \"BBMAP:\", $NF}' >\
+      \ /var/software_versions.txt\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/bbmap_bbsplit/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/bbmap/bbmap_bbsplit"
+  executable: "target/executable/bbmap/bbmap_bbsplit/bbmap_bbsplit"
+  viash_version: "0.9.0"
+  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
+  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-11-g7fb67a9"
+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"
+  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/bbmap/bbmap_bbsplit/bbmap_bbsplit
+++ b/target/executable/bbmap/bbmap_bbsplit/bbmap_bbsplit
--- a/target/executable/bcftools/bcftools_annotate/.config.vsh.yaml
+++ b/target/executable/bcftools/bcftools_annotate/.config.vsh.yaml
@@ -469,9 +469,9 @@ build_info:
  output: "target/executable/bcftools/bcftools_annotate"
  executable: "target/executable/bcftools/bcftools_annotate/bcftools_annotate"
  viash_version: "0.9.0"
-  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
-  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-10-g86333c1"
+  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
+  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-11-g7fb67a9"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bcftools/bcftools_annotate/bcftools_annotate
+++ b/target/executable/bcftools/bcftools_annotate/bcftools_annotate
@@ -650,9 +650,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_annotate"
-LABEL org.opencontainers.image.created="2024-10-16T08:57:43Z"
+LABEL org.opencontainers.image.created="2024-10-18T09:18:48Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
+LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bcftools/bcftools_concat/.config.vsh.yaml
+++ b/target/executable/bcftools/bcftools_concat/.config.vsh.yaml
@@ -335,9 +335,9 @@ build_info:
  output: "target/executable/bcftools/bcftools_concat"
  executable: "target/executable/bcftools/bcftools_concat/bcftools_concat"
  viash_version: "0.9.0"
-  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
-  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-10-g86333c1"
+  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
+  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-11-g7fb67a9"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bcftools/bcftools_concat/bcftools_concat
+++ b/target/executable/bcftools/bcftools_concat/bcftools_concat
@@ -566,9 +566,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_concat"
-LABEL org.opencontainers.image.created="2024-10-16T08:57:39Z"
+LABEL org.opencontainers.image.created="2024-10-18T09:18:49Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
+LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bcftools/bcftools_norm/.config.vsh.yaml
+++ b/target/executable/bcftools/bcftools_norm/.config.vsh.yaml
@@ -416,9 +416,9 @@ build_info:
  output: "target/executable/bcftools/bcftools_norm"
  executable: "target/executable/bcftools/bcftools_norm/bcftools_norm"
  viash_version: "0.9.0"
-  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
-  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-10-g86333c1"
+  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
+  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-11-g7fb67a9"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bcftools/bcftools_norm/bcftools_norm
+++ b/target/executable/bcftools/bcftools_norm/bcftools_norm
@@ -589,9 +589,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_norm"
-LABEL org.opencontainers.image.created="2024-10-16T08:57:40Z"
+LABEL org.opencontainers.image.created="2024-10-18T09:18:49Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
+LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7"
 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
@@ -185,9 +185,9 @@ build_info:
  output: "target/executable/bcftools/bcftools_sort"
  executable: "target/executable/bcftools/bcftools_sort/bcftools_sort"
  viash_version: "0.9.0"
-  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
-  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-10-g86333c1"
+  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
+  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-11-g7fb67a9"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-10-16T08:57:40Z"
+LABEL org.opencontainers.image.created="2024-10-18T09:18:49Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
+LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bcftools/bcftools_stats/.config.vsh.yaml
+++ b/target/executable/bcftools/bcftools_stats/.config.vsh.yaml
@@ -458,9 +458,9 @@ build_info:
  output: "target/executable/bcftools/bcftools_stats"
  executable: "target/executable/bcftools/bcftools_stats/bcftools_stats"
  viash_version: "0.9.0"
-  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
-  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-10-g86333c1"
+  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
+  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-11-g7fb67a9"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bcftools/bcftools_stats/bcftools_stats
+++ b/target/executable/bcftools/bcftools_stats/bcftools_stats
@@ -626,9 +626,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_stats"
-LABEL org.opencontainers.image.created="2024-10-16T08:57:43Z"
+LABEL org.opencontainers.image.created="2024-10-18T09:18:48Z"
 LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
-LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
+LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bcl_convert/.config.vsh.yaml
+++ b/target/executable/bcl_convert/.config.vsh.yaml
@@ -418,9 +418,9 @@ build_info:
  output: "target/executable/bcl_convert"
  executable: "target/executable/bcl_convert/bcl_convert"
  viash_version: "0.9.0"
-  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
-  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-10-g86333c1"
+  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
