diff --git a/CHANGELOG.md b/CHANGELOG.md index 47c786c6..16e79693 100644 --- 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). diff --git a/src/bbmap_bbsplit/config.vsh.yaml b/src/bbmap_bbsplit/config.vsh.yaml new file mode 100644 index 00000000..61336b35 --- /dev/null +++ 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 diff --git a/src/bbmap_bbsplit/help.txt b/src/bbmap_bbsplit/help.txt new file mode 100644 index 00000000..56544a34 --- /dev/null +++ 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= ref_y= +To map: bbsplit.sh build=<1> in= out_x= out_y= + +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= A list of references, or directories containing fasta files. +ref_= 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= Primary reads input; required parameter. +in2= For paired reads in two files. +qin= Set to 33 or 64 to specify input quality value ASCII offset. +interleaved= 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= 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= 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= Quality-trim ends to Q5 before mapping. Options are 'l' (left), 'r' (right), and 'lr' (both). +untrim= Undo trimming after mapping. Untrimmed bases will be soft-clipped in cigar strings. + +Output Parameters: +out_= Output reads that map to the reference to . +basename=prefix%suffix Equivalent to multiple out_%=prefix%suffix expressions, in which each % is replaced by the name of a reference file. +bs= Write a shell script to 'file' that will turn the sam output into a sorted, indexed bam file. +scafstats= Write statistics on how many reads mapped to which scaffold to this file. +refstats= 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. \ No newline at end of file diff --git a/src/bbmap_bbsplit/script.sh b/src/bbmap_bbsplit/script.sh new file mode 100755 index 00000000..ac8542c9 --- /dev/null +++ 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 diff --git a/src/bbmap_bbsplit/test.sh b/src/bbmap_bbsplit/test.sh new file mode 100644 index 00000000..1ad7aac2 --- /dev/null +++ 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 \ No newline at end of file diff --git a/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml b/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml index 6d5842b3..72ea0a76 100644 --- 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" diff --git a/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff b/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff index 96c47390..c795d7ea 100755 --- 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 diff --git a/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml b/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml index 080dd19a..e383351e 100644 --- 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" diff --git a/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff b/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff index 7e9d14eb..20986469 100755 --- 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 diff --git a/target/executable/agat/agat_convert_genscan2gff/.config.vsh.yaml b/target/executable/agat/agat_convert_genscan2gff/.config.vsh.yaml index 506a8bd8..f271bd7b 100644 --- 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" diff --git a/target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff b/target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff index 87ba31d1..2de031e0 100755 --- 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 diff --git a/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml b/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml index 17c91a03..3fc459ca 100644 --- 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" diff --git a/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf b/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf index 3c7849e4..4c687bda 100755 --- a/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf +++ b/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf @@ -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 diff --git a/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml b/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml index 504e5f29..4e108d35 100644 --- 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" diff --git a/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv b/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv index ec79ce76..7d3bc5c7 100755 --- a/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv +++ b/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv @@ -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 diff --git a/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml b/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml index 76855cd1..851308b8 100644 --- 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" diff --git a/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf b/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf index 0b2e9506..8d081218 100755 --- a/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf +++ b/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf @@ -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 diff --git a/target/executable/arriba/.config.vsh.yaml b/target/executable/arriba/.config.vsh.yaml index 88edafcc..ce6efbe2 100644 --- 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" diff --git a/target/executable/arriba/arriba b/target/executable/arriba/arriba index 6dfa6e45..40059e2c 100755 --- 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 diff --git a/target/executable/bbmap/bbmap_bbsplit/.config.vsh.yaml b/target/executable/bbmap/bbmap_bbsplit/.config.vsh.yaml new file mode 100644 index 00000000..39893010 --- /dev/null +++ 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:\", $NF}' >\ + \ /var/software_versions.txt\n" + entrypoint: [] + cmd: null +- type: "native" + id: "native" +build_info: + config: "src/bbmap_bbsplit/config.vsh.yaml" + runner: "executable" + engine: "docker|native" + output: "target/executable/bbmap/bbmap_bbsplit" + executable: "target/executable/bbmap/bbmap_bbsplit/bbmap_bbsplit" + viash_version: "0.9.0" + git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7" + git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-11-g7fb67a9" +package_config: + name: "biobox" + version: "main" + description: "A collection of bioinformatics tools for working with sequence data.\n" + info: null + viash_version: "0.9.0" + source: "src" + target: "target" + config_mods: + - ".requirements.commands := ['ps']\n" + - ".engines += { type: \"native\" }" + - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" + - ".engines[.type == 'docker'].target_tag := 'main'" + keywords: + - "bioinformatics" + - "modules" + - "sequencing" + license: "MIT" + organization: "vsh" + links: + repository: "https://github.com/viash-hub/biobox" + issue_tracker: "https://github.com/viash-hub/biobox/issues" diff --git a/target/executable/bbmap/bbmap_bbsplit/bbmap_bbsplit b/target/executable/bbmap/bbmap_bbsplit/bbmap_bbsplit new file mode 100755 index 00000000..c99ceb0c --- /dev/null +++ b/target/executable/bbmap/bbmap_bbsplit/bbmap_bbsplit @@ -0,0 +1,1739 @@ +#!/usr/bin/env bash + +# bbmap_bbsplit main +# +# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. +# +# The component may contain files which fall under a different license. The +# authors of this component should specify the license in the header of such +# files, or include a separate license file detailing the licenses of all included +# files. + +set -e + +if [ -z "$VIASH_TEMP" ]; then + VIASH_TEMP=${VIASH_TEMP:-$VIASH_TMPDIR} + VIASH_TEMP=${VIASH_TEMP:-$VIASH_TEMPDIR} + VIASH_TEMP=${VIASH_TEMP:-$VIASH_TMP} + VIASH_TEMP=${VIASH_TEMP:-$TMPDIR} + VIASH_TEMP=${VIASH_TEMP:-$TMP} + VIASH_TEMP=${VIASH_TEMP:-$TEMPDIR} + VIASH_TEMP=${VIASH_TEMP:-$TEMP} + VIASH_TEMP=${VIASH_TEMP:-/tmp} +fi + +# define helper functions +# ViashQuote: put quotes around non flag values +# $1 : unquoted string +# return : possibly quoted string +# examples: +# ViashQuote --foo # returns --foo +# ViashQuote bar # returns 'bar' +# Viashquote --foo=bar # returns --foo='bar' +function ViashQuote { + if [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+=.+$ ]]; then + echo "$1" | sed "s#=\(.*\)#='\1'#" + elif [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+$ ]]; then + echo "$1" + else + echo "'$1'" + fi +} +# ViashRemoveFlags: Remove leading flag +# $1 : string with a possible leading flag +# return : string without possible leading flag +# examples: +# ViashRemoveFlags --foo=bar # returns bar +function ViashRemoveFlags { + echo "$1" | sed 's/^--*[a-zA-Z0-9_\-]*=//' +} +# ViashSourceDir: return the path of a bash file, following symlinks +# usage : ViashSourceDir ${BASH_SOURCE[0]} +# $1 : Should always be set to ${BASH_SOURCE[0]} +# returns : The absolute path of the bash file +function ViashSourceDir { + local source="$1" + while [ -h "$source" ]; do + local dir="$( cd -P "$( dirname "$source" )" >/dev/null 2>&1 && pwd )" + source="$(readlink "$source")" + [[ $source != /* ]] && source="$dir/$source" + done + cd -P "$( dirname "$source" )" >/dev/null 2>&1 && pwd +} +# ViashFindTargetDir: return the path of the '.build.yaml' file, following symlinks +# usage : ViashFindTargetDir 'ScriptPath' +# $1 : The location from where to start the upward search +# returns : The absolute path of the '.build.yaml' file +function ViashFindTargetDir { + local source="$1" + while [[ "$source" != "" && ! -e "$source/.build.yaml" ]]; do + source=${source%/*} + done + echo $source +} +# see https://en.wikipedia.org/wiki/Syslog#Severity_level +VIASH_LOGCODE_EMERGENCY=0 +VIASH_LOGCODE_ALERT=1 +VIASH_LOGCODE_CRITICAL=2 +VIASH_LOGCODE_ERROR=3 +VIASH_LOGCODE_WARNING=4 +VIASH_LOGCODE_NOTICE=5 +VIASH_LOGCODE_INFO=6 +VIASH_LOGCODE_DEBUG=7 +VIASH_VERBOSITY=$VIASH_LOGCODE_NOTICE + +# ViashLog: Log events depending on the verbosity level +# usage: ViashLog 1 alert Oh no something went wrong! +# $1: required verbosity level +# $2: display tag +# $3+: messages to display +# stdout: Your input, prepended by '[$2] '. +function ViashLog { + local required_level="$1" + local display_tag="$2" + shift 2 + if [ $VIASH_VERBOSITY -ge $required_level ]; then + >&2 echo "[$display_tag]" "$@" + fi +} + +# ViashEmergency: log events when the system is unstable +# usage: ViashEmergency Oh no something went wrong. +# stdout: Your input, prepended by '[emergency] '. +function ViashEmergency { + ViashLog $VIASH_LOGCODE_EMERGENCY emergency "$@" +} + +# ViashAlert: log events when actions must be taken immediately (e.g. corrupted system database) +# usage: ViashAlert Oh no something went wrong. +# stdout: Your input, prepended by '[alert] '. +function ViashAlert { + ViashLog $VIASH_LOGCODE_ALERT alert "$@" +} + +# ViashCritical: log events when a critical condition occurs +# usage: ViashCritical Oh no something went wrong. +# stdout: Your input, prepended by '[critical] '. +function ViashCritical { + ViashLog $VIASH_LOGCODE_CRITICAL critical "$@" +} + +# ViashError: log events when an error condition occurs +# usage: ViashError Oh no something went wrong. +# stdout: Your input, prepended by '[error] '. +function ViashError { + ViashLog $VIASH_LOGCODE_ERROR error "$@" +} + +# ViashWarning: log potentially abnormal events +# usage: ViashWarning Something may have gone wrong. +# stdout: Your input, prepended by '[warning] '. +function ViashWarning { + ViashLog $VIASH_LOGCODE_WARNING warning "$@" +} + +# ViashNotice: log significant but normal events +# usage: ViashNotice This just happened. +# stdout: Your input, prepended by '[notice] '. +function ViashNotice { + ViashLog $VIASH_LOGCODE_NOTICE notice "$@" +} + +# ViashInfo: log normal events +# usage: ViashInfo This just happened. +# stdout: Your input, prepended by '[info] '. +function ViashInfo { + ViashLog $VIASH_LOGCODE_INFO info "$@" +} + +# ViashDebug: log all events, for debugging purposes +# usage: ViashDebug This just happened. +# stdout: Your input, prepended by '[debug] '. +function ViashDebug { + ViashLog $VIASH_LOGCODE_DEBUG debug "$@" +} + +# find source folder of this component +VIASH_META_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}` + +# find the root of the built components & dependencies +VIASH_TARGET_DIR=`ViashFindTargetDir $VIASH_META_RESOURCES_DIR` + +# define meta fields +VIASH_META_NAME="bbmap_bbsplit" +VIASH_META_FUNCTIONALITY_NAME="bbmap_bbsplit" +VIASH_META_EXECUTABLE="$VIASH_META_RESOURCES_DIR/$VIASH_META_NAME" +VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml" +VIASH_META_TEMP_DIR="$VIASH_TEMP" + + +# ViashHelp: Display helpful explanation about this executable +function ViashHelp { + echo "bbmap_bbsplit main" + echo "" + echo "Split sequencing reads by mapping them to multiple references simultaneously." + echo "" + echo "Input:" + echo " --id" + echo " type: string" + echo " Sample ID" + echo "" + echo " --paired" + echo " type: boolean_true" + echo " Paired fastq files or not?" + echo "" + echo " --input" + echo " type: file, multiple values allowed, file must exist" + echo " example: reads.fastq" + echo " Input fastq files, either one or two (paired), separated by \";\"." + echo "" + echo " --ref" + echo " type: file, multiple values allowed, file must exist" + echo " Reference FASTA files, separated by \";\". The primary reference should be" + echo " specified first." + echo "" + echo " --only_build_index" + echo " type: boolean_true" + echo " If set, only builds the index. Otherwise, mapping is performed." + echo "" + echo " --build" + echo " type: string" + echo " example: 1" + echo " Designate index to use. Corresponds to the number specified when" + echo " building the index." + echo " If building the index, this will be the build's id. If multiple" + echo " references are indexed" + echo " in the same directory, each needs a unique build ID. Default: 1." + echo "" + echo " --qin" + echo " type: string" + echo " Set to 33 or 64 to specify input quality value ASCII offset." + echo " Automatically detected if" + echo " not specified." + echo "" + echo " --interleaved" + echo " type: boolean_true" + echo " True forces paired/interleaved input; false forces single-ended mapping." + echo " If not specified, interleaved status will be autodetected from read" + echo " names." + echo "" + echo " --maxindel" + echo " type: integer" + echo " example: 20" + echo " Don't look for indels longer than this. Lower is faster. Set to >=100k" + echo " for RNA-seq." + echo "" + echo " --minratio" + echo " type: double" + echo " example: 0.56" + echo " Fraction of max alignment score required to keep a site. Higher is" + echo " faster." + echo "" + echo " --minhits" + echo " type: integer" + echo " example: 1" + echo " Minimum number of seed hits required for candidate sites. Higher is" + echo " faster." + echo "" + echo " --ambiguous" + echo " type: string" + echo " example: best" + echo " choices: [ best, toss, random, all ]" + echo " Set behavior on ambiguously-mapped reads (with multiple top-scoring" + echo " mapping locations)." + echo " * best Use the first best site (Default)" + echo " * toss Consider unmapped" + echo " * random Select one top-scoring site randomly" + echo " * all Retain all top-scoring sites. Does not work yet with SAM" + echo " output" + echo "" + echo " --ambiguous2" + echo " type: string" + echo " example: best" + echo " choices: [ best, toss, all, split ]" + echo " Set behavior only for reads that map ambiguously to multiple different" + echo " references." + echo " Normal 'ambiguous=' controls behavior on all ambiguous reads;" + echo " Ambiguous2 excludes reads that map ambiguously within a single" + echo " reference." + echo " * best Use the first best site (Default)" + echo " * toss Consider unmapped" + echo " * all Write a copy to the output for each reference to which it" + echo " maps" + echo " * split Write a copy to the AMBIGUOUS_ output for each reference to" + echo " which it maps" + echo "" + echo " --qtrim" + echo " type: string" + echo " choices: [ l, r, lr ]" + echo " Quality-trim ends to Q5 before mapping. Options are 'l' (left), 'r'" + echo " (right), and 'lr' (both)." + echo "" + echo " --untrim" + echo " type: boolean_true" + echo " Undo trimming after mapping. Untrimmed bases will be soft-clipped in" + echo " cigar strings." + echo "" + echo "Output:" + echo " --fastq_1" + echo " type: file, output, file must exist" + echo " example: read_out1.fastq" + echo " Output file for read 1." + echo "" + echo " --fastq_2" + echo " type: file, output, file must exist" + echo " example: read_out2.fastq" + echo " Output file for read 2." + echo "" + echo " --bs, --sam2bam" + echo " type: file, output, file must exist" + echo " example: script.sh" + echo " Write a shell script to 'file' that will turn the sam output into a" + echo " sorted, indexed bam file." + echo "" + echo " --scafstats" + echo " type: file, output, file must exist" + echo " example: scaffold_stats.txt" + echo " Write statistics on how many reads mapped to which scaffold to this" + echo " file." + echo "" + echo " --refstats" + echo " type: file, output, file must exist" + echo " example: reference_stats.txt" + echo " Write statistics on how many reads were assigned to which reference to" + echo " this file." + echo " Unmapped reads whose mate mapped to a reference are considered assigned" + echo " and will be counted." + echo "" + echo " --nzo" + echo " type: boolean_true" + echo " Only print lines with nonzero coverage." + echo "" + echo " --bbmap_args" + echo " type: string" + echo " Additional arguments from BBMap to pass to BBSplit." +} + +# initialise variables +VIASH_MODE='run' +VIASH_ENGINE_ID='docker' + +######## Helper functions for setting up Docker images for viash ######## +# expects: ViashDockerBuild + +# ViashDockerInstallationCheck: check whether Docker is installed correctly +# +# examples: +# ViashDockerInstallationCheck +function ViashDockerInstallationCheck { + ViashDebug "Checking whether Docker is installed" + if [ ! command -v docker &> /dev/null ]; then + ViashCritical "Docker doesn't seem to be installed. See 'https://docs.docker.com/get-docker/' for instructions." + exit 1 + fi + + ViashDebug "Checking whether the Docker daemon is running" + local save=$-; set +e + local docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null) + local out=$? + [[ $save =~ e ]] && set -e + if [ $out -ne 0 ]; then + ViashCritical "Docker daemon does not seem to be running. Try one of the following:" + ViashCritical "- Try running 'dockerd' in the command line" + ViashCritical "- See https://docs.docker.com/config/daemon/" + exit 1 + fi +} + +# ViashDockerRemoteTagCheck: check whether a Docker image is available +# on a remote. Assumes `docker login` has been performed, if relevant. +# +# $1 : image identifier with format `[registry/]image[:tag]` +# exit code $? : whether or not the image was found +# examples: +# ViashDockerRemoteTagCheck python:latest +# echo $? # returns '0' +# ViashDockerRemoteTagCheck sdaizudceahifu +# echo $? # returns '1' +function ViashDockerRemoteTagCheck { + docker manifest inspect $1 > /dev/null 2> /dev/null +} + +# ViashDockerLocalTagCheck: check whether a Docker image is available locally +# +# $1 : image identifier with format `[registry/]image[:tag]` +# exit code $? : whether or not the image was found +# examples: +# docker pull python:latest +# ViashDockerLocalTagCheck python:latest +# echo $? # returns '0' +# ViashDockerLocalTagCheck sdaizudceahifu +# echo $? # returns '1' +function ViashDockerLocalTagCheck { + [ -n "$(docker images -q $1)" ] +} + +# ViashDockerPull: pull a Docker image +# +# $1 : image identifier with format `[registry/]image[:tag]` +# exit code $? : whether or not the image was found +# examples: +# ViashDockerPull python:latest +# echo $? # returns '0' +# ViashDockerPull sdaizudceahifu +# echo $? # returns '1' +function ViashDockerPull { + ViashNotice "Checking if Docker image is available at '$1'" + if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then + docker pull $1 && return 0 || return 1 + else + local save=$-; set +e + docker pull $1 2> /dev/null > /dev/null + local out=$? + [[ $save =~ e ]] && set -e + if [ $out -ne 0 ]; then + ViashWarning "Could not pull from '$1'. Docker image doesn't exist or is not accessible." + fi + return $out + fi +} + +# ViashDockerPush: push a Docker image +# +# $1 : image identifier with format `[registry/]image[:tag]` +# exit code $? : whether or not the image was found +# examples: +# ViashDockerPush python:latest +# echo $? # returns '0' +# ViashDockerPush sdaizudceahifu +# echo $? # returns '1' +function ViashDockerPush { + ViashNotice "Pushing image to '$1'" + local save=$-; set +e + local out + if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then + docker push $1 + out=$? + else + docker push $1 2> /dev/null > /dev/null + out=$? + fi + [[ $save =~ e ]] && set -e + if [ $out -eq 0 ]; then + ViashNotice "Container '$1' push succeeded." + else + ViashError "Container '$1' push errored. You might not be logged in or have the necessary permissions." + fi + return $out +} + +# ViashDockerPullElseBuild: pull a Docker image, else build it +# +# $1 : image identifier with format `[registry/]image[:tag]` +# ViashDockerBuild : a Bash function which builds a docker image, takes image identifier as argument. +# examples: +# ViashDockerPullElseBuild mynewcomponent +function ViashDockerPullElseBuild { + local save=$-; set +e + ViashDockerPull $1 + local out=$? + [[ $save =~ e ]] && set -e + if [ $out -ne 0 ]; then + ViashDockerBuild $@ + fi +} + +# ViashDockerSetup: create a Docker image, according to specified docker setup strategy +# +# $1 : image identifier with format `[registry/]image[:tag]` +# $2 : docker setup strategy, see DockerSetupStrategy.scala +# examples: +# ViashDockerSetup mynewcomponent alwaysbuild +function ViashDockerSetup { + local image_id="$1" + local setup_strategy="$2" + if [ "$setup_strategy" == "alwaysbuild" -o "$setup_strategy" == "build" -o "$setup_strategy" == "b" ]; then + ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id") + elif [ "$setup_strategy" == "alwayspull" -o "$setup_strategy" == "pull" -o "$setup_strategy" == "p" ]; then + ViashDockerPull $image_id + elif [ "$setup_strategy" == "alwayspullelsebuild" -o "$setup_strategy" == "pullelsebuild" ]; then + ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id") + elif [ "$setup_strategy" == "alwayspullelsecachedbuild" -o "$setup_strategy" == "pullelsecachedbuild" ]; then + ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id") + elif [ "$setup_strategy" == "alwayscachedbuild" -o "$setup_strategy" == "cachedbuild" -o "$setup_strategy" == "cb" ]; then + ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id") + elif [[ "$setup_strategy" =~ ^ifneedbe ]]; then + local save=$-; set +e + ViashDockerLocalTagCheck $image_id + local outCheck=$? + [[ $save =~ e ]] && set -e + if [ $outCheck -eq 0 ]; then + ViashInfo "Image $image_id already exists" + elif [ "$setup_strategy" == "ifneedbebuild" ]; then + ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id") + elif [ "$setup_strategy" == "ifneedbecachedbuild" ]; then + ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id") + elif [ "$setup_strategy" == "ifneedbepull" ]; then + ViashDockerPull $image_id + elif [ "$setup_strategy" == "ifneedbepullelsebuild" ]; then + ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id") + elif [ "$setup_strategy" == "ifneedbepullelsecachedbuild" ]; then + ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id") + else + ViashError "Unrecognised Docker strategy: $setup_strategy" + exit 1 + fi + elif [ "$setup_strategy" == "push" -o "$setup_strategy" == "forcepush" -o "$setup_strategy" == "alwayspush" ]; then + ViashDockerPush "$image_id" + elif [ "$setup_strategy" == "pushifnotpresent" -o "$setup_strategy" == "gentlepush" -o "$setup_strategy" == "maybepush" ]; then + local save=$-; set +e + ViashDockerRemoteTagCheck $image_id + local outCheck=$? + [[ $save =~ e ]] && set -e + if [ $outCheck -eq 0 ]; then + ViashNotice "Container '$image_id' exists, doing nothing." + else + ViashNotice "Container '$image_id' does not yet exist." + ViashDockerPush "$image_id" + fi + elif [ "$setup_strategy" == "donothing" -o "$setup_strategy" == "meh" ]; then + ViashNotice "Skipping setup." + else + ViashError "Unrecognised Docker strategy: $setup_strategy" + exit 1 + fi +} + +# ViashDockerCheckCommands: Check whether a docker container has the required commands +# +# $1 : image identifier with format `[registry/]image[:tag]` +# $@ : commands to verify being present +# examples: +# ViashDockerCheckCommands bash:4.0 bash ps foo +function ViashDockerCheckCommands { + local image_id="$1" + shift 1 + local commands="$@" + local save=$-; set +e + local missing # mark 'missing' as local in advance, otherwise the exit code of the command will be missing and always be '0' + missing=$(docker run --rm --entrypoint=sh "$image_id" -c "for command in $commands; do command -v \$command >/dev/null 2>&1; if [ \$? -ne 0 ]; then echo \$command; exit 1; fi; done") + local outCheck=$? + [[ $save =~ e ]] && set -e + if [ $outCheck -ne 0 ]; then + ViashError "Docker container '$image_id' does not contain command '$missing'." + exit 1 + fi +} + +# ViashDockerBuild: build a docker image +# $1 : image identifier with format `[registry/]image[:tag]` +# $... : additional arguments to pass to docker build +# $VIASH_META_TEMP_DIR : temporary directory to store dockerfile & optional resources in +# $VIASH_META_NAME : name of the component +# $VIASH_META_RESOURCES_DIR : directory containing the resources +# $VIASH_VERBOSITY : verbosity level +# exit code $? : whether or not the image was built successfully +function ViashDockerBuild { + local image_id="$1" + shift 1 + + # create temporary directory to store dockerfile & optional resources in + local tmpdir=$(mktemp -d "$VIASH_META_TEMP_DIR/dockerbuild-$VIASH_META_NAME-XXXXXX") + local dockerfile="$tmpdir/Dockerfile" + function clean_up { + rm -rf "$tmpdir" + } + trap clean_up EXIT + + # store dockerfile and resources + ViashDockerfile "$VIASH_ENGINE_ID" > "$dockerfile" + + # generate the build command + local docker_build_cmd="docker build -t '$image_id' $@ '$VIASH_META_RESOURCES_DIR' -f '$dockerfile'" + + # build the container + ViashNotice "Building container '$image_id' with Dockerfile" + ViashInfo "$docker_build_cmd" + local save=$-; set +e + if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then + eval $docker_build_cmd + else + eval $docker_build_cmd &> "$tmpdir/docker_build.log" + fi + + # check exit code + local out=$? + [[ $save =~ e ]] && set -e + if [ $out -ne 0 ]; then + ViashError "Error occurred while building container '$image_id'" + if [ $VIASH_VERBOSITY -lt $VIASH_LOGCODE_INFO ]; then + ViashError "Transcript: --------------------------------" + cat "$tmpdir/docker_build.log" + ViashError "End of transcript --------------------------" + fi + exit 1 + fi +} + +######## End of helper functions for setting up Docker images for viash ######## + +# ViashDockerFile: print the dockerfile to stdout +# $1 : engine identifier +# return : dockerfile required to run this component +# examples: +# ViashDockerFile +function ViashDockerfile { + local engine_id="$1" + + if [[ "$engine_id" == "docker" ]]; then + cat << 'VIASHDOCKER' +FROM ubuntu:22.04 +ENTRYPOINT [] +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 + +RUN bbsplit.sh --version 2>&1 | awk '/BBMap version/{print "BBMAP:", $NF}' > /var/software_versions.txt + +LABEL org.opencontainers.image.description="Companion container for running component bbmap bbmap_bbsplit" +LABEL org.opencontainers.image.created="2024-10-18T09:18:59Z" +LABEL org.opencontainers.image.source="https://github.com/BioInfoTools/BBMap/blob/master/sh/bbsplit.sh" +LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7" +LABEL org.opencontainers.image.version="main" + +VIASHDOCKER + fi +} + +# ViashDockerBuildArgs: return the arguments to pass to docker build +# $1 : engine identifier +# return : arguments to pass to docker build +function ViashDockerBuildArgs { + local engine_id="$1" + + if [[ "$engine_id" == "docker" ]]; then + echo "" + fi +} + +# ViashAbsolutePath: generate absolute path from relative path +# borrowed from https://stackoverflow.com/a/21951256 +# $1 : relative filename +# return : absolute path +# examples: +# ViashAbsolutePath some_file.txt # returns /path/to/some_file.txt +# ViashAbsolutePath /foo/bar/.. # returns /foo +function ViashAbsolutePath { + local thePath + local parr + local outp + local len + if [[ ! "$1" =~ ^/ ]]; then + thePath="$PWD/$1" + else + thePath="$1" + fi + echo "$thePath" | ( + IFS=/ + read -a parr + declare -a outp + for i in "${parr[@]}"; do + case "$i" in + ''|.) continue ;; + ..) + len=${#outp[@]} + if ((len==0)); then + continue + else + unset outp[$((len-1))] + fi + ;; + *) + len=${#outp[@]} + outp[$len]="$i" + ;; + esac + done + echo /"${outp[*]}" + ) +} +# ViashDockerAutodetectMount: auto configuring docker mounts from parameters +# $1 : The parameter value +# returns : New parameter +# $VIASH_DIRECTORY_MOUNTS : Added another parameter to be passed to docker +# $VIASH_DOCKER_AUTOMOUNT_PREFIX : The prefix to be used for the automounts +# examples: +# ViashDockerAutodetectMount /path/to/bar # returns '/viash_automount/path/to/bar' +# ViashDockerAutodetectMountArg /path/to/bar # returns '--volume="/path/to:/viash_automount/path/to"' +function ViashDockerAutodetectMount { + local abs_path=$(ViashAbsolutePath "$1") + local mount_source + local base_name + if [ -d "$abs_path" ]; then + mount_source="$abs_path" + base_name="" + else + mount_source=`dirname "$abs_path"` + base_name=`basename "$abs_path"` + fi + local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source" + if [ -z "$base_name" ]; then + echo "$mount_target" + else + echo "$mount_target/$base_name" + fi +} +function ViashDockerAutodetectMountArg { + local abs_path=$(ViashAbsolutePath "$1") + local mount_source + local base_name + if [ -d "$abs_path" ]; then + mount_source="$abs_path" + base_name="" + else + mount_source=`dirname "$abs_path"` + base_name=`basename "$abs_path"` + fi + local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source" + ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target" + echo "--volume=\"$mount_source:$mount_target\"" +} +function ViashDockerStripAutomount { + local abs_path=$(ViashAbsolutePath "$1") + echo "${abs_path#$VIASH_DOCKER_AUTOMOUNT_PREFIX}" +} +# initialise variables +VIASH_DIRECTORY_MOUNTS=() + +# configure default docker automount prefix if it is unset +if [ -z "${VIASH_DOCKER_AUTOMOUNT_PREFIX+x}" ]; then + VIASH_DOCKER_AUTOMOUNT_PREFIX="/viash_automount" +fi + +# initialise docker variables +VIASH_DOCKER_RUN_ARGS=(-i --rm) + +# initialise array +VIASH_POSITIONAL_ARGS='' + +while [[ $# -gt 0 ]]; do + case "$1" in + -h|--help) + ViashHelp + exit + ;; + ---v|---verbose) + let "VIASH_VERBOSITY=VIASH_VERBOSITY+1" + shift 1 + ;; + ---verbosity) + VIASH_VERBOSITY="$2" + shift 2 + ;; + ---verbosity=*) + VIASH_VERBOSITY="$(ViashRemoveFlags "$1")" + shift 1 + ;; + --version) + echo "bbmap_bbsplit main" + exit + ;; + --id) + [ -n "$VIASH_PAR_ID" ] && ViashError Bad arguments for option \'--id\': \'$VIASH_PAR_ID\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_ID="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --id. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --id=*) + [ -n "$VIASH_PAR_ID" ] && ViashError Bad arguments for option \'--id=*\': \'$VIASH_PAR_ID\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_ID=$(ViashRemoveFlags "$1") + shift 1 + ;; + --paired) + [ -n "$VIASH_PAR_PAIRED" ] && ViashError Bad arguments for option \'--paired\': \'$VIASH_PAR_PAIRED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_PAIRED=true + shift 1 + ;; + --input) + if [ -z "$VIASH_PAR_INPUT" ]; then + VIASH_PAR_INPUT="$2" + else + VIASH_PAR_INPUT="$VIASH_PAR_INPUT;""$2" + fi + [ $# -lt 2 ] && ViashError Not enough arguments passed to --input. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --input=*) + if [ -z "$VIASH_PAR_INPUT" ]; then + VIASH_PAR_INPUT=$(ViashRemoveFlags "$1") + else + VIASH_PAR_INPUT="$VIASH_PAR_INPUT;"$(ViashRemoveFlags "$1") + fi + shift 1 + ;; + --ref) + if [ -z "$VIASH_PAR_REF" ]; then + VIASH_PAR_REF="$2" + else + VIASH_PAR_REF="$VIASH_PAR_REF;""$2" + fi + [ $# -lt 2 ] && ViashError Not enough arguments passed to --ref. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --ref=*) + if [ -z "$VIASH_PAR_REF" ]; then + VIASH_PAR_REF=$(ViashRemoveFlags "$1") + else + VIASH_PAR_REF="$VIASH_PAR_REF;"$(ViashRemoveFlags "$1") + fi + shift 1 + ;; + --only_build_index) + [ -n "$VIASH_PAR_ONLY_BUILD_INDEX" ] && ViashError Bad arguments for option \'--only_build_index\': \'$VIASH_PAR_ONLY_BUILD_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_ONLY_BUILD_INDEX=true + shift 1 + ;; + --build) + [ -n "$VIASH_PAR_BUILD" ] && ViashError Bad arguments for option \'--build\': \'$VIASH_PAR_BUILD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_BUILD="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --build. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --build=*) + [ -n "$VIASH_PAR_BUILD" ] && ViashError Bad arguments for option \'--build=*\': \'$VIASH_PAR_BUILD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_BUILD=$(ViashRemoveFlags "$1") + shift 1 + ;; + --qin) + [ -n "$VIASH_PAR_QIN" ] && ViashError Bad arguments for option \'--qin\': \'$VIASH_PAR_QIN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_QIN="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --qin. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --qin=*) + [ -n "$VIASH_PAR_QIN" ] && ViashError Bad arguments for option \'--qin=*\': \'$VIASH_PAR_QIN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_QIN=$(ViashRemoveFlags "$1") + shift 1 + ;; + --interleaved) + [ -n "$VIASH_PAR_INTERLEAVED" ] && ViashError Bad arguments for option \'--interleaved\': \'$VIASH_PAR_INTERLEAVED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_INTERLEAVED=true + shift 1 + ;; + --maxindel) + [ -n "$VIASH_PAR_MAXINDEL" ] && ViashError Bad arguments for option \'--maxindel\': \'$VIASH_PAR_MAXINDEL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_MAXINDEL="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --maxindel. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --maxindel=*) + [ -n "$VIASH_PAR_MAXINDEL" ] && ViashError Bad arguments for option \'--maxindel=*\': \'$VIASH_PAR_MAXINDEL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_MAXINDEL=$(ViashRemoveFlags "$1") + shift 1 + ;; + --minratio) + [ -n "$VIASH_PAR_MINRATIO" ] && ViashError Bad arguments for option \'--minratio\': \'$VIASH_PAR_MINRATIO\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_MINRATIO="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --minratio. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --minratio=*) + [ -n "$VIASH_PAR_MINRATIO" ] && ViashError Bad arguments for option \'--minratio=*\': \'$VIASH_PAR_MINRATIO\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_MINRATIO=$(ViashRemoveFlags "$1") + shift 1 + ;; + --minhits) + [ -n "$VIASH_PAR_MINHITS" ] && ViashError Bad arguments for option \'--minhits\': \'$VIASH_PAR_MINHITS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_MINHITS="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --minhits. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --minhits=*) + [ -n "$VIASH_PAR_MINHITS" ] && ViashError Bad arguments for option \'--minhits=*\': \'$VIASH_PAR_MINHITS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_MINHITS=$(ViashRemoveFlags "$1") + shift 1 + ;; + --ambiguous) + [ -n "$VIASH_PAR_AMBIGUOUS" ] && ViashError Bad arguments for option \'--ambiguous\': \'$VIASH_PAR_AMBIGUOUS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_AMBIGUOUS="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --ambiguous. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --ambiguous=*) + [ -n "$VIASH_PAR_AMBIGUOUS" ] && ViashError Bad arguments for option \'--ambiguous=*\': \'$VIASH_PAR_AMBIGUOUS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_AMBIGUOUS=$(ViashRemoveFlags "$1") + shift 1 + ;; + --ambiguous2) + [ -n "$VIASH_PAR_AMBIGUOUS2" ] && ViashError Bad arguments for option \'--ambiguous2\': \'$VIASH_PAR_AMBIGUOUS2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_AMBIGUOUS2="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --ambiguous2. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --ambiguous2=*) + [ -n "$VIASH_PAR_AMBIGUOUS2" ] && ViashError Bad arguments for option \'--ambiguous2=*\': \'$VIASH_PAR_AMBIGUOUS2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_AMBIGUOUS2=$(ViashRemoveFlags "$1") + shift 1 + ;; + --qtrim) + [ -n "$VIASH_PAR_QTRIM" ] && ViashError Bad arguments for option \'--qtrim\': \'$VIASH_PAR_QTRIM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_QTRIM="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --qtrim. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --qtrim=*) + [ -n "$VIASH_PAR_QTRIM" ] && ViashError Bad arguments for option \'--qtrim=*\': \'$VIASH_PAR_QTRIM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_QTRIM=$(ViashRemoveFlags "$1") + shift 1 + ;; + --untrim) + [ -n "$VIASH_PAR_UNTRIM" ] && ViashError Bad arguments for option \'--untrim\': \'$VIASH_PAR_UNTRIM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_UNTRIM=true + shift 1 + ;; + --fastq_1) + [ -n "$VIASH_PAR_FASTQ_1" ] && ViashError Bad arguments for option \'--fastq_1\': \'$VIASH_PAR_FASTQ_1\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_FASTQ_1="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --fastq_1. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --fastq_1=*) + [ -n "$VIASH_PAR_FASTQ_1" ] && ViashError Bad arguments for option \'--fastq_1=*\': \'$VIASH_PAR_FASTQ_1\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_FASTQ_1=$(ViashRemoveFlags "$1") + shift 1 + ;; + --fastq_2) + [ -n "$VIASH_PAR_FASTQ_2" ] && ViashError Bad arguments for option \'--fastq_2\': \'$VIASH_PAR_FASTQ_2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_FASTQ_2="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --fastq_2. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --fastq_2=*) + [ -n "$VIASH_PAR_FASTQ_2" ] && ViashError Bad arguments for option \'--fastq_2=*\': \'$VIASH_PAR_FASTQ_2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_FASTQ_2=$(ViashRemoveFlags "$1") + shift 1 + ;; + --sam2bam) + [ -n "$VIASH_PAR_SAM2BAM" ] && ViashError Bad arguments for option \'--sam2bam\': \'$VIASH_PAR_SAM2BAM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_SAM2BAM="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --sam2bam. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --sam2bam=*) + [ -n "$VIASH_PAR_SAM2BAM" ] && ViashError Bad arguments for option \'--sam2bam=*\': \'$VIASH_PAR_SAM2BAM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_SAM2BAM=$(ViashRemoveFlags "$1") + shift 1 + ;; + --bs) + [ -n "$VIASH_PAR_SAM2BAM" ] && ViashError Bad arguments for option \'--bs\': \'$VIASH_PAR_SAM2BAM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_SAM2BAM="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --bs. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --scafstats) + [ -n "$VIASH_PAR_SCAFSTATS" ] && ViashError Bad arguments for option \'--scafstats\': \'$VIASH_PAR_SCAFSTATS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_SCAFSTATS="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --scafstats. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --scafstats=*) + [ -n "$VIASH_PAR_SCAFSTATS" ] && ViashError Bad arguments for option \'--scafstats=*\': \'$VIASH_PAR_SCAFSTATS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_SCAFSTATS=$(ViashRemoveFlags "$1") + shift 1 + ;; + --refstats) + [ -n "$VIASH_PAR_REFSTATS" ] && ViashError Bad arguments for option \'--refstats\': \'$VIASH_PAR_REFSTATS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_REFSTATS="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --refstats. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --refstats=*) + [ -n "$VIASH_PAR_REFSTATS" ] && ViashError Bad arguments for option \'--refstats=*\': \'$VIASH_PAR_REFSTATS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_REFSTATS=$(ViashRemoveFlags "$1") + shift 1 + ;; + --nzo) + [ -n "$VIASH_PAR_NZO" ] && ViashError Bad arguments for option \'--nzo\': \'$VIASH_PAR_NZO\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_NZO=true + shift 1 + ;; + --bbmap_args) + [ -n "$VIASH_PAR_BBMAP_ARGS" ] && ViashError Bad arguments for option \'--bbmap_args\': \'$VIASH_PAR_BBMAP_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_BBMAP_ARGS="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --bbmap_args. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --bbmap_args=*) + [ -n "$VIASH_PAR_BBMAP_ARGS" ] && ViashError Bad arguments for option \'--bbmap_args=*\': \'$VIASH_PAR_BBMAP_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_BBMAP_ARGS=$(ViashRemoveFlags "$1") + shift 1 + ;; + ---engine) + VIASH_ENGINE_ID="$2" + shift 2 + ;; + ---engine=*) + VIASH_ENGINE_ID="$(ViashRemoveFlags "$1")" + shift 1 + ;; + ---setup) + VIASH_MODE='setup' + VIASH_SETUP_STRATEGY="$2" + shift 2 + ;; + ---setup=*) + VIASH_MODE='setup' + VIASH_SETUP_STRATEGY="$(ViashRemoveFlags "$1")" + shift 1 + ;; + ---dockerfile) + VIASH_MODE='dockerfile' + shift 1 + ;; + ---docker_run_args) + VIASH_DOCKER_RUN_ARGS+=("$2") + shift 2 + ;; + ---docker_run_args=*) + VIASH_DOCKER_RUN_ARGS+=("$(ViashRemoveFlags "$1")") + shift 1 + ;; + ---docker_image_id) + VIASH_MODE='docker_image_id' + shift 1 + ;; + ---debug) + VIASH_MODE='debug' + shift 1 + ;; + ---cpus) + [ -n "$VIASH_META_CPUS" ] && ViashError Bad arguments for option \'---cpus\': \'$VIASH_META_CPUS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_META_CPUS="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to ---cpus. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + ---cpus=*) + [ -n "$VIASH_META_CPUS" ] && ViashError Bad arguments for option \'---cpus=*\': \'$VIASH_META_CPUS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_META_CPUS=$(ViashRemoveFlags "$1") + shift 1 + ;; + ---memory) + [ -n "$VIASH_META_MEMORY" ] && ViashError Bad arguments for option \'---memory\': \'$VIASH_META_MEMORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_META_MEMORY="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to ---memory. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + ---memory=*) + [ -n "$VIASH_META_MEMORY" ] && ViashError Bad arguments for option \'---memory=*\': \'$VIASH_META_MEMORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_META_MEMORY=$(ViashRemoveFlags "$1") + shift 1 + ;; + *) # positional arg or unknown option + # since the positional args will be eval'd, can we always quote, instead of using ViashQuote + VIASH_POSITIONAL_ARGS="$VIASH_POSITIONAL_ARGS '$1'" + [[ $1 == -* ]] && ViashWarning $1 looks like a parameter but is not a defined parameter and will instead be treated as a positional argument. Use "--help" to get more information on the parameters. + shift # past argument + ;; + esac +done + +# parse positional parameters +eval set -- $VIASH_POSITIONAL_ARGS + + +if [ "$VIASH_ENGINE_ID" == "native" ] ; then + VIASH_ENGINE_TYPE='native' +elif [ "$VIASH_ENGINE_ID" == "docker" ] ; then + VIASH_ENGINE_TYPE='docker' +else + ViashError "Engine '$VIASH_ENGINE_ID' is not recognized. Options are: docker, native." + exit 1 +fi + +if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then + # check if docker is installed properly + ViashDockerInstallationCheck + + # determine docker image id + if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bbmap/bbmap_bbsplit:main' + fi + + # print dockerfile + if [ "$VIASH_MODE" == "dockerfile" ]; then + ViashDockerfile "$VIASH_ENGINE_ID" + exit 0 + + elif [ "$VIASH_MODE" == "docker_image_id" ]; then + echo "$VIASH_DOCKER_IMAGE_ID" + exit 0 + + # enter docker container + elif [[ "$VIASH_MODE" == "debug" ]]; then + VIASH_CMD="docker run --entrypoint=bash ${VIASH_DOCKER_RUN_ARGS[@]} -v '$(pwd)':/pwd --workdir /pwd -t $VIASH_DOCKER_IMAGE_ID" + ViashNotice "+ $VIASH_CMD" + eval $VIASH_CMD + exit + + # build docker image + elif [ "$VIASH_MODE" == "setup" ]; then + ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY" + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' + exit 0 + fi + + # check if docker image exists + ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild + ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash' +fi + +# setting computational defaults + +# helper function for parsing memory strings +function ViashMemoryAsBytes { + local memory=`echo "$1" | tr '[:upper:]' '[:lower:]' | tr -d '[:space:]'` + local memory_regex='^([0-9]+)([kmgtp]i?b?|b)$' + if [[ $memory =~ $memory_regex ]]; then + local number=${memory/[^0-9]*/} + local symbol=${memory/*[0-9]/} + + case $symbol in + b) memory_b=$number ;; + kb|k) memory_b=$(( $number * 1000 )) ;; + mb|m) memory_b=$(( $number * 1000 * 1000 )) ;; + gb|g) memory_b=$(( $number * 1000 * 1000 * 1000 )) ;; + tb|t) memory_b=$(( $number * 1000 * 1000 * 1000 * 1000 )) ;; + pb|p) memory_b=$(( $number * 1000 * 1000 * 1000 * 1000 * 1000 )) ;; + kib|ki) memory_b=$(( $number * 1024 )) ;; + mib|mi) memory_b=$(( $number * 1024 * 1024 )) ;; + gib|gi) memory_b=$(( $number * 1024 * 1024 * 1024 )) ;; + tib|ti) memory_b=$(( $number * 1024 * 1024 * 1024 * 1024 )) ;; + pib|pi) memory_b=$(( $number * 1024 * 1024 * 1024 * 1024 * 1024 )) ;; + esac + echo "$memory_b" + fi +} +# compute memory in different units +if [ ! -z ${VIASH_META_MEMORY+x} ]; then + VIASH_META_MEMORY_B=`ViashMemoryAsBytes $VIASH_META_MEMORY` + # do not define other variables if memory_b is an empty string + if [ ! -z "$VIASH_META_MEMORY_B" ]; then + VIASH_META_MEMORY_KB=$(( ($VIASH_META_MEMORY_B+999) / 1000 )) + VIASH_META_MEMORY_MB=$(( ($VIASH_META_MEMORY_KB+999) / 1000 )) + VIASH_META_MEMORY_GB=$(( ($VIASH_META_MEMORY_MB+999) / 1000 )) + VIASH_META_MEMORY_TB=$(( ($VIASH_META_MEMORY_GB+999) / 1000 )) + VIASH_META_MEMORY_PB=$(( ($VIASH_META_MEMORY_TB+999) / 1000 )) + VIASH_META_MEMORY_KIB=$(( ($VIASH_META_MEMORY_B+1023) / 1024 )) + VIASH_META_MEMORY_MIB=$(( ($VIASH_META_MEMORY_KIB+1023) / 1024 )) + VIASH_META_MEMORY_GIB=$(( ($VIASH_META_MEMORY_MIB+1023) / 1024 )) + VIASH_META_MEMORY_TIB=$(( ($VIASH_META_MEMORY_GIB+1023) / 1024 )) + VIASH_META_MEMORY_PIB=$(( ($VIASH_META_MEMORY_TIB+1023) / 1024 )) + else + # unset memory if string is empty + unset $VIASH_META_MEMORY_B + fi +fi +# unset nproc if string is empty +if [ -z "$VIASH_META_CPUS" ]; then + unset $VIASH_META_CPUS +fi + + +# check whether required parameters exist +if [ -z ${VIASH_META_NAME+x} ]; then + ViashError 'name' is a required argument. Use "--help" to get more information on the parameters. + exit 1 +fi +if [ -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then + ViashError 'functionality_name' is a required argument. Use "--help" to get more information on the parameters. + exit 1 +fi +if [ -z ${VIASH_META_RESOURCES_DIR+x} ]; then + ViashError 'resources_dir' is a required argument. Use "--help" to get more information on the parameters. + exit 1 +fi +if [ -z ${VIASH_META_EXECUTABLE+x} ]; then + ViashError 'executable' is a required argument. Use "--help" to get more information on the parameters. + exit 1 +fi +if [ -z ${VIASH_META_CONFIG+x} ]; then + ViashError 'config' is a required argument. Use "--help" to get more information on the parameters. + exit 1 +fi +if [ -z ${VIASH_META_TEMP_DIR+x} ]; then + ViashError 'temp_dir' is a required argument. Use "--help" to get more information on the parameters. + exit 1 +fi + +# filling in defaults +if [ -z ${VIASH_PAR_PAIRED+x} ]; then + VIASH_PAR_PAIRED="false" +fi +if [ -z ${VIASH_PAR_ONLY_BUILD_INDEX+x} ]; then + VIASH_PAR_ONLY_BUILD_INDEX="false" +fi +if [ -z ${VIASH_PAR_INTERLEAVED+x} ]; then + VIASH_PAR_INTERLEAVED="false" +fi +if [ -z ${VIASH_PAR_UNTRIM+x} ]; then + VIASH_PAR_UNTRIM="false" +fi +if [ -z ${VIASH_PAR_NZO+x} ]; then + VIASH_PAR_NZO="false" +fi + +# check whether required files exist +if [ ! -z "$VIASH_PAR_INPUT" ]; then + IFS=';' + set -f + for file in $VIASH_PAR_INPUT; do + unset IFS + if [ ! -e "$file" ]; then + ViashError "Input file '$file' does not exist." + exit 1 + fi + done + set +f +fi +if [ ! -z "$VIASH_PAR_REF" ]; then + IFS=';' + set -f + for file in $VIASH_PAR_REF; do + unset IFS + if [ ! -e "$file" ]; then + ViashError "Input file '$file' does not exist." + exit 1 + fi + done + set +f +fi + +# check whether parameters values are of the right type +if [[ -n "$VIASH_PAR_PAIRED" ]]; then + if ! [[ "$VIASH_PAR_PAIRED" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then + ViashError '--paired' has to be a boolean_true. Use "--help" to get more information on the parameters. + exit 1 + fi +fi +if [[ -n "$VIASH_PAR_ONLY_BUILD_INDEX" ]]; then + if ! [[ "$VIASH_PAR_ONLY_BUILD_INDEX" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then + ViashError '--only_build_index' has to be a boolean_true. Use "--help" to get more information on the parameters. + exit 1 + fi +fi +if [[ -n "$VIASH_PAR_INTERLEAVED" ]]; then + if ! [[ "$VIASH_PAR_INTERLEAVED" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then + ViashError '--interleaved' has to be a boolean_true. Use "--help" to get more information on the parameters. + exit 1 + fi +fi +if [[ -n "$VIASH_PAR_MAXINDEL" ]]; then + if ! [[ "$VIASH_PAR_MAXINDEL" =~ ^[-+]?[0-9]+$ ]]; then + ViashError '--maxindel' has to be an integer. Use "--help" to get more information on the parameters. + exit 1 + fi +fi +if [[ -n "$VIASH_PAR_MINRATIO" ]]; then + if ! [[ "$VIASH_PAR_MINRATIO" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then + ViashError '--minratio' has to be a double. Use "--help" to get more information on the parameters. + exit 1 + fi +fi +if [[ -n "$VIASH_PAR_MINHITS" ]]; then + if ! [[ "$VIASH_PAR_MINHITS" =~ ^[-+]?[0-9]+$ ]]; then + ViashError '--minhits' has to be an integer. Use "--help" to get more information on the parameters. + exit 1 + fi +fi +if [[ -n "$VIASH_PAR_UNTRIM" ]]; then + if ! [[ "$VIASH_PAR_UNTRIM" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then + ViashError '--untrim' has to be a boolean_true. Use "--help" to get more information on the parameters. + exit 1 + fi +fi +if [[ -n "$VIASH_PAR_NZO" ]]; then + if ! [[ "$VIASH_PAR_NZO" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then + ViashError '--nzo' has to be a boolean_true. Use "--help" to get more information on the parameters. + exit 1 + fi +fi +if [[ -n "$VIASH_META_CPUS" ]]; then + if ! [[ "$VIASH_META_CPUS" =~ ^[-+]?[0-9]+$ ]]; then + ViashError 'cpus' has to be an integer. Use "--help" to get more information on the parameters. + exit 1 + fi +fi +if [[ -n "$VIASH_META_MEMORY_B" ]]; then + if ! [[ "$VIASH_META_MEMORY_B" =~ ^[-+]?[0-9]+$ ]]; then + ViashError 'memory_b' has to be a long. Use "--help" to get more information on the parameters. + exit 1 + fi +fi +if [[ -n "$VIASH_META_MEMORY_KB" ]]; then + if ! [[ "$VIASH_META_MEMORY_KB" =~ ^[-+]?[0-9]+$ ]]; then + ViashError 'memory_kb' has to be a long. Use "--help" to get more information on the parameters. + exit 1 + fi +fi +if [[ -n "$VIASH_META_MEMORY_MB" ]]; then + if ! [[ "$VIASH_META_MEMORY_MB" =~ ^[-+]?[0-9]+$ ]]; then + ViashError 'memory_mb' has to be a long. Use "--help" to get more information on the parameters. + exit 1 + fi +fi +if [[ -n "$VIASH_META_MEMORY_GB" ]]; then + if ! [[ "$VIASH_META_MEMORY_GB" =~ ^[-+]?[0-9]+$ ]]; then + ViashError 'memory_gb' has to be a long. Use "--help" to get more information on the parameters. + exit 1 + fi +fi +if [[ -n "$VIASH_META_MEMORY_TB" ]]; then + if ! [[ "$VIASH_META_MEMORY_TB" =~ ^[-+]?[0-9]+$ ]]; then + ViashError 'memory_tb' has to be a long. Use "--help" to get more information on the parameters. + exit 1 + fi +fi +if [[ -n "$VIASH_META_MEMORY_PB" ]]; then + if ! [[ "$VIASH_META_MEMORY_PB" =~ ^[-+]?[0-9]+$ ]]; then + ViashError 'memory_pb' has to be a long. Use "--help" to get more information on the parameters. + exit 1 + fi +fi +if [[ -n "$VIASH_META_MEMORY_KIB" ]]; then + if ! [[ "$VIASH_META_MEMORY_KIB" =~ ^[-+]?[0-9]+$ ]]; then + ViashError 'memory_kib' has to be a long. Use "--help" to get more information on the parameters. + exit 1 + fi +fi +if [[ -n "$VIASH_META_MEMORY_MIB" ]]; then + if ! [[ "$VIASH_META_MEMORY_MIB" =~ ^[-+]?[0-9]+$ ]]; then + ViashError 'memory_mib' has to be a long. Use "--help" to get more information on the parameters. + exit 1 + fi +fi +if [[ -n "$VIASH_META_MEMORY_GIB" ]]; then + if ! [[ "$VIASH_META_MEMORY_GIB" =~ ^[-+]?[0-9]+$ ]]; then + ViashError 'memory_gib' has to be a long. Use "--help" to get more information on the parameters. + exit 1 + fi +fi +if [[ -n "$VIASH_META_MEMORY_TIB" ]]; then + if ! [[ "$VIASH_META_MEMORY_TIB" =~ ^[-+]?[0-9]+$ ]]; then + ViashError 'memory_tib' has to be a long. Use "--help" to get more information on the parameters. + exit 1 + fi +fi +if [[ -n "$VIASH_META_MEMORY_PIB" ]]; then + if ! [[ "$VIASH_META_MEMORY_PIB" =~ ^[-+]?[0-9]+$ ]]; then + ViashError 'memory_pib' has to be a long. Use "--help" to get more information on the parameters. + exit 1 + fi +fi + +# check whether value is belongs to a set of choices +if [ ! -z "$VIASH_PAR_AMBIGUOUS" ]; then + VIASH_PAR_AMBIGUOUS_CHOICES=("best;toss;random;all") + IFS=';' + set -f + if ! [[ ";${VIASH_PAR_AMBIGUOUS_CHOICES[*]};" =~ ";$VIASH_PAR_AMBIGUOUS;" ]]; then + ViashError '--ambiguous' specified value of \'$VIASH_PAR_AMBIGUOUS\' is not in the list of allowed values. Use "--help" to get more information on the parameters. + exit 1 + fi + set +f + unset IFS +fi + +if [ ! -z "$VIASH_PAR_AMBIGUOUS2" ]; then + VIASH_PAR_AMBIGUOUS2_CHOICES=("best;toss;all;split") + IFS=';' + set -f + if ! [[ ";${VIASH_PAR_AMBIGUOUS2_CHOICES[*]};" =~ ";$VIASH_PAR_AMBIGUOUS2;" ]]; then + ViashError '--ambiguous2' specified value of \'$VIASH_PAR_AMBIGUOUS2\' is not in the list of allowed values. Use "--help" to get more information on the parameters. + exit 1 + fi + set +f + unset IFS +fi + +if [ ! -z "$VIASH_PAR_QTRIM" ]; then + VIASH_PAR_QTRIM_CHOICES=("l;r;lr") + IFS=';' + set -f + if ! [[ ";${VIASH_PAR_QTRIM_CHOICES[*]};" =~ ";$VIASH_PAR_QTRIM;" ]]; then + ViashError '--qtrim' specified value of \'$VIASH_PAR_QTRIM\' is not in the list of allowed values. Use "--help" to get more information on the parameters. + exit 1 + fi + set +f + unset IFS +fi + +# create parent directories of output files, if so desired +if [ ! -z "$VIASH_PAR_FASTQ_1" ] && [ ! -d "$(dirname "$VIASH_PAR_FASTQ_1")" ]; then + mkdir -p "$(dirname "$VIASH_PAR_FASTQ_1")" +fi +if [ ! -z "$VIASH_PAR_FASTQ_2" ] && [ ! -d "$(dirname "$VIASH_PAR_FASTQ_2")" ]; then + mkdir -p "$(dirname "$VIASH_PAR_FASTQ_2")" +fi +if [ ! -z "$VIASH_PAR_SAM2BAM" ] && [ ! -d "$(dirname "$VIASH_PAR_SAM2BAM")" ]; then + mkdir -p "$(dirname "$VIASH_PAR_SAM2BAM")" +fi +if [ ! -z "$VIASH_PAR_SCAFSTATS" ] && [ ! -d "$(dirname "$VIASH_PAR_SCAFSTATS")" ]; then + mkdir -p "$(dirname "$VIASH_PAR_SCAFSTATS")" +fi +if [ ! -z "$VIASH_PAR_REFSTATS" ] && [ ! -d "$(dirname "$VIASH_PAR_REFSTATS")" ]; then + mkdir -p "$(dirname "$VIASH_PAR_REFSTATS")" +fi + +if [ "$VIASH_ENGINE_ID" == "native" ] ; then + if [ "$VIASH_MODE" == "run" ]; then + VIASH_CMD="bash" + else + ViashError "Engine '$VIASH_ENGINE_ID' does not support mode '$VIASH_MODE'." + exit 1 + fi +fi + +if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then + # detect volumes from file arguments + VIASH_CHOWN_VARS=() +if [ ! -z "$VIASH_PAR_INPUT" ]; then + VIASH_TEST_INPUT=() + IFS=';' + for var in $VIASH_PAR_INPUT; do + unset IFS + VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" ) + var=$(ViashDockerAutodetectMount "$var") + VIASH_TEST_INPUT+=( "$var" ) + done + VIASH_PAR_INPUT=$(IFS=';' ; echo "${VIASH_TEST_INPUT[*]}") +fi +if [ ! -z "$VIASH_PAR_REF" ]; then + VIASH_TEST_REF=() + IFS=';' + for var in $VIASH_PAR_REF; do + unset IFS + VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" ) + var=$(ViashDockerAutodetectMount "$var") + VIASH_TEST_REF+=( "$var" ) + done + VIASH_PAR_REF=$(IFS=';' ; echo "${VIASH_TEST_REF[*]}") +fi +if [ ! -z "$VIASH_PAR_FASTQ_1" ]; then + VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_FASTQ_1")" ) + VIASH_PAR_FASTQ_1=$(ViashDockerAutodetectMount "$VIASH_PAR_FASTQ_1") + VIASH_CHOWN_VARS+=( "$VIASH_PAR_FASTQ_1" ) +fi +if [ ! -z "$VIASH_PAR_FASTQ_2" ]; then + VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_FASTQ_2")" ) + VIASH_PAR_FASTQ_2=$(ViashDockerAutodetectMount "$VIASH_PAR_FASTQ_2") + VIASH_CHOWN_VARS+=( "$VIASH_PAR_FASTQ_2" ) +fi +if [ ! -z "$VIASH_PAR_SAM2BAM" ]; then + VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_SAM2BAM")" ) + VIASH_PAR_SAM2BAM=$(ViashDockerAutodetectMount "$VIASH_PAR_SAM2BAM") + VIASH_CHOWN_VARS+=( "$VIASH_PAR_SAM2BAM" ) +fi +if [ ! -z "$VIASH_PAR_SCAFSTATS" ]; then + VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_SCAFSTATS")" ) + VIASH_PAR_SCAFSTATS=$(ViashDockerAutodetectMount "$VIASH_PAR_SCAFSTATS") + VIASH_CHOWN_VARS+=( "$VIASH_PAR_SCAFSTATS" ) +fi +if [ ! -z "$VIASH_PAR_REFSTATS" ]; then + VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_REFSTATS")" ) + VIASH_PAR_REFSTATS=$(ViashDockerAutodetectMount "$VIASH_PAR_REFSTATS") + VIASH_CHOWN_VARS+=( "$VIASH_PAR_REFSTATS" ) +fi +if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then + VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_RESOURCES_DIR")" ) + VIASH_META_RESOURCES_DIR=$(ViashDockerAutodetectMount "$VIASH_META_RESOURCES_DIR") +fi +if [ ! -z "$VIASH_META_EXECUTABLE" ]; then + VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_EXECUTABLE")" ) + VIASH_META_EXECUTABLE=$(ViashDockerAutodetectMount "$VIASH_META_EXECUTABLE") +fi +if [ ! -z "$VIASH_META_CONFIG" ]; then + VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_CONFIG")" ) + VIASH_META_CONFIG=$(ViashDockerAutodetectMount "$VIASH_META_CONFIG") +fi +if [ ! -z "$VIASH_META_TEMP_DIR" ]; then + VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_TEMP_DIR")" ) + VIASH_META_TEMP_DIR=$(ViashDockerAutodetectMount "$VIASH_META_TEMP_DIR") +fi + + # get unique mounts + VIASH_UNIQUE_MOUNTS=($(for val in "${VIASH_DIRECTORY_MOUNTS[@]}"; do echo "$val"; done | sort -u)) +fi + +if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then + # change file ownership + function ViashPerformChown { + if (( ${#VIASH_CHOWN_VARS[@]} )); then + set +e + VIASH_CMD="docker run --entrypoint=bash --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_DOCKER_IMAGE_ID -c 'chown $(id -u):$(id -g) --silent --recursive ${VIASH_CHOWN_VARS[@]}'" + ViashDebug "+ $VIASH_CMD" + eval $VIASH_CMD + set -e + fi + } + trap ViashPerformChown EXIT +fi + +if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then + # helper function for filling in extra docker args + if [ ! -z "$VIASH_META_MEMORY_B" ]; then + VIASH_DOCKER_RUN_ARGS+=("--memory=${VIASH_META_MEMORY_B}") + fi + if [ ! -z "$VIASH_META_CPUS" ]; then + VIASH_DOCKER_RUN_ARGS+=("--cpus=${VIASH_META_CPUS}") + fi +fi + +if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then + VIASH_CMD="docker run --entrypoint=bash ${VIASH_DOCKER_RUN_ARGS[@]} ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_DOCKER_IMAGE_ID" +fi + + +# set dependency paths + + +ViashDebug "Running command: $(echo $VIASH_CMD)" +cat << VIASHEOF | eval $VIASH_CMD +set -e +tempscript=\$(mktemp "$VIASH_META_TEMP_DIR/viash-run-bbmap_bbsplit-XXXXXX").sh +function clean_up { + rm "\$tempscript" +} +function interrupt { + echo -e "\nCTRL-C Pressed..." + exit 1 +} +trap clean_up EXIT +trap interrupt INT SIGINT +cat > "\$tempscript" << 'VIASHMAIN' +#!