+  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-11-g7fb67a9"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-10-16T08:57:45Z"
+LABEL org.opencontainers.image.created="2024-10-18T09:18:54Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
+LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7"
 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
@@ -274,9 +274,9 @@ 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"
-  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
-  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-10-g86333c1"
+  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
+  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-11-g7fb67a9"
 package_config:
  name: "biobox"
  version: "main"
--- 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
@@ -554,9 +554,9 @@ RUN VERSION=$(ls -v /var/bd_rhapsody_cwl | grep '^v' | sed 's#v##' | tail -1)
 RUN echo "bdgenomics/rhapsody: \"$VERSION\"" > /var/software_versions.txt
 LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Weiwei Schultz"
 LABEL org.opencontainers.image.description="Companion container for running component bd_rhapsody bd_rhapsody_make_reference"
-LABEL org.opencontainers.image.created="2024-10-16T08:57:47Z"
+LABEL org.opencontainers.image.created="2024-10-18T09:18:52Z"
 LABEL org.opencontainers.image.source="https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1/Extra_Utilities/"
-LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
+LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml
+++ b/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml
@@ -1115,9 +1115,9 @@ build_info:
  output: "target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis"
  executable: "target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/bd_rhapsody_sequence_analysis"
  viash_version: "0.9.0"
-  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
-  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-10-g86333c1"
+  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
+  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-11-g7fb67a9"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/bd_rhapsody_sequence_analysis
+++ b/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/bd_rhapsody_sequence_analysis
@@ -954,9 +954,9 @@ RUN VERSION=$(ls -v /var/bd_rhapsody_cwl | grep '^v' | sed 's#v##' | tail -1)
 RUN echo "bdgenomics/rhapsody: \"$VERSION\"" > /var/software_versions.txt
 LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Weiwei Schultz"
 LABEL org.opencontainers.image.description="Companion container for running component bd_rhapsody bd_rhapsody_sequence_analysis"
-LABEL org.opencontainers.image.created="2024-10-16T08:57:47Z"
+LABEL org.opencontainers.image.created="2024-10-18T09:18:52Z"
 LABEL org.opencontainers.image.source="https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1"
-LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
+LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7"
 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
@@ -187,9 +187,9 @@ build_info:
  output: "target/executable/bedtools/bedtools_bamtofastq"
  executable: "target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq"
  viash_version: "0.9.0"
-  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
-  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-10-g86333c1"
+  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
+  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-11-g7fb67a9"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-10-16T08:57:42Z"
+LABEL org.opencontainers.image.created="2024-10-18T09:18:55Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
+LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7"
 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
@@ -176,9 +176,9 @@ build_info:
  output: "target/executable/bedtools/bedtools_bed12tobed6"
  executable: "target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6"
  viash_version: "0.9.0"
-  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
-  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-10-g86333c1"
+  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
+  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-11-g7fb67a9"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-10-16T08:57:43Z"
+LABEL org.opencontainers.image.created="2024-10-18T09:18:56Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
+LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7"
 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
@@ -214,9 +214,9 @@ build_info:
  output: "target/executable/bedtools/bedtools_bedtobam"
  executable: "target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam"
  viash_version: "0.9.0"
-  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
-  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-10-g86333c1"
+  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
+  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-11-g7fb67a9"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-10-16T08:57:45Z"
+LABEL org.opencontainers.image.created="2024-10-18T09:18:58Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
+LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools/bedtools_genomecov/.config.vsh.yaml
+++ b/target/executable/bedtools/bedtools_genomecov/.config.vsh.yaml
@@ -337,9 +337,9 @@ build_info:
  output: "target/executable/bedtools/bedtools_genomecov"
  executable: "target/executable/bedtools/bedtools_genomecov/bedtools_genomecov"
  viash_version: "0.9.0"
-  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
-  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-10-g86333c1"
+  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
+  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-11-g7fb67a9"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/bedtools/bedtools_genomecov/bedtools_genomecov
+++ b/target/executable/bedtools/bedtools_genomecov/bedtools_genomecov
@@ -591,9 +591,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_genomecov"
-LABEL org.opencontainers.image.created="2024-10-16T08:57:43Z"
+LABEL org.opencontainers.image.created="2024-10-18T09:18:55Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
+LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7"
 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
@@ -232,9 +232,9 @@ build_info:
  output: "target/executable/bedtools/bedtools_getfasta"
  executable: "target/executable/bedtools/bedtools_getfasta/bedtools_getfasta"
  viash_version: "0.9.0"
-  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
-  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-10-g86333c1"
+  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
+  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-11-g7fb67a9"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-10-16T08:57:44Z"
+LABEL org.opencontainers.image.created="2024-10-18T09:18:57Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
+LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7"
 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
@@ -273,9 +273,9 @@ build_info:
  output: "target/executable/bedtools/bedtools_groupby"
  executable: "target/executable/bedtools/bedtools_groupby/bedtools_groupby"
  viash_version: "0.9.0"
-  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
-  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-10-g86333c1"
+  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
+  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-11-g7fb67a9"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-10-16T08:57:44Z"
+LABEL org.opencontainers.image.created="2024-10-18T09:18:57Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
+LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7"
 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
@@ -410,9 +410,9 @@ build_info:
  output: "target/executable/bedtools/bedtools_intersect"
  executable: "target/executable/bedtools/bedtools_intersect/bedtools_intersect"
  viash_version: "0.9.0"
-  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
-  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-10-g86333c1"
+  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
+  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-11-g7fb67a9"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-10-16T08:57:42Z"
+LABEL org.opencontainers.image.created="2024-10-18T09:18:54Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
+LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7"
 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
@@ -210,9 +210,9 @@ build_info:
  output: "target/executable/bedtools/bedtools_links"
  executable: "target/executable/bedtools/bedtools_links/bedtools_links"
  viash_version: "0.9.0"
-  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
-  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-10-g86333c1"
+  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
+  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-11-g7fb67a9"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-10-16T08:57:43Z"
+LABEL org.opencontainers.image.created="2024-10-18T09:18:56Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
+LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7"
 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
@@ -279,9 +279,9 @@ build_info:
  output: "target/executable/bedtools/bedtools_merge"
  executable: "target/executable/bedtools/bedtools_merge/bedtools_merge"
  viash_version: "0.9.0"
-  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
-  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-10-g86333c1"
+  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
+  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-11-g7fb67a9"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-10-16T08:57:44Z"
+LABEL org.opencontainers.image.created="2024-10-18T09:18:57Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
+LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7"
 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
@@ -222,9 +222,9 @@ build_info:
  output: "target/executable/bedtools/bedtools_sort"
  executable: "target/executable/bedtools/bedtools_sort/bedtools_sort"
  viash_version: "0.9.0"
-  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
-  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-10-g86333c1"
+  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
+  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-11-g7fb67a9"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-10-16T08:57:42Z"
+LABEL org.opencontainers.image.created="2024-10-18T09:18:55Z"
 LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
-LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
+LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7"
 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
@@ -158,9 +158,9 @@ build_info:
  output: "target/executable/busco/busco_download_datasets"
  executable: "target/executable/busco/busco_download_datasets/busco_download_datasets"
  viash_version: "0.9.0"
-  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
-  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-10-g86333c1"
+  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
+  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-11-g7fb67a9"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-10-16T08:57:41Z"
+LABEL org.opencontainers.image.created="2024-10-18T09:18:54Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
+LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7"
 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
@@ -145,9 +145,9 @@ build_info:
  output: "target/executable/busco/busco_list_datasets"
  executable: "target/executable/busco/busco_list_datasets/busco_list_datasets"
  viash_version: "0.9.0"
-  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
-  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-10-g86333c1"
+  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