/bin/bash + +## VIASH START +# The following code has been auto-generated by Viash. +$( if [ ! -z ${VIASH_PAR_ID+x} ]; then echo "${VIASH_PAR_ID}" | sed "s#'#'\"'\"'#g;s#.*#par_id='&'#" ; else echo "# par_id="; fi ) +$( if [ ! -z ${VIASH_PAR_PAIRED+x} ]; then echo "${VIASH_PAR_PAIRED}" | sed "s#'#'\"'\"'#g;s#.*#par_paired='&'#" ; else echo "# par_paired="; fi ) +$( if [ ! -z ${VIASH_PAR_INPUT+x} ]; then echo "${VIASH_PAR_INPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_input='&'#" ; else echo "# par_input="; fi ) +$( if [ ! -z ${VIASH_PAR_REF+x} ]; then echo "${VIASH_PAR_REF}" | sed "s#'#'\"'\"'#g;s#.*#par_ref='&'#" ; else echo "# par_ref="; fi ) +$( if [ ! -z ${VIASH_PAR_ONLY_BUILD_INDEX+x} ]; then echo "${VIASH_PAR_ONLY_BUILD_INDEX}" | sed "s#'#'\"'\"'#g;s#.*#par_only_build_index='&'#" ; else echo "# par_only_build_index="; fi ) +$( if [ ! -z ${VIASH_PAR_BUILD+x} ]; then echo "${VIASH_PAR_BUILD}" | sed "s#'#'\"'\"'#g;s#.*#par_build='&'#" ; else echo "# par_build="; fi ) +$( if [ ! -z ${VIASH_PAR_QIN+x} ]; then echo "${VIASH_PAR_QIN}" | sed "s#'#'\"'\"'#g;s#.*#par_qin='&'#" ; else echo "# par_qin="; fi ) +$( if [ ! -z ${VIASH_PAR_INTERLEAVED+x} ]; then echo "${VIASH_PAR_INTERLEAVED}" | sed "s#'#'\"'\"'#g;s#.*#par_interleaved='&'#" ; else echo "# par_interleaved="; fi ) +$( if [ ! -z ${VIASH_PAR_MAXINDEL+x} ]; then echo "${VIASH_PAR_MAXINDEL}" | sed "s#'#'\"'\"'#g;s#.*#par_maxindel='&'#" ; else echo "# par_maxindel="; fi ) +$( if [ ! -z ${VIASH_PAR_MINRATIO+x} ]; then echo "${VIASH_PAR_MINRATIO}" | sed "s#'#'\"'\"'#g;s#.*#par_minratio='&'#" ; else echo "# par_minratio="; fi ) +$( if [ ! -z ${VIASH_PAR_MINHITS+x} ]; then echo "${VIASH_PAR_MINHITS}" | sed "s#'#'\"'\"'#g;s#.*#par_minhits='&'#" ; else echo "# par_minhits="; fi ) +$( if [ ! -z ${VIASH_PAR_AMBIGUOUS+x} ]; then echo "${VIASH_PAR_AMBIGUOUS}" | sed "s#'#'\"'\"'#g;s#.*#par_ambiguous='&'#" ; else echo "# par_ambiguous="; fi ) +$( if [ ! -z ${VIASH_PAR_AMBIGUOUS2+x} ]; then echo "${VIASH_PAR_AMBIGUOUS2}" | sed "s#'#'\"'\"'#g;s#.*#par_ambiguous2='&'#" ; else echo "# par_ambiguous2="; fi ) +$( if [ ! -z ${VIASH_PAR_QTRIM+x} ]; then echo "${VIASH_PAR_QTRIM}" | sed "s#'#'\"'\"'#g;s#.*#par_qtrim='&'#" ; else echo "# par_qtrim="; fi ) +$( if [ ! -z ${VIASH_PAR_UNTRIM+x} ]; then echo "${VIASH_PAR_UNTRIM}" | sed "s#'#'\"'\"'#g;s#.*#par_untrim='&'#" ; else echo "# par_untrim="; fi ) +$( if [ ! -z ${VIASH_PAR_FASTQ_1+x} ]; then echo "${VIASH_PAR_FASTQ_1}" | sed "s#'#'\"'\"'#g;s#.*#par_fastq_1='&'#" ; else echo "# par_fastq_1="; fi ) +$( if [ ! -z ${VIASH_PAR_FASTQ_2+x} ]; then echo "${VIASH_PAR_FASTQ_2}" | sed "s#'#'\"'\"'#g;s#.*#par_fastq_2='&'#" ; else echo "# par_fastq_2="; fi ) +$( if [ ! -z ${VIASH_PAR_SAM2BAM+x} ]; then echo "${VIASH_PAR_SAM2BAM}" | sed "s#'#'\"'\"'#g;s#.*#par_sam2bam='&'#" ; else echo "# par_sam2bam="; fi ) +$( if [ ! -z ${VIASH_PAR_SCAFSTATS+x} ]; then echo "${VIASH_PAR_SCAFSTATS}" | sed "s#'#'\"'\"'#g;s#.*#par_scafstats='&'#" ; else echo "# par_scafstats="; fi ) +$( if [ ! -z ${VIASH_PAR_REFSTATS+x} ]; then echo "${VIASH_PAR_REFSTATS}" | sed "s#'#'\"'\"'#g;s#.*#par_refstats='&'#" ; else echo "# par_refstats="; fi ) +$( if [ ! -z ${VIASH_PAR_NZO+x} ]; then echo "${VIASH_PAR_NZO}" | sed "s#'#'\"'\"'#g;s#.*#par_nzo='&'#" ; else echo "# par_nzo="; fi ) +$( if [ ! -z ${VIASH_PAR_BBMAP_ARGS+x} ]; then echo "${VIASH_PAR_BBMAP_ARGS}" | sed "s#'#'\"'\"'#g;s#.*#par_bbmap_args='&'#" ; else echo "# par_bbmap_args="; fi ) +$( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "${VIASH_META_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_name='&'#" ; else echo "# meta_name="; fi ) +$( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "${VIASH_META_FUNCTIONALITY_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_functionality_name='&'#" ; else echo "# meta_functionality_name="; fi ) +$( if [ ! -z ${VIASH_META_RESOURCES_DIR+x} ]; then echo "${VIASH_META_RESOURCES_DIR}" | sed "s#'#'\"'\"'#g;s#.*#meta_resources_dir='&'#" ; else echo "# meta_resources_dir="; fi ) +$( if [ ! -z ${VIASH_META_EXECUTABLE+x} ]; then echo "${VIASH_META_EXECUTABLE}" | sed "s#'#'\"'\"'#g;s#.*#meta_executable='&'#" ; else echo "# meta_executable="; fi ) +$( if [ ! -z ${VIASH_META_CONFIG+x} ]; then echo "${VIASH_META_CONFIG}" | sed "s#'#'\"'\"'#g;s#.*#meta_config='&'#" ; else echo "# meta_config="; fi ) +$( if [ ! -z ${VIASH_META_TEMP_DIR+x} ]; then echo "${VIASH_META_TEMP_DIR}" | sed "s#'#'\"'\"'#g;s#.*#meta_temp_dir='&'#" ; else echo "# meta_temp_dir="; fi ) +$( if [ ! -z ${VIASH_META_CPUS+x} ]; then echo "${VIASH_META_CPUS}" | sed "s#'#'\"'\"'#g;s#.*#meta_cpus='&'#" ; else echo "# meta_cpus="; fi ) +$( if [ ! -z ${VIASH_META_MEMORY_B+x} ]; then echo "${VIASH_META_MEMORY_B}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_b='&'#" ; else echo "# meta_memory_b="; fi ) +$( if [ ! -z ${VIASH_META_MEMORY_KB+x} ]; then echo "${VIASH_META_MEMORY_KB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_kb='&'#" ; else echo "# meta_memory_kb="; fi ) +$( if [ ! -z ${VIASH_META_MEMORY_MB+x} ]; then echo "${VIASH_META_MEMORY_MB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_mb='&'#" ; else echo "# meta_memory_mb="; fi ) +$( if [ ! -z ${VIASH_META_MEMORY_GB+x} ]; then echo "${VIASH_META_MEMORY_GB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_gb='&'#" ; else echo "# meta_memory_gb="; fi ) +$( if [ ! -z ${VIASH_META_MEMORY_TB+x} ]; then echo "${VIASH_META_MEMORY_TB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_tb='&'#" ; else echo "# meta_memory_tb="; fi ) +$( if [ ! -z ${VIASH_META_MEMORY_PB+x} ]; then echo "${VIASH_META_MEMORY_PB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_pb='&'#" ; else echo "# meta_memory_pb="; fi ) +$( if [ ! -z ${VIASH_META_MEMORY_KIB+x} ]; then echo "${VIASH_META_MEMORY_KIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_kib='&'#" ; else echo "# meta_memory_kib="; fi ) +$( if [ ! -z ${VIASH_META_MEMORY_MIB+x} ]; then echo "${VIASH_META_MEMORY_MIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_mib='&'#" ; else echo "# meta_memory_mib="; fi ) +$( if [ ! -z ${VIASH_META_MEMORY_GIB+x} ]; then echo "${VIASH_META_MEMORY_GIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_gib='&'#" ; else echo "# meta_memory_gib="; fi ) +$( if [ ! -z ${VIASH_META_MEMORY_TIB+x} ]; then echo "${VIASH_META_MEMORY_TIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_tib='&'#" ; else echo "# meta_memory_tib="; fi ) +$( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_pib='&'#" ; else echo "# meta_memory_pib="; fi ) + +## VIASH END + +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 +VIASHMAIN +bash "\$tempscript" & +wait "\$!" + +VIASHEOF + + +if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then + # strip viash automount from file paths + + if [ ! -z "$VIASH_PAR_INPUT" ]; then + unset VIASH_TEST_INPUT + IFS=';' + for var in $VIASH_PAR_INPUT; do + unset IFS + if [ -z "$VIASH_TEST_INPUT" ]; then + VIASH_TEST_INPUT="$(ViashDockerStripAutomount "$var")" + else + VIASH_TEST_INPUT="$VIASH_TEST_INPUT;""$(ViashDockerStripAutomount "$var")" + fi + done + VIASH_PAR_INPUT="$VIASH_TEST_INPUT" + fi + if [ ! -z "$VIASH_PAR_REF" ]; then + unset VIASH_TEST_REF + IFS=';' + for var in $VIASH_PAR_REF; do + unset IFS + if [ -z "$VIASH_TEST_REF" ]; then + VIASH_TEST_REF="$(ViashDockerStripAutomount "$var")" + else + VIASH_TEST_REF="$VIASH_TEST_REF;""$(ViashDockerStripAutomount "$var")" + fi + done + VIASH_PAR_REF="$VIASH_TEST_REF" + fi + if [ ! -z "$VIASH_PAR_FASTQ_1" ]; then + VIASH_PAR_FASTQ_1=$(ViashDockerStripAutomount "$VIASH_PAR_FASTQ_1") + fi + if [ ! -z "$VIASH_PAR_FASTQ_2" ]; then + VIASH_PAR_FASTQ_2=$(ViashDockerStripAutomount "$VIASH_PAR_FASTQ_2") + fi + if [ ! -z "$VIASH_PAR_SAM2BAM" ]; then + VIASH_PAR_SAM2BAM=$(ViashDockerStripAutomount "$VIASH_PAR_SAM2BAM") + fi + if [ ! -z "$VIASH_PAR_SCAFSTATS" ]; then + VIASH_PAR_SCAFSTATS=$(ViashDockerStripAutomount "$VIASH_PAR_SCAFSTATS") + fi + if [ ! -z "$VIASH_PAR_REFSTATS" ]; then + VIASH_PAR_REFSTATS=$(ViashDockerStripAutomount "$VIASH_PAR_REFSTATS") + fi + if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then + VIASH_META_RESOURCES_DIR=$(ViashDockerStripAutomount "$VIASH_META_RESOURCES_DIR") + fi + if [ ! -z "$VIASH_META_EXECUTABLE" ]; then + VIASH_META_EXECUTABLE=$(ViashDockerStripAutomount "$VIASH_META_EXECUTABLE") + fi + if [ ! -z "$VIASH_META_CONFIG" ]; then + VIASH_META_CONFIG=$(ViashDockerStripAutomount "$VIASH_META_CONFIG") + fi + if [ ! -z "$VIASH_META_TEMP_DIR" ]; then + VIASH_META_TEMP_DIR=$(ViashDockerStripAutomount "$VIASH_META_TEMP_DIR") + fi +fi + + +# check whether required files exist +if [ ! -z "$VIASH_PAR_FASTQ_1" ] && [ ! -e "$VIASH_PAR_FASTQ_1" ]; then + ViashError "Output file '$VIASH_PAR_FASTQ_1' does not exist." + exit 1 +fi +if [ ! -z "$VIASH_PAR_FASTQ_2" ] && [ ! -e "$VIASH_PAR_FASTQ_2" ]; then + ViashError "Output file '$VIASH_PAR_FASTQ_2' does not exist." + exit 1 +fi +if [ ! -z "$VIASH_PAR_SAM2BAM" ] && [ ! -e "$VIASH_PAR_SAM2BAM" ]; then + ViashError "Output file '$VIASH_PAR_SAM2BAM' does not exist." + exit 1 +fi +if [ ! -z "$VIASH_PAR_SCAFSTATS" ] && [ ! -e "$VIASH_PAR_SCAFSTATS" ]; then + ViashError "Output file '$VIASH_PAR_SCAFSTATS' does not exist." + exit 1 +fi +if [ ! -z "$VIASH_PAR_REFSTATS" ] && [ ! -e "$VIASH_PAR_REFSTATS" ]; then + ViashError "Output file '$VIASH_PAR_REFSTATS' does not exist." + exit 1 +fi + + +exit 0 diff --git a/target/executable/bcftools/bcftools_annotate/.config.vsh.yaml b/target/executable/bcftools/bcftools_annotate/.config.vsh.yaml index 2ba2e6d0..6c8beba1 100644 --- 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" diff --git a/target/executable/bcftools/bcftools_annotate/bcftools_annotate b/target/executable/bcftools/bcftools_annotate/bcftools_annotate index f9a44dad..6eef6eec 100755 --- a/target/executable/bcftools/bcftools_annotate/bcftools_annotate +++ b/target/executable/bcftools/bcftools_annotate/bcftools_annotate @@ -650,9 +650,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_annotate" -LABEL org.opencontainers.image.created="2024-10-16T08:57:43Z" +LABEL org.opencontainers.image.created="2024-10-18T09:18:48Z" LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools" -LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc" +LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bcftools/bcftools_concat/.config.vsh.yaml b/target/executable/bcftools/bcftools_concat/.config.vsh.yaml index de2bc144..6576e69f 100644 --- a/target/executable/bcftools/bcftools_concat/.config.vsh.yaml +++ b/target/executable/bcftools/bcftools_concat/.config.vsh.yaml @@ -335,9 +335,9 @@ build_info: output: "target/executable/bcftools/bcftools_concat" executable: "target/executable/bcftools/bcftools_concat/bcftools_concat" viash_version: "0.9.0" - git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc" - git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox" - git_tag: "v0.2.0-10-g86333c1" + git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7" + git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-11-g7fb67a9" package_config: name: "biobox" version: "main" diff --git a/target/executable/bcftools/bcftools_concat/bcftools_concat b/target/executable/bcftools/bcftools_concat/bcftools_concat index 24f54c6c..256e1fda 100755 --- a/target/executable/bcftools/bcftools_concat/bcftools_concat +++ b/target/executable/bcftools/bcftools_concat/bcftools_concat @@ -566,9 +566,9 @@ RUN echo "bcftools: \"$(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 diff --git a/target/executable/bcftools/bcftools_norm/.config.vsh.yaml b/target/executable/bcftools/bcftools_norm/.config.vsh.yaml index 8a4f08f5..698c91bb 100644 --- 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" diff --git a/target/executable/bcftools/bcftools_norm/bcftools_norm b/target/executable/bcftools/bcftools_norm/bcftools_norm index eafce02b..7b31c47e 100755 --- a/target/executable/bcftools/bcftools_norm/bcftools_norm +++ b/target/executable/bcftools/bcftools_norm/bcftools_norm @@ -589,9 +589,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_norm" -LABEL org.opencontainers.image.created="2024-10-16T08:57:40Z" +LABEL org.opencontainers.image.created="2024-10-18T09:18:49Z" LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools" -LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc" +LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bcftools/bcftools_sort/.config.vsh.yaml b/target/executable/bcftools/bcftools_sort/.config.vsh.yaml index b1438e05..589abfe4 100644 --- a/target/executable/bcftools/bcftools_sort/.config.vsh.yaml +++ b/target/executable/bcftools/bcftools_sort/.config.vsh.yaml @@ -185,9 +185,9 @@ build_info: output: "target/executable/bcftools/bcftools_sort" executable: "target/executable/bcftools/bcftools_sort/bcftools_sort" viash_version: "0.9.0" - git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc" - git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox" - git_tag: "v0.2.0-10-g86333c1" + git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7" + git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-11-g7fb67a9" package_config: name: "biobox" version: "main" diff --git a/target/executable/bcftools/bcftools_sort/bcftools_sort b/target/executable/bcftools/bcftools_sort/bcftools_sort index 7cf7e81b..2bf2161b 100755 --- a/target/executable/bcftools/bcftools_sort/bcftools_sort +++ b/target/executable/bcftools/bcftools_sort/bcftools_sort @@ -483,9 +483,9 @@ RUN echo "bcftools: \"$(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 diff --git a/target/executable/bcftools/bcftools_stats/.config.vsh.yaml b/target/executable/bcftools/bcftools_stats/.config.vsh.yaml index cdd93b4b..6d66b211 100644 --- 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" diff --git a/target/executable/bcftools/bcftools_stats/bcftools_stats b/target/executable/bcftools/bcftools_stats/bcftools_stats index 7fa2f90b..5f0955b4 100755 --- a/target/executable/bcftools/bcftools_stats/bcftools_stats +++ b/target/executable/bcftools/bcftools_stats/bcftools_stats @@ -626,9 +626,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_stats" -LABEL org.opencontainers.image.created="2024-10-16T08:57:43Z" +LABEL org.opencontainers.image.created="2024-10-18T09:18:48Z" LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools" -LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc" +LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bcl_convert/.config.vsh.yaml b/target/executable/bcl_convert/.config.vsh.yaml index 717ab6b8..91ca5897 100644 --- a/target/executable/bcl_convert/.config.vsh.yaml +++ b/target/executable/bcl_convert/.config.vsh.yaml @@ -418,9 +418,9 @@ build_info: output: "target/executable/bcl_convert" executable: "target/executable/bcl_convert/bcl_convert" viash_version: "0.9.0" - git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc" - git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox" - git_tag: "v0.2.0-10-g86333c1" + git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7" + git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-11-g7fb67a9" package_config: name: "biobox" version: "main" diff --git a/target/executable/bcl_convert/bcl_convert b/target/executable/bcl_convert/bcl_convert index 09fa58fc..066aa6eb 100755 --- a/target/executable/bcl_convert/bcl_convert +++ b/target/executable/bcl_convert/bcl_convert @@ -599,9 +599,9 @@ RUN echo "bcl-convert: \"$(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 diff --git a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml index 0d45449e..38d2a62a 100644 --- a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml +++ b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml @@ -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" diff --git a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference index c103b1d1..caf59e5c 100755 --- a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference +++ b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference @@ -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 diff --git a/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml b/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml index 3ce38aa6..33fab7f9 100644 --- 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" diff --git 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 index 6b8c57a9..eaa8ee43 100755 --- 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 diff --git a/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml b/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml index d3bea49c..97e5273b 100644 --- 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" diff --git a/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq b/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq index ca3627cd..a33b13c1 100755 --- 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 diff --git a/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml b/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml index a99986ac..b7c7761c 100644 --- 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" diff --git a/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6 b/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6 index 5171f565..2fe07ae9 100755 --- 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 diff --git a/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml b/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml index b51233af..00451084 100644 --- 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" diff --git a/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam b/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam index 9ce671cc..44b1462e 100755 --- a/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam +++ b/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam @@ -496,9 +496,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bedtobam" -LABEL org.opencontainers.image.created="2024-10-16T08:57:45Z" +LABEL org.opencontainers.image.created="2024-10-18T09:18:58Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc" +LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bedtools/bedtools_genomecov/.config.vsh.yaml b/target/executable/bedtools/bedtools_genomecov/.config.vsh.yaml index 049cac36..48c78f3c 100644 --- a/target/executable/bedtools/bedtools_genomecov/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_genomecov/.config.vsh.yaml @@ -337,9 +337,9 @@ build_info: output: "target/executable/bedtools/bedtools_genomecov" executable: "target/executable/bedtools/bedtools_genomecov/bedtools_genomecov" viash_version: "0.9.0" - git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc" - git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox" - git_tag: "v0.2.0-10-g86333c1" + git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7" + git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-11-g7fb67a9" package_config: name: "biobox" version: "main" diff --git a/target/executable/bedtools/bedtools_genomecov/bedtools_genomecov b/target/executable/bedtools/bedtools_genomecov/bedtools_genomecov index e19d98fb..76eb9321 100755 --- a/target/executable/bedtools/bedtools_genomecov/bedtools_genomecov +++ b/target/executable/bedtools/bedtools_genomecov/bedtools_genomecov @@ -591,9 +591,9 @@ RUN echo "bedtools: \"$(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 diff --git a/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml b/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml index fb814adb..5475ec26 100644 --- 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" diff --git a/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta b/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta index ffe46b94..c888d898 100755 --- a/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta +++ b/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta @@ -526,9 +526,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_getfasta" -LABEL org.opencontainers.image.created="2024-10-16T08:57:44Z" +LABEL org.opencontainers.image.created="2024-10-18T09:18:57Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc" +LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml b/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml index 9d970ae6..b29b6285 100644 --- a/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml @@ -273,9 +273,9 @@ build_info: output: "target/executable/bedtools/bedtools_groupby" executable: "target/executable/bedtools/bedtools_groupby/bedtools_groupby" viash_version: "0.9.0" - git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc" - git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox" - git_tag: "v0.2.0-10-g86333c1" + git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7" + git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-11-g7fb67a9" package_config: name: "biobox" version: "main" diff --git a/target/executable/bedtools/bedtools_groupby/bedtools_groupby b/target/executable/bedtools/bedtools_groupby/bedtools_groupby index e1ab1d1d..1fce0870 100755 --- a/target/executable/bedtools/bedtools_groupby/bedtools_groupby +++ b/target/executable/bedtools/bedtools_groupby/bedtools_groupby @@ -552,9 +552,9 @@ RUN echo "bedtools: \"$(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 diff --git a/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml b/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml index 5145017e..2e32d5fc 100644 --- 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" diff --git a/target/executable/bedtools/bedtools_intersect/bedtools_intersect b/target/executable/bedtools/bedtools_intersect/bedtools_intersect index 87e47ee0..4dbdf219 100755 --- a/target/executable/bedtools/bedtools_intersect/bedtools_intersect +++ b/target/executable/bedtools/bedtools_intersect/bedtools_intersect @@ -633,9 +633,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_intersect" -LABEL org.opencontainers.image.created="2024-10-16T08:57:42Z" +LABEL org.opencontainers.image.created="2024-10-18T09:18:54Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc" +LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bedtools/bedtools_links/.config.vsh.yaml b/target/executable/bedtools/bedtools_links/.config.vsh.yaml index 66038234..6b5be203 100644 --- a/target/executable/bedtools/bedtools_links/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_links/.config.vsh.yaml @@ -210,9 +210,9 @@ build_info: output: "target/executable/bedtools/bedtools_links" executable: "target/executable/bedtools/bedtools_links/bedtools_links" viash_version: "0.9.0" - git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc" - git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox" - git_tag: "v0.2.0-10-g86333c1" + git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7" + git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-11-g7fb67a9" package_config: name: "biobox" version: "main" diff --git a/target/executable/bedtools/bedtools_links/bedtools_links b/target/executable/bedtools/bedtools_links/bedtools_links index c321dead..27743834 100755 --- a/target/executable/bedtools/bedtools_links/bedtools_links +++ b/target/executable/bedtools/bedtools_links/bedtools_links @@ -500,9 +500,9 @@ RUN echo "bedtools: \"$(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 diff --git a/target/executable/bedtools/bedtools_merge/.config.vsh.yaml b/target/executable/bedtools/bedtools_merge/.config.vsh.yaml index f42602dc..ef8c0d37 100644 --- 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" diff --git a/target/executable/bedtools/bedtools_merge/bedtools_merge b/target/executable/bedtools/bedtools_merge/bedtools_merge index 14287c5b..6bd395f7 100755 --- a/target/executable/bedtools/bedtools_merge/bedtools_merge +++ b/target/executable/bedtools/bedtools_merge/bedtools_merge @@ -558,9 +558,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_merge" -LABEL org.opencontainers.image.created="2024-10-16T08:57:44Z" +LABEL org.opencontainers.image.created="2024-10-18T09:18:57Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc" +LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bedtools/bedtools_sort/.config.vsh.yaml b/target/executable/bedtools/bedtools_sort/.config.vsh.yaml index 2a204915..47a81082 100644 --- a/target/executable/bedtools/bedtools_sort/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_sort/.config.vsh.yaml @@ -222,9 +222,9 @@ build_info: output: "target/executable/bedtools/bedtools_sort" executable: "target/executable/bedtools/bedtools_sort/bedtools_sort" viash_version: "0.9.0" - git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc" - git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox" - git_tag: "v0.2.0-10-g86333c1" + git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7" + git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-11-g7fb67a9" package_config: name: "biobox" version: "main" diff --git a/target/executable/bedtools/bedtools_sort/bedtools_sort b/target/executable/bedtools/bedtools_sort/bedtools_sort index b531a8a8..aa2f0862 100755 --- a/target/executable/bedtools/bedtools_sort/bedtools_sort +++ b/target/executable/bedtools/bedtools_sort/bedtools_sort @@ -509,9 +509,9 @@ RUN echo "bedtools: \"$(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 diff --git a/target/executable/busco/busco_download_datasets/.config.vsh.yaml b/target/executable/busco/busco_download_datasets/.config.vsh.yaml index 8d702428..a65a3b72 100644 --- 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" diff --git a/target/executable/busco/busco_download_datasets/busco_download_datasets b/target/executable/busco/busco_download_datasets/busco_download_datasets index 982aabc5..a41f8792 100755 --- 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 diff --git a/target/executable/busco/busco_list_datasets/.config.vsh.yaml b/target/executable/busco/busco_list_datasets/.config.vsh.yaml index a3733e1b..79542272 100644 --- 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" diff --git a/target/executable/busco/busco_list_datasets/busco_list_datasets