+  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-11-g7fb67a9"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-10-16T08:57:40Z"
+LABEL org.opencontainers.image.created="2024-10-18T09:18:53Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
+LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7"
 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
@@ -423,9 +423,9 @@ build_info:
  output: "target/executable/busco/busco_run"
  executable: "target/executable/busco/busco_run/busco_run"
  viash_version: "0.9.0"
-  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
-  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-10-g86333c1"
+  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
+  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-11-g7fb67a9"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-10-16T08:57:41Z"
+LABEL org.opencontainers.image.created="2024-10-18T09:18:53Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
+LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/cutadapt/.config.vsh.yaml
+++ b/target/executable/cutadapt/.config.vsh.yaml
@@ -740,9 +740,9 @@ build_info:
  output: "target/executable/cutadapt"
  executable: "target/executable/cutadapt/cutadapt"
  viash_version: "0.9.0"
-  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
-  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-10-g86333c1"
+  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
+  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-11-g7fb67a9"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-10-16T08:57:40Z"
+LABEL org.opencontainers.image.created="2024-10-18T09:18:45Z"
 LABEL org.opencontainers.image.source="https://github.com/marcelm/cutadapt"
-LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
+LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/falco/.config.vsh.yaml
+++ b/target/executable/falco/.config.vsh.yaml
@@ -317,9 +317,9 @@ build_info:
  output: "target/executable/falco"
  executable: "target/executable/falco/falco"
  viash_version: "0.9.0"
-  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
-  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-10-g86333c1"
+  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
+  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-11-g7fb67a9"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-10-16T08:57:42Z"
+LABEL org.opencontainers.image.created="2024-10-18T09:18:47Z"
 LABEL org.opencontainers.image.source="https://github.com/smithlabcode/falco"
-LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
+LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/fastp/.config.vsh.yaml
+++ b/target/executable/fastp/.config.vsh.yaml
@@ -1083,9 +1083,9 @@ build_info:
  output: "target/executable/fastp"
  executable: "target/executable/fastp/fastp"
  viash_version: "0.9.0"
-  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
-  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-10-g86333c1"
+  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
+  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-11-g7fb67a9"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-10-16T08:57:46Z"
+LABEL org.opencontainers.image.created="2024-10-18T09:18:51Z"
 LABEL org.opencontainers.image.source="https://github.com/OpenGene/fastp"
-LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
+LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/fastqc/.config.vsh.yaml
+++ b/target/executable/fastqc/.config.vsh.yaml
@@ -340,9 +340,9 @@ build_info:
  output: "target/executable/fastqc"
  executable: "target/executable/fastqc/fastqc"
  viash_version: "0.9.0"
-  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
-  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-10-g86333c1"
+  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
+  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-11-g7fb67a9"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/fastqc/fastqc
+++ b/target/executable/fastqc/fastqc
@@ -601,9 +601,9 @@ RUN echo "fastqc: $(fastqc --version | sed -n 's/^FastQC //p')" > /var/software_

 LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
 LABEL org.opencontainers.image.description="Companion container for running component fastqc"
-LABEL org.opencontainers.image.created="2024-10-16T08:57:43Z"
+LABEL org.opencontainers.image.created="2024-10-18T09:18:52Z"
 LABEL org.opencontainers.image.source="https://github.com/s-andrews/FastQC"
-LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
+LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/featurecounts/.config.vsh.yaml
+++ b/target/executable/featurecounts/.config.vsh.yaml
@@ -645,9 +645,9 @@ build_info:
  output: "target/executable/featurecounts"
  executable: "target/executable/featurecounts/featurecounts"
  viash_version: "0.9.0"
-  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
-  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-10-g86333c1"
+  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
+  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-11-g7fb67a9"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-10-16T08:57:42Z"
+LABEL org.opencontainers.image.created="2024-10-18T09:18:47Z"
 LABEL org.opencontainers.image.source="https://github.com/ShiLab-Bioinformatics/subread"
-LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
+LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/fq_subsample/.config.vsh.yaml
+++ b/target/executable/fq_subsample/.config.vsh.yaml
@@ -190,9 +190,9 @@ build_info:
  output: "target/executable/fq_subsample"
  executable: "target/executable/fq_subsample/fq_subsample"
  viash_version: "0.9.0"
-  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
-  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-10-g86333c1"
+  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
+  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-11-g7fb67a9"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/fq_subsample/fq_subsample
+++ b/target/executable/fq_subsample/fq_subsample
@@ -493,9 +493,9 @@ mv target/release/fq /usr/local/bin/ && \
 cd / && rm -rf /fq

 LABEL org.opencontainers.image.description="Companion container for running component fq_subsample"
-LABEL org.opencontainers.image.created="2024-10-16T08:57:43Z"
+LABEL org.opencontainers.image.created="2024-10-18T09:18:48Z"
 LABEL org.opencontainers.image.source="https://github.com/stjude-rust-labs/fq"
-LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
+LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/gffread/.config.vsh.yaml
+++ b/target/executable/gffread/.config.vsh.yaml
@@ -685,9 +685,9 @@ build_info:
  output: "target/executable/gffread"
  executable: "target/executable/gffread/gffread"
  viash_version: "0.9.0"
-  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
-  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-10-g86333c1"
+  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
+  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-11-g7fb67a9"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-10-16T08:57:42Z"
+LABEL org.opencontainers.image.created="2024-10-18T09:18:51Z"
 LABEL org.opencontainers.image.source="https://github.com/gpertea/gffread"
-LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
+LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/kallisto/kallisto_index/.config.vsh.yaml
+++ b/target/executable/kallisto/kallisto_index/.config.vsh.yaml
@@ -218,9 +218,9 @@ build_info:
  output: "target/executable/kallisto/kallisto_index"
  executable: "target/executable/kallisto/kallisto_index/kallisto_index"
  viash_version: "0.9.0"
-  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
-  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-10-g86333c1"
+  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
+  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-11-g7fb67a9"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/kallisto/kallisto_index/kallisto_index
+++ b/target/executable/kallisto/kallisto_index/kallisto_index
@@ -506,9 +506,9 @@ tar -xzf kallisto_linux-v0.50.1.tar.gz && \
 mv kallisto/kallisto /usr/local/bin/

 LABEL org.opencontainers.image.description="Companion container for running component kallisto kallisto_index"
-LABEL org.opencontainers.image.created="2024-10-16T08:57:44Z"
+LABEL org.opencontainers.image.created="2024-10-18T09:18:57Z"
 LABEL org.opencontainers.image.source="https://github.com/pachterlab/kallisto"
-LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
+LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/kallisto/kallisto_quant/.config.vsh.yaml
+++ b/target/executable/kallisto/kallisto_quant/.config.vsh.yaml
@@ -234,9 +234,9 @@ build_info:
  output: "target/executable/kallisto/kallisto_quant"
  executable: "target/executable/kallisto/kallisto_quant/kallisto_quant"
  viash_version: "0.9.0"
-  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
-  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-10-g86333c1"
+  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
+  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-11-g7fb67a9"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/kallisto/kallisto_quant/kallisto_quant
+++ b/target/executable/kallisto/kallisto_quant/kallisto_quant
@@ -518,9 +518,9 @@ mv kallisto/kallisto /usr/local/bin/
 RUN echo "kallisto: $(kallisto version | sed 's/kallisto, version //')" > /var/software_versions.txt

 LABEL org.opencontainers.image.description="Companion container for running component kallisto kallisto_quant"
-LABEL org.opencontainers.image.created="2024-10-16T08:57:45Z"
+LABEL org.opencontainers.image.created="2024-10-18T09:18:57Z"
 LABEL org.opencontainers.image.source="https://github.com/pachterlab/kallisto"
-LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
+LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7"
 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
@@ -507,9 +507,9 @@ build_info:
  output: "target/executable/lofreq/lofreq_call"
  executable: "target/executable/lofreq/lofreq_call/lofreq_call"
  viash_version: "0.9.0"
-  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
-  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-10-g86333c1"
+  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
+  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-11-g7fb67a9"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-10-16T08:57:45Z"
+LABEL org.opencontainers.image.created="2024-10-18T09:18:58Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
+LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7"
 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
@@ -215,9 +215,9 @@ build_info:
  output: "target/executable/lofreq/lofreq_indelqual"
  executable: "target/executable/lofreq/lofreq_indelqual/lofreq_indelqual"
  viash_version: "0.9.0"
-  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
-  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-10-g86333c1"
+  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
+  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-11-g7fb67a9"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-10-16T08:57:46Z"
+LABEL org.opencontainers.image.created="2024-10-18T09:18:58Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
+LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/multiqc/.config.vsh.yaml
+++ b/target/executable/multiqc/.config.vsh.yaml
@@ -456,9 +456,9 @@ build_info:
  output: "target/executable/multiqc"
  executable: "target/executable/multiqc/multiqc"
  viash_version: "0.9.0"
-  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
-  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-10-g86333c1"
+  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
+  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-11-g7fb67a9"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-10-16T08:57:44Z"
+LABEL org.opencontainers.image.created="2024-10-18T09:18:53Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
-LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
+LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/pear/.config.vsh.yaml
+++ b/target/executable/pear/.config.vsh.yaml
@@ -398,9 +398,9 @@ build_info:
  output: "target/executable/pear"
  executable: "target/executable/pear/pear"
  viash_version: "0.9.0"
-  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
-  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-10-g86333c1"
+  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
+  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-11-g7fb67a9"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-10-16T08:57:39Z"
+LABEL org.opencontainers.image.created="2024-10-18T09:18:44Z"
 LABEL org.opencontainers.image.source="https://github.com/tseemann/PEAR"
-LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
+LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7"
 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
@@ -264,9 +264,9 @@ build_info:
  output: "target/executable/qualimap/qualimap_rnaseq"
  executable: "target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq"
  viash_version: "0.9.0"
-  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
-  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-10-g86333c1"
+  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
+  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-11-g7fb67a9"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-10-16T08:57:43Z"
+LABEL org.opencontainers.image.created="2024-10-18T09:18:49Z"
 LABEL org.opencontainers.image.source="https://bitbucket.org/kokonech/qualimap/commits/branch/master"
-LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
+LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml
+++ b/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml
@@ -852,9 +852,9 @@ build_info:
  output: "target/executable/rsem/rsem_calculate_expression"
  executable: "target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression"
  viash_version: "0.9.0"
-  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
-  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-10-g86333c1"
+  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
+  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-11-g7fb67a9"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression
+++ b/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression
@@ -991,9 +991,9 @@ echo "bowtie: `bowtie --version | grep -oP 'bowtie-align-s version \K\d+\.\d+\.\
 echo "HISAT2: `hisat2 --version | grep -oP 'hisat2-align-s version \K\d+\.\d+\.\d+'`" >> /var/software_versions.txt

 LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_calculate_expression"
-LABEL org.opencontainers.image.created="2024-10-16T08:57:41Z"
+LABEL org.opencontainers.image.created="2024-10-18T09:18:46Z"
 LABEL org.opencontainers.image.source="https://github.com/deweylab/RSEM"
-LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
+LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7"
 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
@@ -416,9 +416,9 @@ build_info:
  output: "target/executable/rsem/rsem_prepare_reference"
  executable: "target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference"
  viash_version: "0.9.0"
-  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
-  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-10-g86333c1"
+  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
+  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-11-g7fb67a9"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-10-16T08:57:41Z"
+LABEL org.opencontainers.image.created="2024-10-18T09:18:46Z"
 LABEL org.opencontainers.image.source="https://github.com/deweylab/RSEM"
-LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
+LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7"
 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
@@ -277,9 +277,9 @@ build_info:
  output: "target/executable/salmon/salmon_index"
  executable: "target/executable/salmon/salmon_index/salmon_index"
  viash_version: "0.9.0"
-  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
-  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-10-g86333c1"
+  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
+  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-11-g7fb67a9"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-10-16T08:57:40Z"
+LABEL org.opencontainers.image.created="2024-10-18T09:18:53Z"
 LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon"
-LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
+LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7"
 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
@@ -1173,9 +1173,9 @@ build_info:
  output: "target/executable/salmon/salmon_quant"
  executable: "target/executable/salmon/salmon_quant/salmon_quant"
  viash_version: "0.9.0"
-  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
-  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-10-g86333c1"
+  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
+  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-11-g7fb67a9"
 package_config:
  name: "biobox"
  version: "main"
--- 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="2024-10-16T08:57:43Z"
+LABEL org.opencontainers.image.created="2024-10-18T09:18:52Z"
 LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon"
-LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
+LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7"
 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
@@ -264,9 +264,9 @@ build_info:
  output: "target/executable/samtools/samtools_collate"
  executable: "target/executable/samtools/samtools_collate/samtools_collate"
  viash_version: "0.9.0"
-  git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
-  git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-10-g86333c1"
+  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
+  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-11-g7fb67a9"
 package_config:
  name: "biobox"
  version: "main"
--- a/Show More
+++ b/Show More