b/target/executable/busco/busco_list_datasets/busco_list_datasets index 48671c03..49dec20f 100755 --- 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 diff --git a/target/executable/busco/busco_run/.config.vsh.yaml b/target/executable/busco/busco_run/.config.vsh.yaml index e21312df..98b45f08 100644 --- 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" diff --git a/target/executable/busco/busco_run/busco_run b/target/executable/busco/busco_run/busco_run index 27520568..6c943bac 100755 --- 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 diff --git a/target/executable/cutadapt/.config.vsh.yaml b/target/executable/cutadapt/.config.vsh.yaml index 437916b0..1c2303a4 100644 --- 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" diff --git a/target/executable/cutadapt/cutadapt b/target/executable/cutadapt/cutadapt index 0b52cf31..7e5feb44 100755 --- 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 diff --git a/target/executable/falco/.config.vsh.yaml b/target/executable/falco/.config.vsh.yaml index ad2e11d5..e8b3ea1c 100644 --- 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" diff --git a/target/executable/falco/falco b/target/executable/falco/falco index 143d92ea..8cec8837 100755 --- a/target/executable/falco/falco +++ b/target/executable/falco/falco @@ -589,9 +589,9 @@ RUN echo "falco: \"$(falco -v | sed -n 's/^falco //p')\"" > /var/software_versio LABEL org.opencontainers.image.authors="Toni Verbeiren" LABEL org.opencontainers.image.description="Companion container for running component falco" -LABEL org.opencontainers.image.created="2024-10-16T08:57:42Z" +LABEL org.opencontainers.image.created="2024-10-18T09:18:47Z" LABEL org.opencontainers.image.source="https://github.com/smithlabcode/falco" -LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc" +LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/fastp/.config.vsh.yaml b/target/executable/fastp/.config.vsh.yaml index a28befd6..fb80d8ad 100644 --- a/target/executable/fastp/.config.vsh.yaml +++ b/target/executable/fastp/.config.vsh.yaml @@ -1083,9 +1083,9 @@ build_info: output: "target/executable/fastp" executable: "target/executable/fastp/fastp" viash_version: "0.9.0" - git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc" - git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox" - git_tag: "v0.2.0-10-g86333c1" + git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7" + git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-11-g7fb67a9" package_config: name: "biobox" version: "main" diff --git a/target/executable/fastp/fastp b/target/executable/fastp/fastp index 8d67cced..aa86be46 100755 --- a/target/executable/fastp/fastp +++ b/target/executable/fastp/fastp @@ -1028,9 +1028,9 @@ RUN fastp --version 2>&1 | sed 's# #: "#;s#$#"#' > /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 diff --git a/target/executable/fastqc/.config.vsh.yaml b/target/executable/fastqc/.config.vsh.yaml index 7bc18283..d09d7f8c 100644 --- 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" diff --git a/target/executable/fastqc/fastqc b/target/executable/fastqc/fastqc index 9b109f32..a5698623 100755 --- 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 diff --git a/target/executable/featurecounts/.config.vsh.yaml b/target/executable/featurecounts/.config.vsh.yaml index 421d69f1..06848158 100644 --- 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" diff --git a/target/executable/featurecounts/featurecounts b/target/executable/featurecounts/featurecounts index 391e6860..ee1ac284 100755 --- 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 diff --git a/target/executable/fq_subsample/.config.vsh.yaml b/target/executable/fq_subsample/.config.vsh.yaml index 708e3370..54b22c07 100644 --- 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" diff --git a/target/executable/fq_subsample/fq_subsample b/target/executable/fq_subsample/fq_subsample index 928b2e12..8106ed60 100755 --- 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 diff --git a/target/executable/gffread/.config.vsh.yaml b/target/executable/gffread/.config.vsh.yaml index a7568d03..a5de0477 100644 --- 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" diff --git a/target/executable/gffread/gffread b/target/executable/gffread/gffread index d5cd0889..6999510f 100755 --- 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 diff --git a/target/executable/kallisto/kallisto_index/.config.vsh.yaml b/target/executable/kallisto/kallisto_index/.config.vsh.yaml index 1f625ee6..5a1a21f5 100644 --- 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" diff --git a/target/executable/kallisto/kallisto_index/kallisto_index b/target/executable/kallisto/kallisto_index/kallisto_index index 5942c8df..3bf66c76 100755 --- 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 diff --git a/target/executable/kallisto/kallisto_quant/.config.vsh.yaml b/target/executable/kallisto/kallisto_quant/.config.vsh.yaml index db647cce..27c29d4b 100644 --- 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" diff --git a/target/executable/kallisto/kallisto_quant/kallisto_quant b/target/executable/kallisto/kallisto_quant/kallisto_quant index 392c23a1..161eb1b9 100755 --- 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 diff --git a/target/executable/lofreq/lofreq_call/.config.vsh.yaml b/target/executable/lofreq/lofreq_call/.config.vsh.yaml index cb7cf288..d27ce62f 100644 --- 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" diff --git a/target/executable/lofreq/lofreq_call/lofreq_call b/target/executable/lofreq/lofreq_call/lofreq_call index ceea54ad..ce8b0ed1 100755 --- 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 diff --git a/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml b/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml index 36c1b1aa..8da4d953 100644 --- 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" diff --git a/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual b/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual index b022f0f5..c590e351 100755 --- 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 diff --git a/target/executable/multiqc/.config.vsh.yaml b/target/executable/multiqc/.config.vsh.yaml index 42fe9796..477eb16c 100644 --- 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" diff --git a/target/executable/multiqc/multiqc b/target/executable/multiqc/multiqc index 4eeb22c5..5eb72c26 100755 --- 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 diff --git a/target/executable/pear/.config.vsh.yaml b/target/executable/pear/.config.vsh.yaml index d89289fb..d1fe7863 100644 --- 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" diff --git a/target/executable/pear/pear b/target/executable/pear/pear index e6961f8c..000c66c4 100755 --- 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 diff --git a/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml b/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml index e94a7ad5..7e39cf28 100644 --- 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" diff --git a/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq b/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq index c6f3cf0a..b258c2e2 100755 --- 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 diff --git a/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml b/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml index c9c3368c..8d2b2888 100644 --- 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" diff --git a/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression b/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression index ea0c6986..9d43a95e 100755 --- 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 diff --git a/target/executable/rsem/rsem_prepare_reference/.config.vsh.yaml b/target/executable/rsem/rsem_prepare_reference/.config.vsh.yaml index c80b5646..645e4f2d 100644 --- 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" diff --git a/target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference b/target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference index b9d3bd44..8004ec1e 100755 --- 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 diff --git a/target/executable/salmon/salmon_index/.config.vsh.yaml b/target/executable/salmon/salmon_index/.config.vsh.yaml index 503888bd..369f2daf 100644 --- 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" diff --git a/target/executable/salmon/salmon_index/salmon_index b/target/executable/salmon/salmon_index/salmon_index index f1f60607..b8a8f5d4 100755 --- 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 diff --git a/target/executable/salmon/salmon_quant/.config.vsh.yaml b/target/executable/salmon/salmon_quant/.config.vsh.yaml index e223d01f..ec745bd0 100644 --- 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" diff --git a/target/executable/salmon/salmon_quant/salmon_quant b/target/executable/salmon/salmon_quant/salmon_quant index 5b226d9c..f8323867 100755 --- 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 diff --git a/target/executable/samtools/samtools_collate/.config.vsh.yaml b/target/executable/samtools/samtools_collate/.config.vsh.yaml index a9998269..d4c49549 100644 --- 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" diff --git a/target/executable/samtools/samtools_collate/samtools_collate b/target/executable/samtools/samtools_collate/samtools_collate index 02e24718..ca72adbc 100755 --- a/target/executable/samtools/samtools_collate/samtools_collate +++ b/target/executable/samtools/samtools_collate/samtools_collate @@ -519,9 +519,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_collate" -LABEL org.opencontainers.image.created="2024-10-16T08:57:41Z" +LABEL org.opencontainers.image.created="2024-10-18T09:18:46Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc" +LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/samtools/samtools_faidx/.config.vsh.yaml b/target/executable/samtools/samtools_faidx/.config.vsh.yaml index 7ea62dec..29c248be 100644 --- a/target/executable/samtools/samtools_faidx/.config.vsh.yaml +++ b/target/executable/samtools/samtools_faidx/.config.vsh.yaml @@ -243,9 +243,9 @@ build_info: output: "target/executable/samtools/samtools_faidx" executable: "target/executable/samtools/samtools_faidx/samtools_faidx" 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" diff --git a/target/executable/samtools/samtools_faidx/samtools_faidx b/target/executable/samtools/samtools_faidx/samtools_faidx index 2ba23246..345d2c70 100755 --- a/target/executable/samtools/samtools_faidx/samtools_faidx +++ b/target/executable/samtools/samtools_faidx/samtools_faidx @@ -512,9 +512,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_faidx" -LABEL org.opencontainers.image.created="2024-10-16T08:57:41Z" +LABEL org.opencontainers.image.created="2024-10-18T09:18:46Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc" +LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/samtools/samtools_fasta/.config.vsh.yaml b/target/executable/samtools/samtools_fasta/.config.vsh.yaml index a7743544..150c5265 100644 --- a/target/executable/samtools/samtools_fasta/.config.vsh.yaml +++ b/target/executable/samtools/samtools_fasta/.config.vsh.yaml @@ -433,9 +433,9 @@ build_info: output: "target/executable/samtools/samtools_fasta" executable: "target/executable/samtools/samtools_fasta/samtools_fasta" 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" diff --git a/target/executable/samtools/samtools_fasta/samtools_fasta b/target/executable/samtools/samtools_fasta/samtools_fasta index a2d8a86b..6e8d9265 100755 --- a/target/executable/samtools/samtools_fasta/samtools_fasta +++ b/target/executable/samtools/samtools_fasta/samtools_fasta @@ -625,9 +625,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_fasta" -LABEL org.opencontainers.image.created="2024-10-16T08:57:41Z" +LABEL org.opencontainers.image.created="2024-10-18T09:18:46Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc" +LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/samtools/samtools_fastq/.config.vsh.yaml b/target/executable/samtools/samtools_fastq/.config.vsh.yaml index ed9b24ec..9d759cbc 100644 --- a/target/executable/samtools/samtools_fastq/.config.vsh.yaml +++ b/target/executable/samtools/samtools_fastq/.config.vsh.yaml @@ -433,9 +433,9 @@ build_info: output: "target/executable/samtools/samtools_fastq" executable: "target/executable/samtools/samtools_fastq/samtools_fastq" 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" diff --git a/target/executable/samtools/samtools_fastq/samtools_fastq b/target/executable/samtools/samtools_fastq/samtools_fastq index fc15b466..0d58e9bb 100755 --- a/target/executable/samtools/samtools_fastq/samtools_fastq +++ b/target/executable/samtools/samtools_fastq/samtools_fastq @@ -626,9 +626,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_fastq" -LABEL org.opencontainers.image.created="2024-10-16T08:57:42Z" +LABEL org.opencontainers.image.created="2024-10-18T09:18:47Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc" +LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/samtools/samtools_flagstat/.config.vsh.yaml b/target/executable/samtools/samtools_flagstat/.config.vsh.yaml index dff8a3d3..9a3d4e20 100644 --- a/target/executable/samtools/samtools_flagstat/.config.vsh.yaml +++ b/target/executable/samtools/samtools_flagstat/.config.vsh.yaml @@ -173,9 +173,9 @@ build_info: output: "target/executable/samtools/samtools_flagstat" executable: "target/executable/samtools/samtools_flagstat/samtools_flagstat" 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" diff --git a/target/executable/samtools/samtools_flagstat/samtools_flagstat b/target/executable/samtools/samtools_flagstat/samtools_flagstat index bfeffd01..9305b316 100755 --- a/target/executable/samtools/samtools_flagstat/samtools_flagstat +++ b/target/executable/samtools/samtools_flagstat/samtools_flagstat @@ -474,9 +474,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_flagstat" -LABEL org.opencontainers.image.created="2024-10-16T08:57:46Z" +LABEL org.opencontainers.image.created="2024-10-18T09:18:58Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc" +LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/samtools/samtools_idxstats/.config.vsh.yaml b/target/executable/samtools/samtools_idxstats/.config.vsh.yaml index c173f04b..5dd3d2a4 100644 --- a/target/executable/samtools/samtools_idxstats/.config.vsh.yaml +++ b/target/executable/samtools/samtools_idxstats/.config.vsh.yaml @@ -183,9 +183,9 @@ build_info: output: "target/executable/samtools/samtools_idxstats" executable: "target/executable/samtools/samtools_idxstats/samtools_idxstats" 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" diff --git a/target/executable/samtools/samtools_idxstats/samtools_idxstats b/target/executable/samtools/samtools_idxstats/samtools_idxstats index 92748376..0165ed38 100755 --- a/target/executable/samtools/samtools_idxstats/samtools_idxstats +++ b/target/executable/samtools/samtools_idxstats/samtools_idxstats @@ -478,9 +478,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_idxstats" -LABEL org.opencontainers.image.created="2024-10-16T08:57:39Z" +LABEL org.opencontainers.image.created="2024-10-18T09:18:59Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc" +LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/samtools/samtools_index/.config.vsh.yaml b/target/executable/samtools/samtools_index/.config.vsh.yaml index d6a9b4bf..c0370865 100644 --- a/target/executable/samtools/samtools_index/.config.vsh.yaml +++ b/target/executable/samtools/samtools_index/.config.vsh.yaml @@ -189,9 +189,9 @@ build_info: output: "target/executable/samtools/samtools_index" executable: "target/executable/samtools/samtools_index/samtools_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" diff --git a/target/executable/samtools/samtools_index/samtools_index b/target/executable/samtools/samtools_index/samtools_index index 49ab00a2..ee03bc9b 100755 --- a/target/executable/samtools/samtools_index/samtools_index +++ b/target/executable/samtools/samtools_index/samtools_index @@ -485,9 +485,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_index" -LABEL org.opencontainers.image.created="2024-10-16T08:57:40Z" +LABEL org.opencontainers.image.created="2024-10-18T09:18:45Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc" +LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/samtools/samtools_sort/.config.vsh.yaml b/target/executable/samtools/samtools_sort/.config.vsh.yaml index 971af32d..5d903f1d 100644 --- a/target/executable/samtools/samtools_sort/.config.vsh.yaml +++ b/target/executable/samtools/samtools_sort/.config.vsh.yaml @@ -332,9 +332,9 @@ build_info: output: "target/executable/samtools/samtools_sort" executable: "target/executable/samtools/samtools_sort/samtools_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" diff --git a/target/executable/samtools/samtools_sort/samtools_sort b/target/executable/samtools/samtools_sort/samtools_sort index 7b0c9271..c0a0c376 100755 --- a/target/executable/samtools/samtools_sort/samtools_sort +++ b/target/executable/samtools/samtools_sort/samtools_sort @@ -556,9 +556,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_sort" -LABEL org.opencontainers.image.created="2024-10-16T08:57:42Z" +LABEL org.opencontainers.image.created="2024-10-18T09:18:47Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc" +LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/samtools/samtools_stats/.config.vsh.yaml b/target/executable/samtools/samtools_stats/.config.vsh.yaml index 011c6798..069e4b4a 100644 --- a/target/executable/samtools/samtools_stats/.config.vsh.yaml +++ b/target/executable/samtools/samtools_stats/.config.vsh.yaml @@ -401,9 +401,9 @@ build_info: output: "target/executable/samtools/samtools_stats" executable: "target/executable/samtools/samtools_stats/samtools_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" diff --git a/target/executable/samtools/samtools_stats/samtools_stats b/target/executable/samtools/samtools_stats/samtools_stats index 90fcebf7..342819fd 100755 --- a/target/executable/samtools/samtools_stats/samtools_stats +++ b/target/executable/samtools/samtools_stats/samtools_stats @@ -575,9 +575,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_stats" -LABEL org.opencontainers.image.created="2024-10-16T08:57:45Z" +LABEL org.opencontainers.image.created="2024-10-18T09:18:58Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc" +LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/samtools/samtools_view/.config.vsh.yaml b/target/executable/samtools/samtools_view/.config.vsh.yaml index 392fb83f..6ea3d7f5 100644 --- a/target/executable/samtools/samtools_view/.config.vsh.yaml +++ b/target/executable/samtools/samtools_view/.config.vsh.yaml @@ -665,9 +665,9 @@ build_info: output: "target/executable/samtools/samtools_view" executable: "target/executable/samtools/samtools_view/samtools_view" 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" diff --git a/target/executable/samtools/samtools_view/samtools_view b/target/executable/samtools/samtools_view/samtools_view index 1ecddb5f..34cc58a2 100755 --- a/target/executable/samtools/samtools_view/samtools_view +++ b/target/executable/samtools/samtools_view/samtools_view @@ -825,9 +825,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_view" -LABEL org.opencontainers.image.created="2024-10-16T08:57:40Z" +LABEL org.opencontainers.image.created="2024-10-18T09:18:45Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc" +LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/seqtk/seqtk_sample/.config.vsh.yaml b/target/executable/seqtk/seqtk_sample/.config.vsh.yaml index a15d3a29..52b7a94d 100644 --- a/target/executable/seqtk/seqtk_sample/.config.vsh.yaml +++ b/target/executable/seqtk/seqtk_sample/.config.vsh.yaml @@ -173,9 +173,9 @@ build_info: output: "target/executable/seqtk/seqtk_sample" executable: "target/executable/seqtk/seqtk_sample/seqtk_sample" 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" diff --git a/target/executable/seqtk/seqtk_sample/seqtk_sample b/target/executable/seqtk/seqtk_sample/seqtk_sample index b5bd1dc2..a7f9a5c3 100755 --- a/target/executable/seqtk/seqtk_sample/seqtk_sample +++ b/target/executable/seqtk/seqtk_sample/seqtk_sample @@ -481,9 +481,9 @@ FROM quay.io/biocontainers/seqtk:1.4--he4a0461_2 ENTRYPOINT [] LABEL org.opencontainers.image.authors="Jakub Majercik" LABEL org.opencontainers.image.description="Companion container for running component seqtk seqtk_sample" -LABEL org.opencontainers.image.created="2024-10-16T08:57:46Z" +LABEL org.opencontainers.image.created="2024-10-18T09:18:58Z" LABEL org.opencontainers.image.source="https://github.com/lh3/seqtk/tree/v1.4" -LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc" +LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml b/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml index 8419794f..a607056d 100644 --- a/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml +++ b/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml @@ -196,9 +196,9 @@ build_info: output: "target/executable/seqtk/seqtk_subseq" executable: "target/executable/seqtk/seqtk_subseq/seqtk_subseq" 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" diff --git a/target/executable/seqtk/seqtk_subseq/seqtk_subseq b/target/executable/seqtk/seqtk_subseq/seqtk_subseq index db0ca1d1..dc7a9780 100755 --- a/target/executable/seqtk/seqtk_subseq/seqtk_subseq +++ b/target/executable/seqtk/seqtk_subseq/seqtk_subseq @@ -491,9 +491,9 @@ RUN echo $(echo $(seqtk 2>&1) | sed -n 's/.*\(Version: [^ ]*\).*/\1/p') > /var/s LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component seqtk seqtk_subseq" -LABEL org.opencontainers.image.created="2024-10-16T08:57:46Z" +LABEL org.opencontainers.image.created="2024-10-18T09:18:59Z" LABEL org.opencontainers.image.source="https://github.com/lh3/seqtk/tree/v1.4" -LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc" +LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/snpeff/.config.vsh.yaml b/target/executable/snpeff/.config.vsh.yaml index 5fca32ca..f168b7f4 100644 --- a/target/executable/snpeff/.config.vsh.yaml +++ b/target/executable/snpeff/.config.vsh.yaml @@ -628,9 +628,9 @@ build_info: output: "target/executable/snpeff" executable: "target/executable/snpeff/snpeff" 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" diff --git a/target/executable/snpeff/snpeff b/target/executable/snpeff/snpeff index 54747663..abe61db9 100755 --- a/target/executable/snpeff/snpeff +++ b/target/executable/snpeff/snpeff @@ -756,9 +756,9 @@ version_trimmed=$(echo "$version" | awk '{print $1, $2}') && \ echo "$version_trimmed" > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component snpeff" -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/pcingola/SnpEff" -LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc" +LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/sortmerna/.config.vsh.yaml b/target/executable/sortmerna/.config.vsh.yaml index 77864c64..daa1700a 100644 --- a/target/executable/sortmerna/.config.vsh.yaml +++ b/target/executable/sortmerna/.config.vsh.yaml @@ -591,9 +591,9 @@ build_info: output: "target/executable/sortmerna" executable: "target/executable/sortmerna/sortmerna" 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" diff --git a/target/executable/sortmerna/sortmerna b/target/executable/sortmerna/sortmerna index d0dd2c56..efc9edb3 100755 --- a/target/executable/sortmerna/sortmerna +++ b/target/executable/sortmerna/sortmerna @@ -744,9 +744,9 @@ wget --no-check-certificate https://github.com/sortmerna/sortmerna/releases/down bash sortmerna-4.3.6-Linux.sh --skip-license LABEL org.opencontainers.image.description="Companion container for running component sortmerna" -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/sortmerna/sortmerna" -LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc" +LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/star/star_align_reads/.config.vsh.yaml b/target/executable/star/star_align_reads/.config.vsh.yaml index 016cb33f..293aa376 100644 --- a/target/executable/star/star_align_reads/.config.vsh.yaml +++ b/target/executable/star/star_align_reads/.config.vsh.yaml @@ -2663,9 +2663,9 @@ build_info: output: "target/executable/star/star_align_reads" executable: "target/executable/star/star_align_reads/star_align_reads" 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" diff --git a/target/executable/star/star_align_reads/star_align_reads b/target/executable/star/star_align_reads/star_align_reads index 903e2441..54a558f7 100755 --- a/target/executable/star/star_align_reads/star_align_reads +++ b/target/executable/star/star_align_reads/star_align_reads @@ -1920,9 +1920,9 @@ RUN STAR --version | sed 's#\(.*\)#star: "\1"#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component star star_align_reads" -LABEL org.opencontainers.image.created="2024-10-16T08:57:44Z" +LABEL org.opencontainers.image.created="2024-10-18T09:18:50Z" LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR" -LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc" +LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/star/star_genome_generate/.config.vsh.yaml b/target/executable/star/star_genome_generate/.config.vsh.yaml index cbecc328..64297536 100644 --- a/target/executable/star/star_genome_generate/.config.vsh.yaml +++ b/target/executable/star/star_genome_generate/.config.vsh.yaml @@ -333,9 +333,9 @@ build_info: output: "target/executable/star/star_genome_generate" executable: "target/executable/star/star_genome_generate/star_genome_generate" 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" diff --git a/target/executable/star/star_genome_generate/star_genome_generate b/target/executable/star/star_genome_generate/star_genome_generate index 1f211397..a5a0ed33 100755 --- a/target/executable/star/star_genome_generate/star_genome_generate +++ b/target/executable/star/star_genome_generate/star_genome_generate @@ -577,9 +577,9 @@ RUN STAR --version | sed 's#\(.*\)#star: "\1"#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa" LABEL org.opencontainers.image.description="Companion container for running component star star_genome_generate" -LABEL org.opencontainers.image.created="2024-10-16T08:57:44Z" +LABEL org.opencontainers.image.created="2024-10-18T09:18:49Z" LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR" -LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc" +LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/trimgalore/.config.vsh.yaml b/target/executable/trimgalore/.config.vsh.yaml index 393d2294..db3d7b9d 100644 --- a/target/executable/trimgalore/.config.vsh.yaml +++ b/target/executable/trimgalore/.config.vsh.yaml @@ -770,9 +770,9 @@ build_info: output: "target/executable/trimgalore" executable: "target/executable/trimgalore/trimgalore" 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" diff --git a/target/executable/trimgalore/trimgalore b/target/executable/trimgalore/trimgalore index ddc48234..fc3d5545 100755 --- a/target/executable/trimgalore/trimgalore +++ b/target/executable/trimgalore/trimgalore @@ -881,9 +881,9 @@ RUN echo "TrimGalore: `trim_galore --version | sed -n 's/.*version\s\+\([0-9]\+\ LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa" LABEL org.opencontainers.image.description="Companion container for running component trimgalore" -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/FelixKrueger/TrimGalore" -LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc" +LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml b/target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml index 66119970..9f2c7f8c 100644 --- a/target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml +++ b/target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml @@ -611,9 +611,9 @@ build_info: output: "target/executable/umi_tools/umi_tools_dedup" executable: "target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup" viash_version: "0.9.0" - 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" diff --git a/target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup b/target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup index 2373dac7..a029da00 100755 --- a/target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup +++ b/target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup @@ -770,9 +770,9 @@ RUN umi_tools -v | sed 's/ version//g' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component umi_tools umi_tools_dedup" -LABEL org.opencontainers.image.created="2024-10-16T08:57:41Z" +LABEL org.opencontainers.image.created="2024-10-18T09:18:50Z" LABEL org.opencontainers.image.source="https://github.com/CGATOxford/UMI-tools" -LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc" +LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml b/target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml index 5a06cd00..d6076dd9 100644 --- a/target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml +++ b/target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml @@ -449,9 +449,9 @@ build_info: output: "target/executable/umi_tools/umi_tools_extract" executable: "target/executable/umi_tools/umi_tools_extract/umi_tools_extract" viash_version: "0.9.0" - 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" diff --git a/target/executable/umi_tools/umi_tools_extract/umi_tools_extract b/target/executable/umi_tools/umi_tools_extract/umi_tools_extract index 3ba9db0e..7ad6609c 100755 --- a/target/executable/umi_tools/umi_tools_extract/umi_tools_extract +++ b/target/executable/umi_tools/umi_tools_extract/umi_tools_extract @@ -637,9 +637,9 @@ ENTRYPOINT [] RUN umi_tools -v | sed 's/ version//g' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component umi_tools umi_tools_extract" -LABEL org.opencontainers.image.created="2024-10-16T08:57:41Z" +LABEL org.opencontainers.image.created="2024-10-18T09:18:50Z" LABEL org.opencontainers.image.source="https://github.com/CGATOxford/UMI-tools" -LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc" +LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml b/target/executable/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml index 3a38e82c..d168dc82 100644 --- a/target/executable/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml +++ b/target/executable/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml @@ -256,9 +256,9 @@ build_info: output: "target/executable/umi_tools/umi_tools_prepareforrsem" executable: "target/executable/umi_tools/umi_tools_prepareforrsem/umi_tools_prepareforrsem" 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" diff --git a/target/executable/umi_tools/umi_tools_prepareforrsem/umi_tools_prepareforrsem b/target/executable/umi_tools/umi_tools_prepareforrsem/umi_tools_prepareforrsem index 48ab393f..b194e52e 100755 --- a/target/executable/umi_tools/umi_tools_prepareforrsem/umi_tools_prepareforrsem +++ b/target/executable/umi_tools/umi_tools_prepareforrsem/umi_tools_prepareforrsem @@ -519,9 +519,9 @@ ENTRYPOINT [] RUN umi_tools -v | sed 's/ version//g' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component umi_tools umi_tools_prepareforrsem" -LABEL org.opencontainers.image.created="2024-10-16T08:57:41Z" +LABEL org.opencontainers.image.created="2024-10-18T09:18:50Z" LABEL org.opencontainers.image.source="https://github.com/CGATOxford/UMI-tools" -LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc" +LABEL org.opencontainers.image.revision="7fb67a98539868b9af788338fb5f46d34ab742f7" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/nextflow/agat/agat_convert_bed2gff/.config.vsh.yaml b/target/nextflow/agat/agat_convert_bed2gff/.config.vsh.yaml index 99030b48..8cfbadb2 100644 --- a/target/nextflow/agat/agat_convert_bed2gff/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_bed2gff/.config.vsh.yaml @@ -235,9 +235,9 @@ build_info: output: "target/nextflow/agat/agat_convert_bed2gff" executable: "target/nextflow/agat/agat_convert_bed2gff/main.nf" 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" diff --git a/target/nextflow/agat/agat_convert_bed2gff/main.nf b/target/nextflow/agat/agat_convert_bed2gff/main.nf index 30a022e0..f374d2d6 100644 --- a/target/nextflow/agat/agat_convert_bed2gff/main.nf +++ b/target/nextflow/agat/agat_convert_bed2gff/main.nf @@ -3092,9 +3092,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/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", diff --git a/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml b/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml index 38450003..7e64221e 100644 --- a/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml @@ -225,9 +225,9 @@ build_info: output: "target/nextflow/agat/agat_convert_embl2gff" executable: "target/nextflow/agat/agat_convert_embl2gff/main.nf" 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" diff --git a/target/nextflow/agat/agat_convert_embl2gff/main.nf b/target/nextflow/agat/agat_convert_embl2gff/main.nf index 5af54d74..6f9d0d7a 100644 --- a/target/nextflow/agat/agat_convert_embl2gff/main.nf +++ b/target/nextflow/agat/agat_convert_embl2gff/main.nf @@ -3085,9 +3085,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/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", diff --git a/target/nextflow/agat/agat_convert_genscan2gff/.config.vsh.yaml b/target/nextflow/agat/agat_convert_genscan2gff/.config.vsh.yaml index fc1bffa0..f0cb7284 100644 --- a/target/nextflow/agat/agat_convert_genscan2gff/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_genscan2gff/.config.vsh.yaml @@ -230,9 +230,9 @@ build_info: output: "target/nextflow/agat/agat_convert_genscan2gff" executable: "target/nextflow/agat/agat_convert_genscan2gff/main.nf" 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" diff --git a/target/nextflow/agat/agat_convert_genscan2gff/main.nf b/target/nextflow/agat/agat_convert_genscan2gff/main.nf index 806bfad1..461e61fb 100644 --- a/target/nextflow/agat/agat_convert_genscan2gff/main.nf +++ b/target/nextflow/agat/agat_convert_genscan2gff/main.nf @@ -3087,9 +3087,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/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", diff --git a/target/nextflow/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml b/target/nextflow/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml index 7a092537..ab568264 100644 --- a/target/nextflow/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml @@ -228,9 +228,9 @@ build_info: output: "target/nextflow/agat/agat_convert_sp_gff2gtf" executable: "target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf" viash_version: "0.9.0" - 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" diff --git a/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf b/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf index 4aee64f2..0dc9dcbe 100644 --- a/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf +++ b/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf @@ -3068,9 +3068,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/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", diff --git a/target/nextflow/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml b/target/nextflow/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml index d077c854..36fe78cb 100644 --- a/target/nextflow/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml @@ -188,9 +188,9 @@ build_info: output: "target/nextflow/agat/agat_convert_sp_gff2tsv" executable: "target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf" viash_version: "0.9.0" - 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" diff --git a/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf b/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf index 9c41c532..fe3a7b4e 100644 --- a/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf +++ b/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf @@ -3046,9 +3046,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/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", diff --git a/target/nextflow/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml b/target/nextflow/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml index 554505e1..ab5d057b 100644 --- a/target/nextflow/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml @@ -195,9 +195,9 @@ build_info: output: "target/nextflow/agat/agat_convert_sp_gxf2gxf" executable: "target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf" viash_version: "0.9.0" - 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" diff --git a/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf b/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf index 89813b41..ef4e3017 100644 --- a/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf +++ b/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf @@ -3046,9 +3046,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/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", diff --git a/target/nextflow/arriba/.config.vsh.yaml b/target/nextflow/arriba/.config.vsh.yaml index fb154e50..39830d87 100644 --- a/target/nextflow/arriba/.config.vsh.yaml +++ b/target/nextflow/arriba/.config.vsh.yaml @@ -706,9 +706,9 @@ build_info: output: "target/nextflow/arriba" executable: "target/nextflow/arriba/main.nf" 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" diff --git a/target/nextflow/arriba/main.nf b/target/nextflow/arriba/main.nf index 82b3570f..c6f59769 100644 --- a/target/nextflow/arriba/main.nf +++ b/target/nextflow/arriba/main.nf @@ -3592,9 +3592,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/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", diff --git a/target/nextflow/bbmap/bbmap_bbsplit/.config.vsh.yaml b/target/nextflow/bbmap/bbmap_bbsplit/.config.vsh.yaml new file mode 100644 index 00000000..a94ce928 --- /dev/null +++ b/target/nextflow/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: "nextflow" + engine: "docker|native" + output: "target/nextflow/bbmap/bbmap_bbsplit" + executable: "target/nextflow/bbmap/bbmap_bbsplit/main.nf" + 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" diff --git a/target/nextflow/bbmap/bbmap_bbsplit/main.nf b/target/nextflow/bbmap/bbmap_bbsplit/main.nf new file mode 100644 index 00000000..3341a376 --- /dev/null +++ b/target/nextflow/bbmap/bbmap_bbsplit/main.nf @@ -0,0 +1,3864 @@ +// bbmap_bbsplit main +// +// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative +// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +// Intuitive. +// +// The component may contain files which fall under a different license. The +// authors of this component should specify the license in the header of such +// files, or include a separate license file detailing the licenses of all included +// files. + +//////////////////////////// +// VDSL3 helper functions // +//////////////////////////// + +// helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_checkArgumentType.nf' +class UnexpectedArgumentTypeException extends Exception { + String errorIdentifier + String stage + String plainName + String expectedClass + String foundClass + + // ${key ? " in module '$key'" : ""}${id ? " id '$id'" : ""} + UnexpectedArgumentTypeException(String errorIdentifier, String stage, String plainName, String expectedClass, String foundClass) { + super("Error${errorIdentifier ? " $errorIdentifier" : ""}:${stage ? " $stage" : "" } argument '${plainName}' has the wrong type. " + + "Expected type: ${expectedClass}. Found type: ${foundClass}") + this.errorIdentifier = errorIdentifier + this.stage = stage + this.plainName = plainName + this.expectedClass = expectedClass + this.foundClass = foundClass + } +} + +/** + * Checks if the given value is of the expected type. If not, an exception is thrown. + * + * @param stage The stage of the argument (input or output) + * @param par The parameter definition + * @param value The value to check + * @param errorIdentifier The identifier to use in the error message + * @return The value, if it is of the expected type + * @throws UnexpectedArgumentTypeException If the value is not of the expected type +*/ +def _checkArgumentType(String stage, Map par, Object value, String errorIdentifier) { + // expectedClass will only be != null if value is not of the expected type + def expectedClass = null + def foundClass = null + + // todo: split if need be + + if (!par.required && value == null) { + expectedClass = null + } else if (par.multiple) { + if (value !instanceof Collection) { + value = [value] + } + + // split strings + value = value.collectMany{ val -> + if (val instanceof String) { + // collect() to ensure that the result is a List and not simply an array + val.split(par.multiple_sep).collect() + } else { + [val] + } + } + + // process globs + if (par.type == "file" && par.direction == "input") { + value = value.collect{ it instanceof String ? file(it, hidden: true) : it }.flatten() + } + + // check types of elements in list + try { + value = value.collect { listVal -> + _checkArgumentType(stage, par + [multiple: false], listVal, errorIdentifier) + } + } catch (UnexpectedArgumentTypeException e) { + expectedClass = "List[${e.expectedClass}]" + foundClass = "List[${e.foundClass}]" + } + } else if (par.type == "string") { + // cast to string if need be + if (value instanceof GString) { + value = value.toString() + } + expectedClass = value instanceof String ? null : "String" + } else if (par.type == "integer") { + // cast to integer if need be + if (value instanceof String) { + try { + value = value.toInteger() + } catch (NumberFormatException e) { + // do nothing + } + } + if (value instanceof java.math.BigInteger) { + value = value.intValue() + } + expectedClass = value instanceof Integer ? null : "Integer" + } else if (par.type == "long") { + // cast to long if need be + if (value instanceof String) { + try { + value = value.toLong() + } catch (NumberFormatException e) { + // do nothing + } + } + if (value instanceof Integer) { + value = value.toLong() + } + expectedClass = value instanceof Long ? null : "Long" + } else if (par.type == "double") { + // cast to double if need be + if (value instanceof String) { + try { + value = value.toDouble() + } catch (NumberFormatException e) { + // do nothing + } + } + if (value instanceof java.math.BigDecimal) { + value = value.doubleValue() + } + if (value instanceof Float) { + value = value.toDouble() + } + expectedClass = value instanceof Double ? null : "Double" + } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { + // cast to boolean if need be + if (value instanceof String) { + def valueLower = value.toLowerCase() + if (valueLower == "true") { + value = true + } else if (valueLower == "false") { + value = false + } + } + expectedClass = value instanceof Boolean ? null : "Boolean" + } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { + // cast to path if need be + if (value instanceof String) { + value = file(value, hidden: true) + } + if (value instanceof File) { + value = value.toPath() + } + expectedClass = value instanceof Path ? null : "Path" + } else if (par.type == "file" && stage == "input" && par.direction == "output") { + // cast to string if need be + if (value instanceof GString) { + value = value.toString() + } + expectedClass = value instanceof String ? null : "String" + } else { + // didn't find a match for par.type + expectedClass = par.type + } + + if (expectedClass != null) { + if (foundClass == null) { + foundClass = value.getClass().getName() + } + throw new UnexpectedArgumentTypeException(errorIdentifier, stage, par.plainName, expectedClass, foundClass) + } + + return value +} +// helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processInputValues.nf' +Map _processInputValues(Map inputs, Map config, String id, String key) { + if (!workflow.stubRun) { + config.allArguments.each { arg -> + if (arg.required) { + assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : + "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing" + } + } + + inputs = inputs.collectEntries { name, value -> + def par = config.allArguments.find { it.plainName == name && (it.direction == "input" || it.type == "file") } + assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid input argument" + + value = _checkArgumentType("input", par, value, "in module '$key' id '$id'") + + [ name, value ] + } + } + return inputs +} + +// helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf' +Map _processOutputValues(Map outputs, Map config, String id, String key) { + if (!workflow.stubRun) { + config.allArguments.each { arg -> + if (arg.direction == "output" && arg.required) { + assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : + "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing" + } + } + + outputs = outputs.collectEntries { name, value -> + def par = config.allArguments.find { it.plainName == name && it.direction == "output" } + assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument" + + value = _checkArgumentType("output", par, value, "in module '$key' id '$id'") + + [ name, value ] + } + } + return outputs +} + +// helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf' +class IDChecker { + final def items = [] as Set + + @groovy.transform.WithWriteLock + boolean observe(String item) { + if (items.contains(item)) { + return false + } else { + items << item + return true + } + } + + @groovy.transform.WithReadLock + boolean contains(String item) { + return items.contains(item) + } + + @groovy.transform.WithReadLock + Set getItems() { + return items.clone() + } +} +// helper file: 'src/main/resources/io/viash/runners/nextflow/channel/_checkUniqueIds.nf' + +/** + * Check if the ids are unique across parameter sets + * + * @param parameterSets a list of parameter sets. + */ +private void _checkUniqueIds(List>> parameterSets) { + def ppIds = parameterSets.collect{it[0]} + assert ppIds.size() == ppIds.unique().size() : "All argument sets should have unique ids. Detected ids: $ppIds" +} + +// helper file: 'src/main/resources/io/viash/runners/nextflow/channel/_getChild.nf' + +// helper functions for reading params from file // +def _getChild(parent, child) { + if (child.contains("://") || java.nio.file.Paths.get(child).isAbsolute()) { + child + } else { + def parentAbsolute = java.nio.file.Paths.get(parent).toAbsolutePath().toString() + parentAbsolute.replaceAll('/[^/]*$', "/") + child + } +} + +// helper file: 'src/main/resources/io/viash/runners/nextflow/channel/_parseParamList.nf' +/** + * Figure out the param list format based on the file extension + * + * @param param_list A String containing the path to the parameter list file. + * + * @return A String containing the format of the parameter list file. + */ +def _paramListGuessFormat(param_list) { + if (param_list !instanceof String) { + "asis" + } else if (param_list.endsWith(".csv")) { + "csv" + } else if (param_list.endsWith(".json") || param_list.endsWith(".jsn")) { + "json" + } else if (param_list.endsWith(".yaml") || param_list.endsWith(".yml")) { + "yaml" + } else { + "yaml_blob" + } +} + + +/** + * Read the param list + * + * @param param_list One of the following: + * - A String containing the path to the parameter list file (csv, json or yaml), + * - A yaml blob of a list of maps (yaml_blob), + * - Or a groovy list of maps (asis). + * @param config A Map of the Viash configuration. + * + * @return A List of Maps containing the parameters. + */ +def _parseParamList(param_list, Map config) { + // first determine format by extension + def paramListFormat = _paramListGuessFormat(param_list) + + def paramListPath = (paramListFormat != "asis" && paramListFormat != "yaml_blob") ? + file(param_list, hidden: true) : + null + + // get the correct parser function for the detected params_list format + def paramSets = [] + if (paramListFormat == "asis") { + paramSets = param_list + } else if (paramListFormat == "yaml_blob") { + paramSets = readYamlBlob(param_list) + } else if (paramListFormat == "yaml") { + paramSets = readYaml(paramListPath) + } else if (paramListFormat == "json") { + paramSets = readJson(paramListPath) + } else if (paramListFormat == "csv") { + paramSets = readCsv(paramListPath) + } else { + error "Format of provided --param_list not recognised.\n" + + "Found: '$paramListFormat'.\n" + + "Expected: a csv file, a json file, a yaml file,\n" + + "a yaml blob or a groovy list of maps." + } + + // data checks + assert paramSets instanceof List: "--param_list should contain a list of maps" + for (value in paramSets) { + assert value instanceof Map: "--param_list should contain a list of maps" + } + + // id is argument + def idIsArgument = config.allArguments.any{it.plainName == "id"} + + // Reformat from List to List> by adding the ID as first element of a Tuple2 + paramSets = paramSets.collect({ data -> + def id = data.id + if (!idIsArgument) { + data = data.findAll{k, v -> k != "id"} + } + [id, data] + }) + + // Split parameters with 'multiple: true' + paramSets = paramSets.collect({ id, data -> + data = _splitParams(data, config) + [id, data] + }) + + // The paths of input files inside a param_list file may have been specified relatively to the + // location of the param_list file. These paths must be made absolute. + if (paramListPath) { + paramSets = paramSets.collect({ id, data -> + def new_data = data.collectEntries{ parName, parValue -> + def par = config.allArguments.find{it.plainName == parName} + if (par && par.type == "file" && par.direction == "input") { + if (parValue instanceof Collection) { + parValue = parValue.collectMany{path -> + def x = _resolveSiblingIfNotAbsolute(path, paramListPath) + x instanceof Collection ? x : [x] + } + } else { + parValue = _resolveSiblingIfNotAbsolute(parValue, paramListPath) + } + } + [parName, parValue] + } + [id, new_data] + }) + } + + return paramSets +} + +// helper file: 'src/main/resources/io/viash/runners/nextflow/channel/_splitParams.nf' +/** + * Split parameters for arguments that accept multiple values using their separator + * + * @param paramList A Map containing parameters to split. + * @param config A Map of the Viash configuration. This Map can be generated from the config file + * using the readConfig() function. + * + * @return A Map of parameters where the parameter values have been split into a list using + * their seperator. + */ +Map _splitParams(Map parValues, Map config){ + def parsedParamValues = parValues.collectEntries { parName, parValue -> + def parameterSettings = config.allArguments.find({it.plainName == parName}) + + if (!parameterSettings) { + // if argument is not found, do not alter + return [parName, parValue] + } + if (parameterSettings.multiple) { // Check if parameter can accept multiple values + if (parValue instanceof Collection) { + parValue = parValue.collect{it instanceof String ? it.split(parameterSettings.multiple_sep) : it } + } else if (parValue instanceof String) { + parValue = parValue.split(parameterSettings.multiple_sep) + } else if (parValue == null) { + parValue = [] + } else { + parValue = [ parValue ] + } + parValue = parValue.flatten() + } + // For all parameters check if multiple values are only passed for + // arguments that allow it. Quietly simplify lists of length 1. + if (!parameterSettings.multiple && parValue instanceof Collection) { + assert parValue.size() == 1 : + "Error: argument ${parName} has too many values.\n" + + " Expected amount: 1. Found: ${parValue.size()}" + parValue = parValue[0] + } + [parName, parValue] + } + return parsedParamValues +} + +// helper file: 'src/main/resources/io/viash/runners/nextflow/channel/channelFromParams.nf' +/** + * Parse nextflow parameters based on settings defined in a viash config. + * Return a list of parameter sets, each parameter set corresponding to + * an event in a nextflow channel. The output from this function can be used + * with Channel.fromList to create a nextflow channel with Vdsl3 formatted + * events. + * + * This function performs: + * - A filtering of the params which can be found in the config file. + * - Process the params_list argument which allows a user to to initialise + * a Vsdl3 channel with multiple parameter sets. Possible formats are + * csv, json, yaml, or simply a yaml_blob. A csv should have column names + * which correspond to the different arguments of this pipeline. A json or a yaml + * file should be a list of maps, each of which has keys corresponding to the + * arguments of the pipeline. A yaml blob can also be passed directly as a parameter. + * When passing a csv, json or yaml, relative path names are relativized to the + * location of the parameter file. + * - Combine the parameter sets into a vdsl3 Channel. + * + * @param params Input parameters. Can optionaly contain a 'param_list' key that + * provides a list of arguments that can be split up into multiple events + * in the output channel possible formats of param_lists are: a csv file, + * json file, a yaml file or a yaml blob. Each parameters set (event) must + * have a unique ID. + * @param config A Map of the Viash configuration. This Map can be generated from the config file + * using the readConfig() function. + * + * @return A list of parameters with the first element of the event being + * the event ID and the second element containing a map of the parsed parameters. + */ + +private List>> _paramsToParamSets(Map params, Map config){ + // todo: fetch key from run args + def key_ = config.name + + /* parse regular parameters (not in param_list) */ + /*************************************************/ + def globalParams = config.allArguments + .findAll { params.containsKey(it.plainName) } + .collectEntries { [ it.plainName, params[it.plainName] ] } + def globalID = params.get("id", null) + + /* process params_list arguments */ + /*********************************/ + def paramList = params.containsKey("param_list") && params.param_list != null ? + params.param_list : [] + // if (paramList instanceof String) { + // paramList = [paramList] + // } + // def paramSets = paramList.collectMany{ _parseParamList(it, config) } + // TODO: be able to process param_list when it is a list of strings + def paramSets = _parseParamList(paramList, config) + if (paramSets.isEmpty()) { + paramSets = [[null, [:]]] + } + + /* combine arguments into channel */ + /**********************************/ + def processedParams = paramSets.indexed().collect{ index, tup -> + // Process ID + def id = tup[0] ?: globalID + + if (workflow.stubRun && !id) { + // if stub run, explicitly add an id if missing + id = "stub${index}" + } + assert id != null: "Each parameter set should have at least an 'id'" + + // Process params + def parValues = globalParams + tup[1] + // // Remove parameters which are null, if the default is also null + // parValues = parValues.collectEntries{paramName, paramValue -> + // parameterSettings = config.functionality.allArguments.find({it.plainName == paramName}) + // if ( paramValue != null || parameterSettings.get("default", null) != null ) { + // [paramName, paramValue] + // } + // } + parValues = parValues.collectEntries { name, value -> + def par = config.allArguments.find { it.plainName == name && (it.direction == "input" || it.type == "file") } + assert par != null : "Error in module '${key_}' id '${id}': '${name}' is not a valid input argument" + + if (par == null) { + return [:] + } + value = _checkArgumentType("input", par, value, "in module '$key_' id '$id'") + + [ name, value ] + } + + [id, parValues] + } + + // Check if ids (first element of each list) is unique + _checkUniqueIds(processedParams) + return processedParams +} + +/** + * Parse nextflow parameters based on settings defined in a viash config + * and return a nextflow channel. + * + * @param params Input parameters. Can optionaly contain a 'param_list' key that + * provides a list of arguments that can be split up into multiple events + * in the output channel possible formats of param_lists are: a csv file, + * json file, a yaml file or a yaml blob. Each parameters set (event) must + * have a unique ID. + * @param config A Map of the Viash configuration. This Map can be generated from the config file + * using the readConfig() function. + * + * @return A nextflow Channel with events. Events are formatted as a tuple that contains + * first contains the ID of the event and as second element holds a parameter map. + * + * + */ +def channelFromParams(Map params, Map config) { + def processedParams = _paramsToParamSets(params, config) + return Channel.fromList(processedParams) +} + +// helper file: 'src/main/resources/io/viash/runners/nextflow/channel/checkUniqueIds.nf' +def checkUniqueIds(Map args) { + def stopOnError = args.stopOnError == null ? args.stopOnError : true + + def idChecker = new IDChecker() + + return filter { tup -> + if (!idChecker.observe(tup[0])) { + if (stopOnError) { + error "Duplicate id: ${tup[0]}" + } else { + log.warn "Duplicate id: ${tup[0]}, removing duplicate entry" + return false + } + } + return true + } +} +// helper file: 'src/main/resources/io/viash/runners/nextflow/channel/preprocessInputs.nf' +// This helper file will be deprecated soon +preprocessInputsDeprecationWarningPrinted = false + +def preprocessInputsDeprecationWarning() { + if (!preprocessInputsDeprecationWarningPrinted) { + preprocessInputsDeprecationWarningPrinted = true + System.err.println("Warning: preprocessInputs() is deprecated and will be removed in Viash 0.9.0.") + } +} + +/** + * Generate a nextflow Workflow that allows processing a channel of + * Vdsl3 formatted events and apply a Viash config to them: + * - Gather default parameters from the Viash config and make + * sure that they are correctly formatted (see applyConfig method). + * - Format the input parameters (also using the applyConfig method). + * - Apply the default parameter to the input parameters. + * - Do some assertions: + * ~ Check if the event IDs in the channel are unique. + * + * The events in the channel are formatted as tuples, with the + * first element of the tuples being a unique id of the parameter set, + * and the second element containg the the parameters themselves. + * Optional extra elements of the tuples will be passed to the output as is. + * + * @param args A map that must contain a 'config' key that points + * to a parsed config (see readConfig()). Optionally, a + * 'key' key can be provided which can be used to create a unique + * name for the workflow process. + * + * @return A workflow that allows processing a channel of Vdsl3 formatted events + * and apply a Viash config to them. + */ +def preprocessInputs(Map args) { + preprocessInputsDeprecationWarning() + + def config = args.config + assert config instanceof Map : + "Error in preprocessInputs: config must be a map. " + + "Expected class: Map. Found: config.getClass() is ${config.getClass()}" + def key_ = args.key ?: config.name + + // Get different parameter types (used throughout this function) + def defaultArgs = config.allArguments + .findAll { it.containsKey("default") } + .collectEntries { [ it.plainName, it.default ] } + + map { tup -> + def id = tup[0] + def data = tup[1] + def passthrough = tup.drop(2) + + def new_data = (defaultArgs + data).collectEntries { name, value -> + def par = config.allArguments.find { it.plainName == name && (it.direction == "input" || it.type == "file") } + + if (par != null) { + value = _checkArgumentType("input", par, value, "in module '$key_' id '$id'") + } + + [ name, value ] + } + + [ id, new_data ] + passthrough + } +} + +// helper file: 'src/main/resources/io/viash/runners/nextflow/channel/runComponents.nf' +/** + * Run a list of components on a stream of data. + * + * @param components: list of Viash VDSL3 modules to run + * @param fromState: a closure, a map or a list of keys to extract from the input data. + * If a closure, it will be called with the id, the data and the component config. + * @param toState: a closure, a map or a list of keys to extract from the output data + * If a closure, it will be called with the id, the output data, the old state and the component config. + * @param filter: filter function to apply to the input. + * It will be called with the id, the data and the component config. + * @param id: id to use for the output data + * If a closure, it will be called with the id, the data and the component config. + * @param auto: auto options to pass to the components + * + * @return: a workflow that runs the components + **/ +def runComponents(Map args) { + log.warn("runComponents is deprecated, use runEach instead") + assert args.components: "runComponents should be passed a list of components to run" + + def components_ = args.components + if (components_ !instanceof List) { + components_ = [ components_ ] + } + assert components_.size() > 0: "pass at least one component to runComponents" + + def fromState_ = args.fromState + def toState_ = args.toState + def filter_ = args.filter + def id_ = args.id + + workflow runComponentsWf { + take: input_ch + main: + + // generate one channel per method + out_chs = components_.collect{ comp_ -> + def comp_config = comp_.config + + def filter_ch = filter_ + ? input_ch | filter{tup -> + filter_(tup[0], tup[1], comp_config) + } + : input_ch + def id_ch = id_ + ? filter_ch | map{tup -> + // def new_id = id_(tup[0], tup[1], comp_config) + def new_id = tup[0] + if (id_ instanceof String) { + new_id = id_ + } else if (id_ instanceof Closure) { + new_id = id_(new_id, tup[1], comp_config) + } + [new_id] + tup.drop(1) + } + : filter_ch + def data_ch = id_ch | map{tup -> + def new_data = tup[1] + if (fromState_ instanceof Map) { + new_data = fromState_.collectEntries{ key0, key1 -> + [key0, new_data[key1]] + } + } else if (fromState_ instanceof List) { + new_data = fromState_.collectEntries{ key -> + [key, new_data[key]] + } + } else if (fromState_ instanceof Closure) { + new_data = fromState_(tup[0], new_data, comp_config) + } + tup.take(1) + [new_data] + tup.drop(1) + } + def out_ch = data_ch + | comp_.run( + auto: (args.auto ?: [:]) + [simplifyInput: false, simplifyOutput: false] + ) + def post_ch = toState_ + ? out_ch | map{tup -> + def output = tup[1] + def old_state = tup[2] + def new_state = null + if (toState_ instanceof Map) { + new_state = old_state + toState_.collectEntries{ key0, key1 -> + [key0, output[key1]] + } + } else if (toState_ instanceof List) { + new_state = old_state + toState_.collectEntries{ key -> + [key, output[key]] + } + } else if (toState_ instanceof Closure) { + new_state = toState_(tup[0], output, old_state, comp_config) + } + [tup[0], new_state] + tup.drop(3) + } + : out_ch + + post_ch + } + + // mix all results + output_ch = + (out_chs.size == 1) + ? out_chs[0] + : out_chs[0].mix(*out_chs.drop(1)) + + emit: output_ch + } + + return runComponentsWf +} + +// helper file: 'src/main/resources/io/viash/runners/nextflow/channel/runEach.nf' +/** + * Run a list of components on a stream of data. + * + * @param components: list of Viash VDSL3 modules to run + * @param fromState: a closure, a map or a list of keys to extract from the input data. + * If a closure, it will be called with the id, the data and the component itself. + * @param toState: a closure, a map or a list of keys to extract from the output data + * If a closure, it will be called with the id, the output data, the old state and the component itself. + * @param filter: filter function to apply to the input. + * It will be called with the id, the data and the component itself. + * @param id: id to use for the output data + * If a closure, it will be called with the id, the data and the component itself. + * @param auto: auto options to pass to the components + * + * @return: a workflow that runs the components + **/ +def runEach(Map args) { + assert args.components: "runEach should be passed a list of components to run" + + def components_ = args.components + if (components_ !instanceof List) { + components_ = [ components_ ] + } + assert components_.size() > 0: "pass at least one component to runEach" + + def fromState_ = args.fromState + def toState_ = args.toState + def filter_ = args.filter + def runIf_ = args.runIf + def id_ = args.id + + assert !runIf_ || runIf_ instanceof Closure: "runEach: must pass a Closure to runIf." + + workflow runEachWf { + take: input_ch + main: + + // generate one channel per method + out_chs = components_.collect{ comp_ -> + def filter_ch = filter_ + ? input_ch | filter{tup -> + filter_(tup[0], tup[1], comp_) + } + : input_ch + def id_ch = id_ + ? filter_ch | map{tup -> + def new_id = id_ + if (new_id instanceof Closure) { + new_id = new_id(tup[0], tup[1], comp_) + } + assert new_id instanceof String : "Error in runEach: id should be a String or a Closure that returns a String. Expected: id instanceof String. Found: ${new_id.getClass()}" + [new_id] + tup.drop(1) + } + : filter_ch + def chPassthrough = null + def chRun = null + if (runIf_) { + def idRunIfBranch = id_ch.branch{ tup -> + run: runIf_(tup[0], tup[1], comp_) + passthrough: true + } + chPassthrough = idRunIfBranch.passthrough + chRun = idRunIfBranch.run + } else { + chRun = id_ch + chPassthrough = Channel.empty() + } + def data_ch = chRun | map{tup -> + def new_data = tup[1] + if (fromState_ instanceof Map) { + new_data = fromState_.collectEntries{ key0, key1 -> + [key0, new_data[key1]] + } + } else if (fromState_ instanceof List) { + new_data = fromState_.collectEntries{ key -> + [key, new_data[key]] + } + } else if (fromState_ instanceof Closure) { + new_data = fromState_(tup[0], new_data, comp_) + } + tup.take(1) + [new_data] + tup.drop(1) + } + def out_ch = data_ch + | comp_.run( + auto: (args.auto ?: [:]) + [simplifyInput: false, simplifyOutput: false] + ) + def post_ch = toState_ + ? out_ch | map{tup -> + def output = tup[1] + def old_state = tup[2] + def new_state = null + if (toState_ instanceof Map) { + new_state = old_state + toState_.collectEntries{ key0, key1 -> + [key0, output[key1]] + } + } else if (toState_ instanceof List) { + new_state = old_state + toState_.collectEntries{ key -> + [key, output[key]] + } + } else if (toState_ instanceof Closure) { + new_state = toState_(tup[0], output, old_state, comp_) + } + [tup[0], new_state] + tup.drop(3) + } + : out_ch + + def return_ch = post_ch + | concat(chPassthrough) + + return_ch + } + + // mix all results + output_ch = + (out_chs.size == 1) + ? out_chs[0] + : out_chs[0].mix(*out_chs.drop(1)) + + emit: output_ch + } + + return runEachWf +} + +// helper file: 'src/main/resources/io/viash/runners/nextflow/channel/safeJoin.nf' +/** + * Join sourceChannel to targetChannel + * + * This function joins the sourceChannel to the targetChannel. + * However, each id in the targetChannel must be present in the + * sourceChannel. If _meta.join_id exists in the targetChannel, that is + * used as an id instead. If the id doesn't match any id in the sourceChannel, + * an error is thrown. + */ + +def safeJoin(targetChannel, sourceChannel, key) { + def sourceIDs = new IDChecker() + + def sourceCheck = sourceChannel + | map { tup -> + sourceIDs.observe(tup[0]) + tup + } + def targetCheck = targetChannel + | map { tup -> + def id = tup[0] + + if (!sourceIDs.contains(id)) { + error ( + "Error in module '${key}' when merging output with original state.\n" + + " Reason: output with id '${id}' could not be joined with source channel.\n" + + " If the IDs in the output channel differ from the input channel,\n" + + " please set `tup[1]._meta.join_id to the original ID.\n" + + " Original IDs in input channel: ['${sourceIDs.getItems().join("', '")}'].\n" + + " Unexpected ID in the output channel: '${id}'.\n" + + " Example input event: [\"id\", [input: file(...)]],\n" + + " Example output event: [\"newid\", [output: file(...), _meta: [join_id: \"id\"]]]" + ) + } + // TODO: add link to our documentation on how to fix this + + tup + } + + sourceCheck.cross(targetChannel) + | map{ left, right -> + right + left.drop(1) + } +} + +// helper file: 'src/main/resources/io/viash/runners/nextflow/config/_processArgument.nf' +def _processArgument(arg) { + arg.multiple = arg.multiple != null ? arg.multiple : false + arg.required = arg.required != null ? arg.required : false + arg.direction = arg.direction != null ? arg.direction : "input" + arg.multiple_sep = arg.multiple_sep != null ? arg.multiple_sep : ";" + arg.plainName = arg.name.replaceAll("^-*", "") + + if (arg.type == "file") { + arg.must_exist = arg.must_exist != null ? arg.must_exist : true + arg.create_parent = arg.create_parent != null ? arg.create_parent : true + } + + // add default values to output files which haven't already got a default + if (arg.type == "file" && arg.direction == "output" && arg.default == null) { + def mult = arg.multiple ? "_*" : "" + def extSearch = "" + if (arg.default != null) { + extSearch = arg.default + } else if (arg.example != null) { + extSearch = arg.example + } + if (extSearch instanceof List) { + extSearch = extSearch[0] + } + def extSearchResult = extSearch.find("\\.[^\\.]+\$") + def ext = extSearchResult != null ? extSearchResult : "" + arg.default = "\$id.\$key.${arg.plainName}${mult}${ext}" + if (arg.multiple) { + arg.default = [arg.default] + } + } + + if (!arg.multiple) { + if (arg.default != null && arg.default instanceof List) { + arg.default = arg.default[0] + } + if (arg.example != null && arg.example instanceof List) { + arg.example = arg.example[0] + } + } + + if (arg.type == "boolean_true") { + arg.default = false + } + if (arg.type == "boolean_false") { + arg.default = true + } + + arg +} + +// helper file: 'src/main/resources/io/viash/runners/nextflow/config/addGlobalParams.nf' +def addGlobalArguments(config) { + def localConfig = [ + "argument_groups": [ + [ + "name": "Nextflow input-output arguments", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "arguments" : [ + [ + 'name': '--publish_dir', + 'required': true, + 'type': 'string', + 'description': 'Path to an output directory.', + 'example': 'output/', + 'multiple': false + ], + [ + 'name': '--param_list', + 'required': false, + 'type': 'string', + 'description': '''Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob. + | + |* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ ['id': 'foo', 'input': 'foo.txt'], ['id': 'bar', 'input': 'bar.txt'] ]`. + |* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`. + |* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {'id': 'foo', 'input': 'foo.txt'}, {'id': 'bar', 'input': 'bar.txt'} ]`. + |* A yaml blob can also be passed directly as a string. Example: `--param_list "[ {'id': 'foo', 'input': 'foo.txt'}, {'id': 'bar', 'input': 'bar.txt'} ]"`. + | + |When passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.'''.stripMargin(), + 'example': 'my_params.yaml', + 'multiple': false, + 'hidden': true + ] + // TODO: allow multiple: true in param_list? + // TODO: allow to specify a --param_list_regex to filter the param_list? + // TODO: allow to specify a --param_list_from_state to remap entries in the param_list? + ] + ] + ] + ] + + return processConfig(_mergeMap(config, localConfig)) +} + +def _mergeMap(Map lhs, Map rhs) { + return rhs.inject(lhs.clone()) { map, entry -> + if (map[entry.key] instanceof Map && entry.value instanceof Map) { + map[entry.key] = _mergeMap(map[entry.key], entry.value) + } else if (map[entry.key] instanceof Collection && entry.value instanceof Collection) { + map[entry.key] += entry.value + } else { + map[entry.key] = entry.value + } + return map + } +} + +// helper file: 'src/main/resources/io/viash/runners/nextflow/config/generateHelp.nf' +def _generateArgumentHelp(param) { + // alternatives are not supported + // def names = param.alternatives ::: List(param.name) + + def unnamedProps = [ + ["required parameter", param.required], + ["multiple values allowed", param.multiple], + ["output", param.direction.toLowerCase() == "output"], + ["file must exist", param.type == "file" && param.must_exist] + ].findAll{it[1]}.collect{it[0]} + + def dflt = null + if (param.default != null) { + if (param.default instanceof List) { + dflt = param.default.join(param.multiple_sep != null ? param.multiple_sep : ", ") + } else { + dflt = param.default.toString() + } + } + def example = null + if (param.example != null) { + if (param.example instanceof List) { + example = param.example.join(param.multiple_sep != null ? param.multiple_sep : ", ") + } else { + example = param.example.toString() + } + } + def min = param.min?.toString() + def max = param.max?.toString() + + def escapeChoice = { choice -> + def s1 = choice.replaceAll("\\n", "\\\\n") + def s2 = s1.replaceAll("\"", """\\\"""") + s2.contains(",") || s2 != choice ? "\"" + s2 + "\"" : s2 + } + def choices = param.choices == null ? + null : + "[ " + param.choices.collect{escapeChoice(it.toString())}.join(", ") + " ]" + + def namedPropsStr = [ + ["type", ([param.type] + unnamedProps).join(", ")], + ["default", dflt], + ["example", example], + ["choices", choices], + ["min", min], + ["max", max] + ] + .findAll{it[1]} + .collect{"\n " + it[0] + ": " + it[1].replaceAll("\n", "\\n")} + .join("") + + def descStr = param.description == null ? + "" : + _paragraphWrap("\n" + param.description.trim(), 80 - 8).join("\n ") + + "\n --" + param.plainName + + namedPropsStr + + descStr +} + +// Based on Helper.generateHelp() in Helper.scala +def _generateHelp(config) { + def fun = config + + // PART 1: NAME AND VERSION + def nameStr = fun.name + + (fun.version == null ? "" : " " + fun.version) + + // PART 2: DESCRIPTION + def descrStr = fun.description == null ? + "" : + "\n\n" + _paragraphWrap(fun.description.trim(), 80).join("\n") + + // PART 3: Usage + def usageStr = fun.usage == null ? + "" : + "\n\nUsage:\n" + fun.usage.trim() + + // PART 4: Options + def argGroupStrs = fun.allArgumentGroups.collect{argGroup -> + def name = argGroup.name + def descriptionStr = argGroup.description == null ? + "" : + "\n " + _paragraphWrap(argGroup.description.trim(), 80-4).join("\n ") + "\n" + def arguments = argGroup.arguments.collect{arg -> + arg instanceof String ? fun.allArguments.find{it.plainName == arg} : arg + }.findAll{it != null} + def argumentStrs = arguments.collect{param -> _generateArgumentHelp(param)} + + "\n\n$name:" + + descriptionStr + + argumentStrs.join("\n") + } + + // FINAL: combine + def out = nameStr + + descrStr + + usageStr + + argGroupStrs.join("") + + return out +} + +// based on Format._paragraphWrap +def _paragraphWrap(str, maxLength) { + def outLines = [] + str.split("\n").each{par -> + def words = par.split("\\s").toList() + + def word = null + def line = words.pop() + while(!words.isEmpty()) { + word = words.pop() + if (line.length() + word.length() + 1 <= maxLength) { + line = line + " " + word + } else { + outLines.add(line) + line = word + } + } + if (words.isEmpty()) { + outLines.add(line) + } + } + return outLines +} + +def helpMessage(config) { + if (params.containsKey("help") && params.help) { + def mergedConfig = addGlobalArguments(config) + def helpStr = _generateHelp(mergedConfig) + println(helpStr) + exit 0 + } +} + +// helper file: 'src/main/resources/io/viash/runners/nextflow/config/processConfig.nf' +def processConfig(config) { + // set defaults for arguments + config.arguments = + (config.arguments ?: []).collect{_processArgument(it)} + + // set defaults for argument_group arguments + config.argument_groups = + (config.argument_groups ?: []).collect{grp -> + grp.arguments = (grp.arguments ?: []).collect{_processArgument(it)} + grp + } + + // create combined arguments list + config.allArguments = + config.arguments + + config.argument_groups.collectMany{it.arguments} + + // add missing argument groups (based on Functionality::allArgumentGroups()) + def argGroups = config.argument_groups + if (argGroups.any{it.name.toLowerCase() == "arguments"}) { + argGroups = argGroups.collect{ grp -> + if (grp.name.toLowerCase() == "arguments") { + grp = grp + [ + arguments: grp.arguments + config.arguments + ] + } + grp + } + } else { + argGroups = argGroups + [ + name: "Arguments", + arguments: config.arguments + ] + } + config.allArgumentGroups = argGroups + + config +} + +// helper file: 'src/main/resources/io/viash/runners/nextflow/config/readConfig.nf' + +def readConfig(file) { + def config = readYaml(file ?: moduleDir.resolve("config.vsh.yaml")) + processConfig(config) +} + +// helper file: 'src/main/resources/io/viash/runners/nextflow/functions/_resolveSiblingIfNotAbsolute.nf' +/** + * Resolve a path relative to the current file. + * + * @param str The path to resolve, as a String. + * @param parentPath The path to resolve relative to, as a Path. + * + * @return The path that may have been resovled, as a Path. + */ +def _resolveSiblingIfNotAbsolute(str, parentPath) { + if (str !instanceof String) { + return str + } + if (!_stringIsAbsolutePath(str)) { + return parentPath.resolveSibling(str) + } else { + return file(str, hidden: true) + } +} + +// helper file: 'src/main/resources/io/viash/runners/nextflow/functions/_stringIsAbsolutePath.nf' +/** + * Check whether a path as a string is absolute. + * + * In the past, we tried using `file(., relative: true).isAbsolute()`, + * but the 'relative' option was added in 22.10.0. + * + * @param path The path to check, as a String. + * + * @return Whether the path is absolute, as a boolean. + */ +def _stringIsAbsolutePath(path) { + def _resolve_URL_PROTOCOL = ~/^([a-zA-Z][a-zA-Z0-9]*:)?\\/.+/ + + assert path instanceof String + return _resolve_URL_PROTOCOL.matcher(path).matches() +} + +// helper file: 'src/main/resources/io/viash/runners/nextflow/functions/collectTraces.nf' +class CustomTraceObserver implements nextflow.trace.TraceObserver { + List traces + + CustomTraceObserver(List traces) { + this.traces = traces + } + + @Override + void onProcessComplete(nextflow.processor.TaskHandler handler, nextflow.trace.TraceRecord trace) { + def trace2 = trace.store.clone() + trace2.script = null + traces.add(trace2) + } + + @Override + void onProcessCached(nextflow.processor.TaskHandler handler, nextflow.trace.TraceRecord trace) { + def trace2 = trace.store.clone() + trace2.script = null + traces.add(trace2) + } +} + +def collectTraces() { + def traces = Collections.synchronizedList([]) + + // add custom trace observer which stores traces in the traces object + session.observers.add(new CustomTraceObserver(traces)) + + traces +} + +// helper file: 'src/main/resources/io/viash/runners/nextflow/functions/deepClone.nf' +/** + * Performs a deep clone of the given object. + * @param x an object + */ +def deepClone(x) { + iterateMap(x, {it instanceof Cloneable ? it.clone() : it}) +} +// helper file: 'src/main/resources/io/viash/runners/nextflow/functions/getPublishDir.nf' +def getPublishDir() { + return params.containsKey("publish_dir") ? params.publish_dir : + params.containsKey("publishDir") ? params.publishDir : + null +} + +// helper file: 'src/main/resources/io/viash/runners/nextflow/functions/getRootDir.nf' + +// Recurse upwards until we find a '.build.yaml' file +def _findBuildYamlFile(pathPossiblySymlink) { + def path = pathPossiblySymlink.toRealPath() + def child = path.resolve(".build.yaml") + if (java.nio.file.Files.isDirectory(path) && java.nio.file.Files.exists(child)) { + return child + } else { + def parent = path.getParent() + if (parent == null) { + return null + } else { + return _findBuildYamlFile(parent) + } + } +} + +// get the root of the target folder +def getRootDir() { + def dir = _findBuildYamlFile(meta.resources_dir) + assert dir != null: "Could not find .build.yaml in the folder structure" + dir.getParent() +} + +// helper file: 'src/main/resources/io/viash/runners/nextflow/functions/iterateMap.nf' +/** + * Recursively apply a function over the leaves of an object. + * @param obj The object to iterate over. + * @param fun The function to apply to each value. + * @return The object with the function applied to each value. + */ +def iterateMap(obj, fun) { + if (obj instanceof List && obj !instanceof String) { + return obj.collect{item -> + iterateMap(item, fun) + } + } else if (obj instanceof Map) { + return obj.collectEntries{key, item -> + [key.toString(), iterateMap(item, fun)] + } + } else { + return fun(obj) + } +} + +// helper file: 'src/main/resources/io/viash/runners/nextflow/functions/niceView.nf' +/** + * A view for printing the event of each channel as a YAML blob. + * This is useful for debugging. + */ +def niceView() { + workflow niceViewWf { + take: input + main: + output = input + | view{toYamlBlob(it)} + emit: output + } + return niceViewWf +} + +// helper file: 'src/main/resources/io/viash/runners/nextflow/readwrite/readCsv.nf' + +def readCsv(file_path) { + def output = [] + def inputFile = file_path !instanceof Path ? file(file_path, hidden: true) : file_path + + // todo: allow escaped quotes in string + // todo: allow single quotes? + def splitRegex = java.util.regex.Pattern.compile(''',(?=(?:[^"]*"[^"]*")*[^"]*$)''') + def removeQuote = java.util.regex.Pattern.compile('''"(.*)"''') + + def br = java.nio.file.Files.newBufferedReader(inputFile) + + def row = -1 + def header = null + while (br.ready() && header == null) { + def line = br.readLine() + row++ + if (!line.startsWith("#")) { + header = splitRegex.split(line, -1).collect{field -> + m = removeQuote.matcher(field) + m.find() ? m.replaceFirst('$1') : field + } + } + } + assert header != null: "CSV file should contain a header" + + while (br.ready()) { + def line = br.readLine() + row++ + if (line == null) { + br.close() + break + } + + if (!line.startsWith("#")) { + def predata = splitRegex.split(line, -1) + def data = predata.collect{field -> + if (field == "") { + return null + } + def m = removeQuote.matcher(field) + if (m.find()) { + return m.replaceFirst('$1') + } else { + return field + } + } + assert header.size() == data.size(): "Row $row should contain the same number as fields as the header" + + def dataMap = [header, data].transpose().collectEntries().findAll{it.value != null} + output.add(dataMap) + } + } + + output +} + +// helper file: 'src/main/resources/io/viash/runners/nextflow/readwrite/readJson.nf' +def readJson(file_path) { + def inputFile = file_path !instanceof Path ? file(file_path, hidden: true) : file_path + def jsonSlurper = new groovy.json.JsonSlurper() + jsonSlurper.parse(inputFile) +} + +// helper file: 'src/main/resources/io/viash/runners/nextflow/readwrite/readJsonBlob.nf' +def readJsonBlob(str) { + def jsonSlurper = new groovy.json.JsonSlurper() + jsonSlurper.parseText(str) +} + +// helper file: 'src/main/resources/io/viash/runners/nextflow/readwrite/readTaggedYaml.nf' +// Custom constructor to modify how certain objects are parsed from YAML +class CustomConstructor extends org.yaml.snakeyaml.constructor.Constructor { + Path root + + class ConstructPath extends org.yaml.snakeyaml.constructor.AbstractConstruct { + public Object construct(org.yaml.snakeyaml.nodes.Node node) { + String filename = (String) constructScalar(node); + if (root != null) { + return root.resolve(filename); + } + return java.nio.file.Paths.get(filename); + } + } + + CustomConstructor(org.yaml.snakeyaml.LoaderOptions options, Path root) { + super(options) + this.root = root + // Handling !file tag and parse it back to a File type + this.yamlConstructors.put(new org.yaml.snakeyaml.nodes.Tag("!file"), new ConstructPath()) + } +} + +def readTaggedYaml(Path path) { + def options = new org.yaml.snakeyaml.LoaderOptions() + def constructor = new CustomConstructor(options, path.getParent()) + def yaml = new org.yaml.snakeyaml.Yaml(constructor) + return yaml.load(path.text) +} + +// helper file: 'src/main/resources/io/viash/runners/nextflow/readwrite/readYaml.nf' +def readYaml(file_path) { + def inputFile = file_path !instanceof Path ? file(file_path, hidden: true) : file_path + def yamlSlurper = new org.yaml.snakeyaml.Yaml() + yamlSlurper.load(inputFile) +} + +// helper file: 'src/main/resources/io/viash/runners/nextflow/readwrite/readYamlBlob.nf' +def readYamlBlob(str) { + def yamlSlurper = new org.yaml.snakeyaml.Yaml() + yamlSlurper.load(str) +} + +// helper file: 'src/main/resources/io/viash/runners/nextflow/readwrite/toJsonBlob.nf' +String toJsonBlob(data) { + return groovy.json.JsonOutput.toJson(data) +} + +// helper file: 'src/main/resources/io/viash/runners/nextflow/readwrite/toTaggedYamlBlob.nf' +// Custom representer to modify how certain objects are represented in YAML +class CustomRepresenter extends org.yaml.snakeyaml.representer.Representer { + Path relativizer + + class RepresentPath implements org.yaml.snakeyaml.representer.Represent { + public String getFileName(Object obj) { + if (obj instanceof File) { + obj = ((File) obj).toPath(); + } + if (obj !instanceof Path) { + throw new IllegalArgumentException("Object: " + obj + " is not a Path or File"); + } + def path = (Path) obj; + + if (relativizer != null) { + return relativizer.relativize(path).toString() + } else { + return path.toString() + } + } + + public org.yaml.snakeyaml.nodes.Node representData(Object data) { + String filename = getFileName(data); + def tag = new org.yaml.snakeyaml.nodes.Tag("!file"); + return representScalar(tag, filename); + } + } + CustomRepresenter(org.yaml.snakeyaml.DumperOptions options, Path relativizer) { + super(options) + this.relativizer = relativizer + this.representers.put(sun.nio.fs.UnixPath, new RepresentPath()) + this.representers.put(Path, new RepresentPath()) + this.representers.put(File, new RepresentPath()) + } +} + +String toTaggedYamlBlob(data) { + return toRelativeTaggedYamlBlob(data, null) +} +String toRelativeTaggedYamlBlob(data, Path relativizer) { + def options = new org.yaml.snakeyaml.DumperOptions() + options.setDefaultFlowStyle(org.yaml.snakeyaml.DumperOptions.FlowStyle.BLOCK) + def representer = new CustomRepresenter(options, relativizer) + def yaml = new org.yaml.snakeyaml.Yaml(representer, options) + return yaml.dump(data) +} + +// helper file: 'src/main/resources/io/viash/runners/nextflow/readwrite/toYamlBlob.nf' +String toYamlBlob(data) { + def options = new org.yaml.snakeyaml.DumperOptions() + options.setDefaultFlowStyle(org.yaml.snakeyaml.DumperOptions.FlowStyle.BLOCK) + options.setPrettyFlow(true) + def yaml = new org.yaml.snakeyaml.Yaml(options) + def cleanData = iterateMap(data, { it instanceof Path ? it.toString() : it }) + return yaml.dump(cleanData) +} + +// helper file: 'src/main/resources/io/viash/runners/nextflow/readwrite/writeJson.nf' +void writeJson(data, file) { + assert data: "writeJson: data should not be null" + assert file: "writeJson: file should not be null" + file.write(toJsonBlob(data)) +} + +// helper file: 'src/main/resources/io/viash/runners/nextflow/readwrite/writeYaml.nf' +void writeYaml(data, file) { + assert data: "writeYaml: data should not be null" + assert file: "writeYaml: file should not be null" + file.write(toYamlBlob(data)) +} + +// helper file: 'src/main/resources/io/viash/runners/nextflow/states/findStates.nf' +def findStates(Map params, Map config) { + def auto_config = deepClone(config) + def auto_params = deepClone(params) + + auto_config = auto_config.clone() + // override arguments + auto_config.argument_groups = [] + auto_config.arguments = [ + [ + type: "string", + name: "--id", + description: "A dummy identifier", + required: false + ], + [ + type: "file", + name: "--input_states", + example: "/path/to/input/directory/**/state.yaml", + description: "Path to input directory containing the datasets to be integrated.", + required: true, + multiple: true, + multiple_sep: ";" + ], + [ + type: "string", + name: "--filter", + example: "foo/.*/state.yaml", + description: "Regex to filter state files by path.", + required: false + ], + // to do: make this a yaml blob? + [ + type: "string", + name: "--rename_keys", + example: ["newKey1:oldKey1", "newKey2:oldKey2"], + description: "Rename keys in the detected input files. This is useful if the input files do not match the set of input arguments of the workflow.", + required: false, + multiple: true, + multiple_sep: ";" + ], + [ + type: "string", + name: "--settings", + example: '{"output_dataset": "dataset.h5ad", "k": 10}', + description: "Global arguments as a JSON glob to be passed to all components.", + required: false + ] + ] + if (!(auto_params.containsKey("id"))) { + auto_params["id"] = "auto" + } + + // run auto config through processConfig once more + auto_config = processConfig(auto_config) + + workflow findStatesWf { + helpMessage(auto_config) + + output_ch = + channelFromParams(auto_params, auto_config) + | flatMap { autoId, args -> + + def globalSettings = args.settings ? readYamlBlob(args.settings) : [:] + + // look for state files in input dir + def stateFiles = args.input_states + + // filter state files by regex + if (args.filter) { + stateFiles = stateFiles.findAll{ stateFile -> + def stateFileStr = stateFile.toString() + def matcher = stateFileStr =~ args.filter + matcher.matches()} + } + + // read in states + def states = stateFiles.collect { stateFile -> + def state_ = readTaggedYaml(stateFile) + [state_.id, state_] + } + + // construct renameMap + if (args.rename_keys) { + def renameMap = args.rename_keys.collectEntries{renameString -> + def split = renameString.split(":") + assert split.size() == 2: "Argument 'rename_keys' should be of the form 'newKey:oldKey', or 'newKey:oldKey;newKey:oldKey' in case of multiple values" + split + } + + // rename keys in state, only let states through which have all keys + // also add global settings + states = states.collectMany{id, state -> + def newState = [:] + + for (key in renameMap.keySet()) { + def origKey = renameMap[key] + if (!(state.containsKey(origKey))) { + return [] + } + newState[key] = state[origKey] + } + + [[id, globalSettings + newState]] + } + } + + states + } + emit: + output_ch + } + + return findStatesWf +} + +// helper file: 'src/main/resources/io/viash/runners/nextflow/states/joinStates.nf' +def joinStates(Closure apply_) { + workflow joinStatesWf { + take: input_ch + main: + output_ch = input_ch + | toSortedList + | filter{ it.size() > 0 } + | map{ tups -> + def ids = tups.collect{it[0]} + def states = tups.collect{it[1]} + apply_(ids, states) + } + + emit: output_ch + } + return joinStatesWf +} +// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf' +def collectFiles(obj) { + if (obj instanceof java.io.File || obj instanceof Path) { + return [obj] + } else if (obj instanceof List && obj !instanceof String) { + return obj.collectMany{item -> + collectFiles(item) + } + } else if (obj instanceof Map) { + return obj.collectMany{key, item -> + collectFiles(item) + } + } else { + return [] + } +} + +/** + * Recurse through a state and collect all input files and their target output filenames. + * @param obj The state to recurse through. + * @param prefix The prefix to prepend to the output filenames. + */ +def collectInputOutputPaths(obj, prefix) { + if (obj instanceof File || obj instanceof Path) { + def path = obj instanceof Path ? obj : obj.toPath() + def ext = path.getFileName().toString().find("\\.[^\\.]+\$") ?: "" + def newFilename = prefix + ext + return [[obj, newFilename]] + } else if (obj instanceof List && obj !instanceof String) { + return obj.withIndex().collectMany{item, ix -> + collectInputOutputPaths(item, prefix + "_" + ix) + } + } else if (obj instanceof Map) { + return obj.collectMany{key, item -> + collectInputOutputPaths(item, prefix + "." + key) + } + } else { + return [] + } +} + +def publishStates(Map args) { + def key_ = args.get("key") + def yamlTemplate_ = args.get("output_state", args.get("outputState", '$id.$key.state.yaml')) + + assert key_ != null : "publishStates: key must be specified" + + workflow publishStatesWf { + take: input_ch + main: + input_ch + | map { tup -> + def id_ = tup[0] + def state_ = tup[1] + + // the input files and the target output filenames + def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose() + def inputFiles_ = inputoutputFilenames_[0] + def outputFilenames_ = inputoutputFilenames_[1] + + def yamlFilename = yamlTemplate_ + .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) + .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) + + // TODO: do the pathnames in state_ match up with the outputFilenames_? + + // convert state to yaml blob + def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename)) + + [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_] + } + | publishStatesProc + emit: input_ch + } + return publishStatesWf +} +process publishStatesProc { + // todo: check publishpath? + publishDir path: "${getPublishDir()}/", mode: "copy" + tag "$id" + input: + tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles) + output: + tuple val(id), path{[yamlFile] + outputFiles} + script: + def copyCommands = [ + inputFiles instanceof List ? inputFiles : [inputFiles], + outputFiles instanceof List ? outputFiles : [outputFiles] + ] + .transpose() + .collectMany{infile, outfile -> + if (infile.toString() != outfile.toString()) { + [ + "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"", + "cp -r '${infile.toString()}' '${outfile.toString()}'" + ] + } else { + // no need to copy if infile is the same as outfile + [] + } + } + """ +mkdir -p "\$(dirname '${yamlFile}')" +echo "Storing state as yaml" +echo '${yamlBlob}' > '${yamlFile}' +echo "Copying output files to destination folder" +${copyCommands.join("\n ")} +""" +} + + +// this assumes that the state contains no other values other than those specified in the config +def publishStatesByConfig(Map args) { + def config = args.get("config") + assert config != null : "publishStatesByConfig: config must be specified" + + def key_ = args.get("key", config.name) + assert key_ != null : "publishStatesByConfig: key must be specified" + + workflow publishStatesSimpleWf { + take: input_ch + main: + input_ch + | map { tup -> + def id_ = tup[0] + def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10] + def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad'] + + // TODO: allow overriding the state.yaml template + // TODO TODO: if auto.publish == "state", add output_state as an argument + def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' + def yamlFilename = yamlTemplate + .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) + .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) + def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() + + // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where + // - key is a String + // - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path) + // - inputPath is a List[Path] + // - outputFilename is a List[String] + // - (key, value) are the tuples that will be saved to the state.yaml file + // - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml) + def processedState = + config.allArguments + .findAll { it.direction == "output" } + .collectMany { par -> + def plainName_ = par.plainName + // if the state does not contain the key, it's an + // optional argument for which the component did + // not generate any output + if (!state_.containsKey(plainName_)) { + return [] + } + def value = state_[plainName_] + // if the parameter is not a file, it should be stored + // in the state as-is, but is not something that needs + // to be copied from the source path to the dest path + if (par.type != "file") { + return [[key: plainName_, value: value, inputPath: [], outputFilename: []]] + } + // if the orig state does not contain this filename, + // it's an optional argument for which the user specified + // that it should not be returned as a state + if (!origState_.containsKey(plainName_)) { + return [] + } + def filenameTemplate = origState_[plainName_] + // if the pararameter is multiple: true, fetch the template + if (par.multiple && filenameTemplate instanceof List) { + filenameTemplate = filenameTemplate[0] + } + // instantiate the template + def filename = filenameTemplate + .replaceAll('\\$id', id_) + .replaceAll('\\$\\{id\\}', id_) + .replaceAll('\\$key', key_) + .replaceAll('\\$\\{key\\}', key_) + if (par.multiple) { + // if the parameter is multiple: true, the filename + // should contain a wildcard '*' that is replaced with + // the index of the file + assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}" + def outputPerFile = value.withIndex().collect{ val, ix -> + def filename_ix = filename.replace("*", ix.toString()) + def value_ = java.nio.file.Paths.get(filename_ix) + // if id contains a slash + if (yamlDir != null) { + value_ = yamlDir.relativize(value_) + } + def inputPath = val instanceof File ? val.toPath() : val + [value: value_, inputPath: inputPath, outputFilename: filename_ix] + } + def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> + [key, outputPerFile.collect{dic -> dic[key]}] + } + return [[key: plainName_] + transposedOutputs] + } else { + def value_ = java.nio.file.Paths.get(filename) + // if id contains a slash + if (yamlDir != null) { + value_ = yamlDir.relativize(value_) + } + def inputPath = value instanceof File ? value.toPath() : value + return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]] + } + } + + def updatedState_ = processedState.collectEntries{[it.key, it.value]} + def inputPaths = processedState.collectMany{it.inputPath} + def outputFilenames = processedState.collectMany{it.outputFilename} + + // convert state to yaml blob + def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_) + + [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames] + } + | publishStatesProc + emit: input_ch + } + return publishStatesSimpleWf +} + +// helper file: 'src/main/resources/io/viash/runners/nextflow/states/setState.nf' +def setState(fun) { + assert fun instanceof Closure || fun instanceof Map || fun instanceof List : + "Error in setState: Expected process argument to be a Closure, a Map, or a List. Found: class ${fun.getClass()}" + + // if fun is a List, convert to map + if (fun instanceof List) { + // check whether fun is a list[string] + assert fun.every{it instanceof CharSequence} : "Error in setState: argument is a List, but not all elements are Strings" + fun = fun.collectEntries{[it, it]} + } + + // if fun is a map, convert to closure + if (fun instanceof Map) { + // check whether fun is a map[string, string] + assert fun.values().every{it instanceof CharSequence} : "Error in setState: argument is a Map, but not all values are Strings" + assert fun.keySet().every{it instanceof CharSequence} : "Error in setState: argument is a Map, but not all keys are Strings" + def funMap = fun.clone() + // turn the map into a closure to be used later on + fun = { id_, state_ -> + assert state_ instanceof Map : "Error in setState: the state is not a Map" + funMap.collectMany{newkey, origkey -> + if (state_.containsKey(origkey)) { + [[newkey, state_[origkey]]] + } else { + [] + } + }.collectEntries() + } + } + + map { tup -> + def id = tup[0] + def state = tup[1] + def unfilteredState = fun(id, state) + def newState = unfilteredState.findAll{key, val -> val != null} + [id, newState] + tup.drop(2) + } +} + +// helper file: 'src/main/resources/io/viash/runners/nextflow/workflowFactory/processAuto.nf' +// TODO: unit test processAuto +def processAuto(Map auto) { + // remove null values + auto = auto.findAll{k, v -> v != null} + + // check for unexpected keys + def expectedKeys = ["simplifyInput", "simplifyOutput", "transcript", "publish"] + def unexpectedKeys = auto.keySet() - expectedKeys + assert unexpectedKeys.isEmpty(), "unexpected keys in auto: '${unexpectedKeys.join("', '")}'" + + // check auto.simplifyInput + assert auto.simplifyInput instanceof Boolean, "auto.simplifyInput must be a boolean" + + // check auto.simplifyOutput + assert auto.simplifyOutput instanceof Boolean, "auto.simplifyOutput must be a boolean" + + // check auto.transcript + assert auto.transcript instanceof Boolean, "auto.transcript must be a boolean" + + // check auto.publish + assert auto.publish instanceof Boolean || auto.publish == "state", "auto.publish must be a boolean or 'state'" + + return auto.subMap(expectedKeys) +} + +// helper file: 'src/main/resources/io/viash/runners/nextflow/workflowFactory/processDirectives.nf' +def assertMapKeys(map, expectedKeys, requiredKeys, mapName) { + assert map instanceof Map : "Expected argument '$mapName' to be a Map. Found: class ${map.getClass()}" + map.forEach { key, val -> + assert key in expectedKeys : "Unexpected key '$key' in ${mapName ? mapName + " " : ""}map" + } + requiredKeys.forEach { requiredKey -> + assert map.containsKey(requiredKey) : "Missing required key '$key' in ${mapName ? mapName + " " : ""}map" + } +} + +// TODO: unit test processDirectives +def processDirectives(Map drctv) { + // remove null values + drctv = drctv.findAll{k, v -> v != null} + + // check for unexpected keys + def expectedKeys = [ + "accelerator", "afterScript", "beforeScript", "cache", "conda", "container", "containerOptions", "cpus", "disk", "echo", "errorStrategy", "executor", "machineType", "maxErrors", "maxForks", "maxRetries", "memory", "module", "penv", "pod", "publishDir", "queue", "label", "scratch", "storeDir", "stageInMode", "stageOutMode", "tag", "time" + ] + def unexpectedKeys = drctv.keySet() - expectedKeys + assert unexpectedKeys.isEmpty() : "Unexpected keys in process directive: '${unexpectedKeys.join("', '")}'" + + /* DIRECTIVE accelerator + accepted examples: + - [ limit: 4, type: "nvidia-tesla-k80" ] + */ + if (drctv.containsKey("accelerator")) { + assertMapKeys(drctv["accelerator"], ["type", "limit", "request", "runtime"], [], "accelerator") + } + + /* DIRECTIVE afterScript + accepted examples: + - "source /cluster/bin/cleanup" + */ + if (drctv.containsKey("afterScript")) { + assert drctv["afterScript"] instanceof CharSequence + } + + /* DIRECTIVE beforeScript + accepted examples: + - "source /cluster/bin/setup" + */ + if (drctv.containsKey("beforeScript")) { + assert drctv["beforeScript"] instanceof CharSequence + } + + /* DIRECTIVE cache + accepted examples: + - true + - false + - "deep" + - "lenient" + */ + if (drctv.containsKey("cache")) { + assert drctv["cache"] instanceof CharSequence || drctv["cache"] instanceof Boolean + if (drctv["cache"] instanceof CharSequence) { + assert drctv["cache"] in ["deep", "lenient"] : "Unexpected value for cache" + } + } + + /* DIRECTIVE conda + accepted examples: + - "bwa=0.7.15" + - "bwa=0.7.15 fastqc=0.11.5" + - ["bwa=0.7.15", "fastqc=0.11.5"] + */ + if (drctv.containsKey("conda")) { + if (drctv["conda"] instanceof List) { + drctv["conda"] = drctv["conda"].join(" ") + } + assert drctv["conda"] instanceof CharSequence + } + + /* DIRECTIVE container + accepted examples: + - "foo/bar:tag" + - [ registry: "reg", image: "im", tag: "ta" ] + is transformed to "reg/im:ta" + - [ image: "im" ] + is transformed to "im:latest" + */ + if (drctv.containsKey("container")) { + assert drctv["container"] instanceof Map || drctv["container"] instanceof CharSequence + if (drctv["container"] instanceof Map) { + def m = drctv["container"] + assertMapKeys(m, [ "registry", "image", "tag" ], ["image"], "container") + def part1 = + System.getenv('OVERRIDE_CONTAINER_REGISTRY') ? System.getenv('OVERRIDE_CONTAINER_REGISTRY') + "/" : + params.containsKey("override_container_registry") ? params["override_container_registry"] + "/" : // todo: remove? + m.registry ? m.registry + "/" : + "" + def part2 = m.image + def part3 = m.tag ? ":" + m.tag : ":latest" + drctv["container"] = part1 + part2 + part3 + } + } + + /* DIRECTIVE containerOptions + accepted examples: + - "--foo bar" + - ["--foo bar", "-f b"] + */ + if (drctv.containsKey("containerOptions")) { + if (drctv["containerOptions"] instanceof List) { + drctv["containerOptions"] = drctv["containerOptions"].join(" ") + } + assert drctv["containerOptions"] instanceof CharSequence + } + + /* DIRECTIVE cpus + accepted examples: + - 1 + - 10 + */ + if (drctv.containsKey("cpus")) { + assert drctv["cpus"] instanceof Integer + } + + /* DIRECTIVE disk + accepted examples: + - "1 GB" + - "2TB" + - "3.2KB" + - "10.B" + */ + if (drctv.containsKey("disk")) { + assert drctv["disk"] instanceof CharSequence + // assert drctv["disk"].matches("[0-9]+(\\.[0-9]*)? *[KMGTPEZY]?B") + // ^ does not allow closures + } + + /* DIRECTIVE echo + accepted examples: + - true + - false + */ + if (drctv.containsKey("echo")) { + assert drctv["echo"] instanceof Boolean + } + + /* DIRECTIVE errorStrategy + accepted examples: + - "terminate" + - "finish" + */ + if (drctv.containsKey("errorStrategy")) { + assert drctv["errorStrategy"] instanceof CharSequence + assert drctv["errorStrategy"] in ["terminate", "finish", "ignore", "retry"] : "Unexpected value for errorStrategy" + } + + /* DIRECTIVE executor + accepted examples: + - "local" + - "sge" + */ + if (drctv.containsKey("executor")) { + assert drctv["executor"] instanceof CharSequence + assert drctv["executor"] in ["local", "sge", "uge", "lsf", "slurm", "pbs", "pbspro", "moab", "condor", "nqsii", "ignite", "k8s", "awsbatch", "google-pipelines"] : "Unexpected value for executor" + } + + /* DIRECTIVE machineType + accepted examples: + - "n1-highmem-8" + */ + if (drctv.containsKey("machineType")) { + assert drctv["machineType"] instanceof CharSequence + } + + /* DIRECTIVE maxErrors + accepted examples: + - 1 + - 3 + */ + if (drctv.containsKey("maxErrors")) { + assert drctv["maxErrors"] instanceof Integer + } + + /* DIRECTIVE maxForks + accepted examples: + - 1 + - 3 + */ + if (drctv.containsKey("maxForks")) { + assert drctv["maxForks"] instanceof Integer + } + + /* DIRECTIVE maxRetries + accepted examples: + - 1 + - 3 + */ + if (drctv.containsKey("maxRetries")) { + assert drctv["maxRetries"] instanceof Integer + } + + /* DIRECTIVE memory + accepted examples: + - "1 GB" + - "2TB" + - "3.2KB" + - "10.B" + */ + if (drctv.containsKey("memory")) { + assert drctv["memory"] instanceof CharSequence + // assert drctv["memory"].matches("[0-9]+(\\.[0-9]*)? *[KMGTPEZY]?B") + // ^ does not allow closures + } + + /* DIRECTIVE module + accepted examples: + - "ncbi-blast/2.2.27" + - "ncbi-blast/2.2.27:t_coffee/10.0" + - ["ncbi-blast/2.2.27", "t_coffee/10.0"] + */ + if (drctv.containsKey("module")) { + if (drctv["module"] instanceof List) { + drctv["module"] = drctv["module"].join(":") + } + assert drctv["module"] instanceof CharSequence + } + + /* DIRECTIVE penv + accepted examples: + - "smp" + */ + if (drctv.containsKey("penv")) { + assert drctv["penv"] instanceof CharSequence + } + + /* DIRECTIVE pod + accepted examples: + - [ label: "key", value: "val" ] + - [ annotation: "key", value: "val" ] + - [ env: "key", value: "val" ] + - [ [label: "l", value: "v"], [env: "e", value: "v"]] + */ + if (drctv.containsKey("pod")) { + if (drctv["pod"] instanceof Map) { + drctv["pod"] = [ drctv["pod"] ] + } + assert drctv["pod"] instanceof List + drctv["pod"].forEach { pod -> + assert pod instanceof Map + // TODO: should more checks be added? + // See https://www.nextflow.io/docs/latest/process.html?highlight=directives#pod + // e.g. does it contain 'label' and 'value', or 'annotation' and 'value', or ...? + } + } + + /* DIRECTIVE publishDir + accepted examples: + - [] + - [ [ path: "foo", enabled: true ], [ path: "bar", enabled: false ] ] + - "/path/to/dir" + is transformed to [[ path: "/path/to/dir" ]] + - [ path: "/path/to/dir", mode: "cache" ] + is transformed to [[ path: "/path/to/dir", mode: "cache" ]] + */ + // TODO: should we also look at params["publishDir"]? + if (drctv.containsKey("publishDir")) { + def pblsh = drctv["publishDir"] + + // check different options + assert pblsh instanceof List || pblsh instanceof Map || pblsh instanceof CharSequence + + // turn into list if not already so + // for some reason, 'if (!pblsh instanceof List) pblsh = [ pblsh ]' doesn't work. + pblsh = pblsh instanceof List ? pblsh : [ pblsh ] + + // check elements of publishDir + pblsh = pblsh.collect{ elem -> + // turn into map if not already so + elem = elem instanceof CharSequence ? [ path: elem ] : elem + + // check types and keys + assert elem instanceof Map : "Expected publish argument '$elem' to be a String or a Map. Found: class ${elem.getClass()}" + assertMapKeys(elem, [ "path", "mode", "overwrite", "pattern", "saveAs", "enabled" ], ["path"], "publishDir") + + // check elements in map + assert elem.containsKey("path") + assert elem["path"] instanceof CharSequence + if (elem.containsKey("mode")) { + assert elem["mode"] instanceof CharSequence + assert elem["mode"] in [ "symlink", "rellink", "link", "copy", "copyNoFollow", "move" ] + } + if (elem.containsKey("overwrite")) { + assert elem["overwrite"] instanceof Boolean + } + if (elem.containsKey("pattern")) { + assert elem["pattern"] instanceof CharSequence + } + if (elem.containsKey("saveAs")) { + assert elem["saveAs"] instanceof CharSequence //: "saveAs as a Closure is currently not supported. Surround your closure with single quotes to get the desired effect. Example: '\{ foo \}'" + } + if (elem.containsKey("enabled")) { + assert elem["enabled"] instanceof Boolean + } + + // return final result + elem + } + // store final directive + drctv["publishDir"] = pblsh + } + + /* DIRECTIVE queue + accepted examples: + - "long" + - "short,long" + - ["short", "long"] + */ + if (drctv.containsKey("queue")) { + if (drctv["queue"] instanceof List) { + drctv["queue"] = drctv["queue"].join(",") + } + assert drctv["queue"] instanceof CharSequence + } + + /* DIRECTIVE label + accepted examples: + - "big_mem" + - "big_cpu" + - ["big_mem", "big_cpu"] + */ + if (drctv.containsKey("label")) { + if (drctv["label"] instanceof CharSequence) { + drctv["label"] = [ drctv["label"] ] + } + assert drctv["label"] instanceof List + drctv["label"].forEach { label -> + assert label instanceof CharSequence + // assert label.matches("[a-zA-Z0-9]([a-zA-Z0-9_]*[a-zA-Z0-9])?") + // ^ does not allow closures + } + } + + /* DIRECTIVE scratch + accepted examples: + - true + - "/path/to/scratch" + - '$MY_PATH_TO_SCRATCH' + - "ram-disk" + */ + if (drctv.containsKey("scratch")) { + assert drctv["scratch"] == true || drctv["scratch"] instanceof CharSequence + } + + /* DIRECTIVE storeDir + accepted examples: + - "/path/to/storeDir" + */ + if (drctv.containsKey("storeDir")) { + assert drctv["storeDir"] instanceof CharSequence + } + + /* DIRECTIVE stageInMode + accepted examples: + - "copy" + - "link" + */ + if (drctv.containsKey("stageInMode")) { + assert drctv["stageInMode"] instanceof CharSequence + assert drctv["stageInMode"] in ["copy", "link", "symlink", "rellink"] + } + + /* DIRECTIVE stageOutMode + accepted examples: + - "copy" + - "link" + */ + if (drctv.containsKey("stageOutMode")) { + assert drctv["stageOutMode"] instanceof CharSequence + assert drctv["stageOutMode"] in ["copy", "move", "rsync"] + } + + /* DIRECTIVE tag + accepted examples: + - "foo" + - '$id' + */ + if (drctv.containsKey("tag")) { + assert drctv["tag"] instanceof CharSequence + } + + /* DIRECTIVE time + accepted examples: + - "1h" + - "2days" + - "1day 6hours 3minutes 30seconds" + */ + if (drctv.containsKey("time")) { + assert drctv["time"] instanceof CharSequence + // todo: validation regex? + } + + return drctv +} + +// helper file: 'src/main/resources/io/viash/runners/nextflow/workflowFactory/processWorkflowArgs.nf' +def processWorkflowArgs(Map args, Map defaultWfArgs, Map meta) { + // override defaults with args + def workflowArgs = defaultWfArgs + args + + // check whether 'key' exists + assert workflowArgs.containsKey("key") : "Error in module '${meta.config.name}': key is a required argument" + + // if 'key' is a closure, apply it to the original key + if (workflowArgs["key"] instanceof Closure) { + workflowArgs["key"] = workflowArgs["key"](meta.config.name) + } + def key = workflowArgs["key"] + assert key instanceof CharSequence : "Expected process argument 'key' to be a String. Found: class ${key.getClass()}" + assert key ==~ /^[a-zA-Z_]\w*$/ : "Error in module '$key': Expected process argument 'key' to consist of only letters, digits or underscores. Found: ${key}" + + // check for any unexpected keys + def expectedKeys = ["key", "directives", "auto", "map", "mapId", "mapData", "mapPassthrough", "filter", "runIf", "fromState", "toState", "args", "renameKeys", "debug"] + def unexpectedKeys = workflowArgs.keySet() - expectedKeys + assert unexpectedKeys.isEmpty() : "Error in module '$key': unexpected arguments to the '.run()' function: '${unexpectedKeys.join("', '")}'" + + // check whether directives exists and apply defaults + assert workflowArgs.containsKey("directives") : "Error in module '$key': directives is a required argument" + assert workflowArgs["directives"] instanceof Map : "Error in module '$key': Expected process argument 'directives' to be a Map. Found: class ${workflowArgs['directives'].getClass()}" + workflowArgs["directives"] = processDirectives(defaultWfArgs.directives + workflowArgs["directives"]) + + // check whether directives exists and apply defaults + assert workflowArgs.containsKey("auto") : "Error in module '$key': auto is a required argument" + assert workflowArgs["auto"] instanceof Map : "Error in module '$key': Expected process argument 'auto' to be a Map. Found: class ${workflowArgs['auto'].getClass()}" + workflowArgs["auto"] = processAuto(defaultWfArgs.auto + workflowArgs["auto"]) + + // auto define publish, if so desired + if (workflowArgs.auto.publish == true && (workflowArgs.directives.publishDir != null ? workflowArgs.directives.publishDir : [:]).isEmpty()) { + // can't assert at this level thanks to the no_publish profile + // assert params.containsKey("publishDir") || params.containsKey("publish_dir") : + // "Error in module '${workflowArgs['key']}': if auto.publish is true, params.publish_dir needs to be defined.\n" + + // " Example: params.publish_dir = \"./output/\"" + def publishDir = getPublishDir() + + if (publishDir != null) { + workflowArgs.directives.publishDir = [[ + path: publishDir, + saveAs: "{ it.startsWith('.') ? null : it }", // don't publish hidden files, by default + mode: "copy" + ]] + } + } + + // auto define transcript, if so desired + if (workflowArgs.auto.transcript == true) { + // can't assert at this level thanks to the no_publish profile + // assert params.containsKey("transcriptsDir") || params.containsKey("transcripts_dir") || params.containsKey("publishDir") || params.containsKey("publish_dir") : + // "Error in module '${workflowArgs['key']}': if auto.transcript is true, either params.transcripts_dir or params.publish_dir needs to be defined.\n" + + // " Example: params.transcripts_dir = \"./transcripts/\"" + def transcriptsDir = + params.containsKey("transcripts_dir") ? params.transcripts_dir : + params.containsKey("transcriptsDir") ? params.transcriptsDir : + params.containsKey("publish_dir") ? params.publish_dir + "/_transcripts" : + params.containsKey("publishDir") ? params.publishDir + "/_transcripts" : + null + if (transcriptsDir != null) { + def timestamp = nextflow.Nextflow.getSession().getWorkflowMetadata().start.format('yyyy-MM-dd_HH-mm-ss') + def transcriptsPublishDir = [ + path: "$transcriptsDir/$timestamp/\${task.process.replaceAll(':', '-')}/\${id}/", + saveAs: "{ it.startsWith('.') ? it.replaceAll('^.', '') : null }", + mode: "copy" + ] + def publishDirs = workflowArgs.directives.publishDir != null ? workflowArgs.directives.publishDir : null ? workflowArgs.directives.publishDir : [] + workflowArgs.directives.publishDir = publishDirs + transcriptsPublishDir + } + } + + // if this is a stubrun, remove certain directives? + if (workflow.stubRun) { + workflowArgs.directives.keySet().removeAll(["publishDir", "cpus", "memory", "label"]) + } + + for (nam in ["map", "mapId", "mapData", "mapPassthrough", "filter", "runIf"]) { + if (workflowArgs.containsKey(nam) && workflowArgs[nam]) { + assert workflowArgs[nam] instanceof Closure : "Error in module '$key': Expected process argument '$nam' to be null or a Closure. Found: class ${workflowArgs[nam].getClass()}" + } + } + + // TODO: should functions like 'map', 'mapId', 'mapData', 'mapPassthrough' be deprecated as well? + for (nam in ["map", "mapData", "mapPassthrough", "renameKeys"]) { + if (workflowArgs.containsKey(nam) && workflowArgs[nam] != null) { + log.warn "module '$key': workflow argument '$nam' is deprecated and will be removed in Viash 0.9.0. Please use 'fromState' and 'toState' instead." + } + } + + // check fromState + workflowArgs["fromState"] = _processFromState(workflowArgs.get("fromState"), key, meta.config) + + // check toState + workflowArgs["toState"] = _processToState(workflowArgs.get("toState"), key, meta.config) + + // return output + return workflowArgs +} + +def _processFromState(fromState, key_, config_) { + assert fromState == null || fromState instanceof Closure || fromState instanceof Map || fromState instanceof List : + "Error in module '$key_': Expected process argument 'fromState' to be null, a Closure, a Map, or a List. Found: class ${fromState.getClass()}" + if (fromState == null) { + return null + } + + // if fromState is a List, convert to map + if (fromState instanceof List) { + // check whether fromstate is a list[string] + assert fromState.every{it instanceof CharSequence} : "Error in module '$key_': fromState is a List, but not all elements are Strings" + fromState = fromState.collectEntries{[it, it]} + } + + // if fromState is a map, convert to closure + if (fromState instanceof Map) { + // check whether fromstate is a map[string, string] + assert fromState.values().every{it instanceof CharSequence} : "Error in module '$key_': fromState is a Map, but not all values are Strings" + assert fromState.keySet().every{it instanceof CharSequence} : "Error in module '$key_': fromState is a Map, but not all keys are Strings" + def fromStateMap = fromState.clone() + def requiredInputNames = meta.config.allArguments.findAll{it.required && it.direction == "Input"}.collect{it.plainName} + // turn the map into a closure to be used later on + fromState = { it -> + def state = it[1] + assert state instanceof Map : "Error in module '$key_': the state is not a Map" + def data = fromStateMap.collectMany{newkey, origkey -> + // check whether newkey corresponds to a required argument + if (state.containsKey(origkey)) { + [[newkey, state[origkey]]] + } else if (!requiredInputNames.contains(origkey)) { + [] + } else { + throw new Exception("Error in module '$key_': fromState key '$origkey' not found in current state") + } + }.collectEntries() + data + } + } + + return fromState +} + +def _processToState(toState, key_, config_) { + if (toState == null) { + toState = { tup -> tup[1] } + } + + // toState should be a closure, map[string, string], or list[string] + assert toState instanceof Closure || toState instanceof Map || toState instanceof List : + "Error in module '$key_': Expected process argument 'toState' to be a Closure, a Map, or a List. Found: class ${toState.getClass()}" + + // if toState is a List, convert to map + if (toState instanceof List) { + // check whether toState is a list[string] + assert toState.every{it instanceof CharSequence} : "Error in module '$key_': toState is a List, but not all elements are Strings" + toState = toState.collectEntries{[it, it]} + } + + // if toState is a map, convert to closure + if (toState instanceof Map) { + // check whether toState is a map[string, string] + assert toState.values().every{it instanceof CharSequence} : "Error in module '$key_': toState is a Map, but not all values are Strings" + assert toState.keySet().every{it instanceof CharSequence} : "Error in module '$key_': toState is a Map, but not all keys are Strings" + def toStateMap = toState.clone() + def requiredOutputNames = config_.allArguments.findAll{it.required && it.direction == "Output"}.collect{it.plainName} + // turn the map into a closure to be used later on + toState = { it -> + def output = it[1] + def state = it[2] + assert output instanceof Map : "Error in module '$key_': the output is not a Map" + assert state instanceof Map : "Error in module '$key_': the state is not a Map" + def extraEntries = toStateMap.collectMany{newkey, origkey -> + // check whether newkey corresponds to a required argument + if (output.containsKey(origkey)) { + [[newkey, output[origkey]]] + } else if (!requiredOutputNames.contains(origkey)) { + [] + } else { + throw new Exception("Error in module '$key_': toState key '$origkey' not found in current output") + } + }.collectEntries() + state + extraEntries + } + } + + return toState +} + +// helper file: 'src/main/resources/io/viash/runners/nextflow/workflowFactory/workflowFactory.nf' +def _debug(workflowArgs, debugKey) { + if (workflowArgs.debug) { + view { "process '${workflowArgs.key}' $debugKey tuple: $it" } + } else { + map { it } + } +} + +// depends on: innerWorkflowFactory +def workflowFactory(Map args, Map defaultWfArgs, Map meta) { + def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta) + def key_ = workflowArgs["key"] + + workflow workflowInstance { + take: input_ + + main: + def chModified = input_ + | checkUniqueIds([:]) + | _debug(workflowArgs, "input") + | map { tuple -> + tuple = deepClone(tuple) + + if (workflowArgs.map) { + tuple = workflowArgs.map(tuple) + } + if (workflowArgs.mapId) { + tuple[0] = workflowArgs.mapId(tuple[0]) + } + if (workflowArgs.mapData) { + tuple[1] = workflowArgs.mapData(tuple[1]) + } + if (workflowArgs.mapPassthrough) { + tuple = tuple.take(2) + workflowArgs.mapPassthrough(tuple.drop(2)) + } + + // check tuple + assert tuple instanceof List : + "Error in module '${key_}': element in channel should be a tuple [id, data, ...otherargs...]\n" + + " Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" + + " Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}" + assert tuple.size() >= 2 : + "Error in module '${key_}': expected length of tuple in input channel to be two or greater.\n" + + " Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" + + " Found: tuple.size() == ${tuple.size()}" + + // check id field + if (tuple[0] instanceof GString) { + tuple[0] = tuple[0].toString() + } + assert tuple[0] instanceof CharSequence : + "Error in module '${key_}': first element of tuple in channel should be a String\n" + + " Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" + + " Found: ${tuple[0]}" + + // match file to input file + if (workflowArgs.auto.simplifyInput && (tuple[1] instanceof Path || tuple[1] instanceof List)) { + def inputFiles = meta.config.allArguments + .findAll { it.type == "file" && it.direction == "input" } + + assert inputFiles.size() == 1 : + "Error in module '${key_}' id '${tuple[0]}'.\n" + + " Anonymous file inputs are only allowed when the process has exactly one file input.\n" + + " Expected: inputFiles.size() == 1. Found: inputFiles.size() is ${inputFiles.size()}" + + tuple[1] = [[ inputFiles[0].plainName, tuple[1] ]].collectEntries() + } + + // check data field + assert tuple[1] instanceof Map : + "Error in module '${key_}' id '${tuple[0]}': second element of tuple in channel should be a Map\n" + + " Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" + + " Expected class: Map. Found: tuple[1].getClass() is ${tuple[1].getClass()}" + + // rename keys of data field in tuple + if (workflowArgs.renameKeys) { + assert workflowArgs.renameKeys instanceof Map : + "Error renaming data keys in module '${key_}' id '${tuple[0]}'.\n" + + " Example: renameKeys: ['new_key': 'old_key'].\n" + + " Expected class: Map. Found: renameKeys.getClass() is ${workflowArgs.renameKeys.getClass()}" + assert tuple[1] instanceof Map : + "Error renaming data keys in module '${key_}' id '${tuple[0]}'.\n" + + " Expected class: Map. Found: tuple[1].getClass() is ${tuple[1].getClass()}" + + // TODO: allow renameKeys to be a function? + workflowArgs.renameKeys.each { newKey, oldKey -> + assert newKey instanceof CharSequence : + "Error renaming data keys in module '${key_}' id '${tuple[0]}'.\n" + + " Example: renameKeys: ['new_key': 'old_key'].\n" + + " Expected class of newKey: String. Found: newKey.getClass() is ${newKey.getClass()}" + assert oldKey instanceof CharSequence : + "Error renaming data keys in module '${key_}' id '${tuple[0]}'.\n" + + " Example: renameKeys: ['new_key': 'old_key'].\n" + + " Expected class of oldKey: String. Found: oldKey.getClass() is ${oldKey.getClass()}" + assert tuple[1].containsKey(oldKey) : + "Error renaming data keys in module '${key}' id '${tuple[0]}'.\n" + + " Key '$oldKey' is missing in the data map. tuple[1].keySet() is '${tuple[1].keySet()}'" + tuple[1].put(newKey, tuple[1][oldKey]) + } + tuple[1].keySet().removeAll(workflowArgs.renameKeys.collect{ newKey, oldKey -> oldKey }) + } + tuple + } + + + def chRun = null + def chPassthrough = null + if (workflowArgs.runIf) { + def runIfBranch = chModified.branch{ tup -> + run: workflowArgs.runIf(tup[0], tup[1]) + passthrough: true + } + chRun = runIfBranch.run + chPassthrough = runIfBranch.passthrough + } else { + chRun = chModified + chPassthrough = Channel.empty() + } + + def chRunFiltered = workflowArgs.filter ? + chRun | filter{workflowArgs.filter(it)} : + chRun + + def chArgs = workflowArgs.fromState ? + chRunFiltered | map{ + def new_data = workflowArgs.fromState(it.take(2)) + [it[0], new_data] + } : + chRunFiltered | map {tup -> tup.take(2)} + + // fill in defaults + def chArgsWithDefaults = chArgs + | map { tuple -> + def id_ = tuple[0] + def data_ = tuple[1] + + // TODO: could move fromState to here + + // fetch default params from functionality + def defaultArgs = meta.config.allArguments + .findAll { it.containsKey("default") } + .collectEntries { [ it.plainName, it.default ] } + + // fetch overrides in params + def paramArgs = meta.config.allArguments + .findAll { par -> + def argKey = key_ + "__" + par.plainName + params.containsKey(argKey) + } + .collectEntries { [ it.plainName, params[key_ + "__" + it.plainName] ] } + + // fetch overrides in data + def dataArgs = meta.config.allArguments + .findAll { data_.containsKey(it.plainName) } + .collectEntries { [ it.plainName, data_[it.plainName] ] } + + // combine params + def combinedArgs = defaultArgs + paramArgs + workflowArgs.args + dataArgs + + // remove arguments with explicit null values + combinedArgs + .removeAll{_, val -> val == null || val == "viash_no_value" || val == "force_null"} + + combinedArgs = _processInputValues(combinedArgs, meta.config, id_, key_) + + [id_, combinedArgs] + tuple.drop(2) + } + + // TODO: move some of the _meta.join_id wrangling to the safeJoin() function. + def chInitialOutput = chArgsWithDefaults + | _debug(workflowArgs, "processed") + // run workflow + | innerWorkflowFactory(workflowArgs) + // check output tuple + | map { id_, output_ -> + + // see if output map contains metadata + def meta_ = + output_ instanceof Map && output_.containsKey("_meta") ? + output_["_meta"] : + [:] + def join_id = meta_.join_id ?: id_ + + // remove metadata + output_ = output_.findAll{k, v -> k != "_meta"} + + // check value types + output_ = _processOutputValues(output_, meta.config, id_, key_) + + // simplify output if need be + if (workflowArgs.auto.simplifyOutput && output_.size() == 1) { + output_ = output_.values()[0] + } + + [join_id, id_, output_] + } + // | view{"chInitialOutput: ${it.take(3)}"} + + // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...] + def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_) + // input tuple format: [join_id, id, output, prev_state, ...] + // output tuple format: [join_id, id, new_state, ...] + | map{ tup -> + def new_state = workflowArgs.toState(tup.drop(1).take(3)) + tup.take(2) + [new_state] + tup.drop(4) + } + + if (workflowArgs.auto.publish == "state") { + def chPublish = chNewState + // input tuple format: [join_id, id, new_state, ...] + // output tuple format: [join_id, id, new_state] + | map{ tup -> + tup.take(3) + } + + safeJoin(chPublish, chArgsWithDefaults, key_) + // input tuple format: [join_id, id, new_state, orig_state, ...] + // output tuple format: [id, new_state, orig_state] + | map { tup -> + tup.drop(1).take(3) + } + | publishStatesByConfig(key: key_, config: meta.config) + } + + // remove join_id and meta + chReturn = chNewState + | map { tup -> + // input tuple format: [join_id, id, new_state, ...] + // output tuple format: [id, new_state, ...] + tup.drop(1) + } + | _debug(workflowArgs, "output") + | concat(chPassthrough) + + emit: chReturn + } + + def wf = workflowInstance.cloneWithName(key_) + + // add factory function + wf.metaClass.run = { runArgs -> + workflowFactory(runArgs, workflowArgs, meta) + } + // add config to module for later introspection + wf.metaClass.config = meta.config + + return wf +} + +nextflow.enable.dsl=2 + +// START COMPONENT-SPECIFIC CODE + +// create meta object +meta = [ + "resources_dir": moduleDir.toRealPath().normalize(), + "config": processConfig(readJsonBlob('''{ + "name" : "bbmap_bbsplit", + "namespace" : "bbmap", + "version" : "main", + "argument_groups" : [ + { + "name" : "Input", + "arguments" : [ + { + "type" : "string", + "name" : "--id", + "description" : "Sample ID", + "required" : false, + "direction" : "input", + "multiple" : false, + "multiple_sep" : ";" + }, + { + "type" : "boolean_true", + "name" : "--paired", + "description" : "Paired fastq files or not?", + "direction" : "input" + }, + { + "type" : "file", + "name" : "--input", + "description" : "Input fastq files, either one or two (paired), separated by \\";\\".", + "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.", + "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.", + "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", + "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", + "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", + "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", + "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", + "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", + "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", + "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;\nAmbiguous2 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", + "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", + "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.", + "direction" : "input" + } + ] + }, + { + "name" : "Output", + "arguments" : [ + { + "type" : "file", + "name" : "--fastq_1", + "description" : "Output file for read 1.\n", + "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", + "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", + "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", + "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", + "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.", + "direction" : "input" + }, + { + "type" : "string", + "name" : "--bbmap_args", + "description" : "Additional arguments from BBMap to pass to BBSplit.\n", + "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 + } + ], + "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:\\", $NF}' > /var/software_versions.txt\n" + ] + } + ] + }, + { + "type" : "native", + "id" : "native" + } + ], + "build_info" : { + "config" : "/workdir/root/repo/src/bbmap_bbsplit/config.vsh.yaml", + "runner" : "nextflow", + "engine" : "docker|native", + "output" : "target/nextflow/bbmap/bbmap_bbsplit", + "viash_version" : "0.9.0", + "git_commit" : "7fb67a98539868b9af788338fb5f46d34ab742f7", + "git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-11-g7fb67a9" + }, + "package_config" : { + "name" : "biobox", + "version" : "main", + "description" : "A collection of bioinformatics tools for working with sequence data.\n", + "viash_version" : "0.9.0", + "source" : "src", + "target" : "target", + "config_mods" : [ + ".requirements.commands := ['ps']\n", + ".engines += { type: \\"native\\" }", + ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", + ".engines[.type == 'docker'].target_tag := 'main'" + ], + "keywords" : [ + "bioinformatics", + "modules", + "sequencing" + ], + "license" : "MIT", + "organization" : "vsh", + "links" : { + "repository" : "https://github.com/viash-hub/biobox", + "issue_tracker" : "https://github.com/viash-hub/biobox/issues" + } + } +}''')) +] + +// resolve dependencies dependencies (if any) + + +// inner workflow +// inner workflow hook +def innerWorkflowFactory(args) { + def rawScript = '''set -e +tempscript=".viash_script.sh" +cat > "$tempscript" << VIASHMAIN +#!/bin/bash + +## VIASH START +# The following code has been auto-generated by Viash. +$( if [ ! -z ${VIASH_PAR_ID+x} ]; then echo "${VIASH_PAR_ID}" | sed "s#'#'\\"'\\"'#g;s#.*#par_id='&'#" ; else echo "# par_id="; fi ) +$( if [ ! -z ${VIASH_PAR_PAIRED+x} ]; then echo "${VIASH_PAR_PAIRED}" | sed "s#'#'\\"'\\"'#g;s#.*#par_paired='&'#" ; else echo "# par_paired="; fi ) +$( if [ ! -z ${VIASH_PAR_INPUT+x} ]; then echo "${VIASH_PAR_INPUT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_input='&'#" ; else echo "# par_input="; fi ) +$( if [ ! -z ${VIASH_PAR_REF+x} ]; then echo "${VIASH_PAR_REF}" | sed "s#'#'\\"'\\"'#g;s#.*#par_ref='&'#" ; else echo "# par_ref="; fi ) +$( if [ ! -z ${VIASH_PAR_ONLY_BUILD_INDEX+x} ]; then echo "${VIASH_PAR_ONLY_BUILD_INDEX}" | sed "s#'#'\\"'\\"'#g;s#.*#par_only_build_index='&'#" ; else echo "# par_only_build_index="; fi ) +$( if [ ! -z ${VIASH_PAR_BUILD+x} ]; then echo "${VIASH_PAR_BUILD}" | sed "s#'#'\\"'\\"'#g;s#.*#par_build='&'#" ; else echo "# par_build="; fi ) +$( if [ ! -z ${VIASH_PAR_QIN+x} ]; then echo "${VIASH_PAR_QIN}" | sed "s#'#'\\"'\\"'#g;s#.*#par_qin='&'#" ; else echo "# par_qin="; fi ) +$( if [ ! -z ${VIASH_PAR_INTERLEAVED+x} ]; then echo "${VIASH_PAR_INTERLEAVED}" | sed "s#'#'\\"'\\"'#g;s#.*#par_interleaved='&'#" ; else echo "# par_interleaved="; fi ) +$( if [ ! -z ${VIASH_PAR_MAXINDEL+x} ]; then echo "${VIASH_PAR_MAXINDEL}" | sed "s#'#'\\"'\\"'#g;s#.*#par_maxindel='&'#" ; else echo "# par_maxindel="; fi ) +$( if [ ! -z ${VIASH_PAR_MINRATIO+x} ]; then echo "${VIASH_PAR_MINRATIO}" | sed "s#'#'\\"'\\"'#g;s#.*#par_minratio='&'#" ; else echo "# par_minratio="; fi ) +$( if [ ! -z ${VIASH_PAR_MINHITS+x} ]; then echo "${VIASH_PAR_MINHITS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_minhits='&'#" ; else echo "# par_minhits="; fi ) +$( if [ ! -z ${VIASH_PAR_AMBIGUOUS+x} ]; then echo "${VIASH_PAR_AMBIGUOUS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_ambiguous='&'#" ; else echo "# par_ambiguous="; fi ) +$( if [ ! -z ${VIASH_PAR_AMBIGUOUS2+x} ]; then echo "${VIASH_PAR_AMBIGUOUS2}" | sed "s#'#'\\"'\\"'#g;s#.*#par_ambiguous2='&'#" ; else echo "# par_ambiguous2="; fi ) +$( if [ ! -z ${VIASH_PAR_QTRIM+x} ]; then echo "${VIASH_PAR_QTRIM}" | sed "s#'#'\\"'\\"'#g;s#.*#par_qtrim='&'#" ; else echo "# par_qtrim="; fi ) +$( if [ ! -z ${VIASH_PAR_UNTRIM+x} ]; then echo "${VIASH_PAR_UNTRIM}" | sed "s#'#'\\"'\\"'#g;s#.*#par_untrim='&'#" ; else echo "# par_untrim="; fi ) +$( if [ ! -z ${VIASH_PAR_FASTQ_1+x} ]; then echo "${VIASH_PAR_FASTQ_1}" | sed "s#'#'\\"'\\"'#g;s#.*#par_fastq_1='&'#" ; else echo "# par_fastq_1="; fi ) +$( if [ ! -z ${VIASH_PAR_FASTQ_2+x} ]; then echo "${VIASH_PAR_FASTQ_2}" | sed "s#'#'\\"'\\"'#g;s#.*#par_fastq_2='&'#" ; else echo "# par_fastq_2="; fi ) +$( if [ ! -z ${VIASH_PAR_SAM2BAM+x} ]; then echo "${VIASH_PAR_SAM2BAM}" | sed "s#'#'\\"'\\"'#g;s#.*#par_sam2bam='&'#" ; else echo "# par_sam2bam="; fi ) +$( if [ ! -z ${VIASH_PAR_SCAFSTATS+x} ]; then echo "${VIASH_PAR_SCAFSTATS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_scafstats='&'#" ; else echo "# par_scafstats="; fi ) +$( if [ ! -z ${VIASH_PAR_REFSTATS+x} ]; then echo "${VIASH_PAR_REFSTATS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_refstats='&'#" ; else echo "# par_refstats="; fi ) +$( if [ ! -z ${VIASH_PAR_NZO+x} ]; then echo "${VIASH_PAR_NZO}" | sed "s#'#'\\"'\\"'#g;s#.*#par_nzo='&'#" ; else echo "# par_nzo="; fi ) +$( if [ ! -z ${VIASH_PAR_BBMAP_ARGS+x} ]; then echo "${VIASH_PAR_BBMAP_ARGS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_bbmap_args='&'#" ; else echo "# par_bbmap_args="; fi ) +$( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "${VIASH_META_NAME}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_name='&'#" ; else echo "# meta_name="; fi ) +$( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "${VIASH_META_FUNCTIONALITY_NAME}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_functionality_name='&'#" ; else echo "# meta_functionality_name="; fi ) +$( if [ ! -z ${VIASH_META_RESOURCES_DIR+x} ]; then echo "${VIASH_META_RESOURCES_DIR}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_resources_dir='&'#" ; else echo "# meta_resources_dir="; fi ) +$( if [ ! -z ${VIASH_META_EXECUTABLE+x} ]; then echo "${VIASH_META_EXECUTABLE}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_executable='&'#" ; else echo "# meta_executable="; fi ) +$( if [ ! -z ${VIASH_META_CONFIG+x} ]; then echo "${VIASH_META_CONFIG}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_config='&'#" ; else echo "# meta_config="; fi ) +$( if [ ! -z ${VIASH_META_TEMP_DIR+x} ]; then echo "${VIASH_META_TEMP_DIR}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_temp_dir='&'#" ; else echo "# meta_temp_dir="; fi ) +$( if [ ! -z ${VIASH_META_CPUS+x} ]; then echo "${VIASH_META_CPUS}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_cpus='&'#" ; else echo "# meta_cpus="; fi ) +$( if [ ! -z ${VIASH_META_MEMORY_B+x} ]; then echo "${VIASH_META_MEMORY_B}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_memory_b='&'#" ; else echo "# meta_memory_b="; fi ) +$( if [ ! -z ${VIASH_META_MEMORY_KB+x} ]; then echo "${VIASH_META_MEMORY_KB}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_memory_kb='&'#" ; else echo "# meta_memory_kb="; fi ) +$( if [ ! -z ${VIASH_META_MEMORY_MB+x} ]; then echo "${VIASH_META_MEMORY_MB}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_memory_mb='&'#" ; else echo "# meta_memory_mb="; fi ) +$( if [ ! -z ${VIASH_META_MEMORY_GB+x} ]; then echo "${VIASH_META_MEMORY_GB}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_memory_gb='&'#" ; else echo "# meta_memory_gb="; fi ) +$( if [ ! -z ${VIASH_META_MEMORY_TB+x} ]; then echo "${VIASH_META_MEMORY_TB}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_memory_tb='&'#" ; else echo "# meta_memory_tb="; fi ) +$( if [ ! -z ${VIASH_META_MEMORY_PB+x} ]; then echo "${VIASH_META_MEMORY_PB}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_memory_pb='&'#" ; else echo "# meta_memory_pb="; fi ) +$( if [ ! -z ${VIASH_META_MEMORY_KIB+x} ]; then echo "${VIASH_META_MEMORY_KIB}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_memory_kib='&'#" ; else echo "# meta_memory_kib="; fi ) +$( if [ ! -z ${VIASH_META_MEMORY_MIB+x} ]; then echo "${VIASH_META_MEMORY_MIB}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_memory_mib='&'#" ; else echo "# meta_memory_mib="; fi ) +$( if [ ! -z ${VIASH_META_MEMORY_GIB+x} ]; then echo "${VIASH_META_MEMORY_GIB}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_memory_gib='&'#" ; else echo "# meta_memory_gib="; fi ) +$( if [ ! -z ${VIASH_META_MEMORY_TIB+x} ]; then echo "${VIASH_META_MEMORY_TIB}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_memory_tib='&'#" ; else echo "# meta_memory_tib="; fi ) +$( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_memory_pib='&'#" ; else echo "# meta_memory_pib="; fi ) + +## VIASH END + +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 +VIASHMAIN +bash "$tempscript" +''' + + return vdsl3WorkflowFactory(args, meta, rawScript) +} + + + +/** + * Generate a workflow for VDSL3 modules. + * + * This function is called by the workflowFactory() function. + * + * Input channel: [id, input_map] + * Output channel: [id, output_map] + * + * Internally, this workflow will convert the input channel + * to a format which the Nextflow module will be able to handle. + */ +def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { + def key = args["key"] + def processObj = null + + workflow processWf { + take: input_ + main: + + if (processObj == null) { + processObj = _vdsl3ProcessFactory(args, meta, rawScript) + } + + output_ = input_ + | map { tuple -> + def id = tuple[0] + def data_ = tuple[1] + + if (workflow.stubRun) { + // add id if missing + data_ = [id: 'stub'] + data_ + } + + // process input files separately + def inputPaths = meta.config.allArguments + .findAll { it.type == "file" && it.direction == "input" } + .collect { par -> + def val = data_.containsKey(par.plainName) ? data_[par.plainName] : [] + def inputFiles = [] + if (val == null) { + inputFiles = [] + } else if (val instanceof List) { + inputFiles = val + } else if (val instanceof Path) { + inputFiles = [ val ] + } else { + inputFiles = [] + } + if (!workflow.stubRun) { + // throw error when an input file doesn't exist + inputFiles.each{ file -> + assert file.exists() : + "Error in module '${key}' id '${id}' argument '${par.plainName}'.\n" + + " Required input file does not exist.\n" + + " Path: '$file'.\n" + + " Expected input file to exist" + } + } + inputFiles + } + + // remove input files + def argsExclInputFiles = meta.config.allArguments + .findAll { (it.type != "file" || it.direction != "input") && data_.containsKey(it.plainName) } + .collectEntries { par -> + def parName = par.plainName + def val = data_[parName] + if (par.multiple && val instanceof Collection) { + val = val.join(par.multiple_sep) + } + if (par.direction == "output" && par.type == "file") { + val = val + .replaceAll('\\$id', id) + .replaceAll('\\$\\{id\\}', id) + .replaceAll('\\$key', key) + .replaceAll('\\$\\{key\\}', key) + } + [parName, val] + } + + [ id ] + inputPaths + [ argsExclInputFiles, meta.resources_dir ] + } + | processObj + | map { output -> + def outputFiles = meta.config.allArguments + .findAll { it.type == "file" && it.direction == "output" } + .indexed() + .collectEntries{ index, par -> + def out = output[index + 1] + // strip dummy '.exitcode' file from output (see nextflow-io/nextflow#2678) + if (!out instanceof List || out.size() <= 1) { + if (par.multiple) { + out = [] + } else { + assert !par.required : + "Error in module '${key}' id '${output[0]}' argument '${par.plainName}'.\n" + + " Required output file is missing" + out = null + } + } else if (out.size() == 2 && !par.multiple) { + out = out[1] + } else { + out = out.drop(1) + } + [ par.plainName, out ] + } + + // drop null outputs + outputFiles.removeAll{it.value == null} + + [ output[0], outputFiles ] + } + emit: output_ + } + + return processWf +} + +// depends on: session? +def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { + // autodetect process key + def wfKey = workflowArgs["key"] + def procKeyPrefix = "${wfKey}_process" + def scriptMeta = nextflow.script.ScriptMeta.current() + def existing = scriptMeta.getProcessNames().findAll{it.startsWith(procKeyPrefix)} + def numbers = existing.collect{it.replace(procKeyPrefix, "0").toInteger()} + def newNumber = (numbers + [-1]).max() + 1 + + def procKey = newNumber == 0 ? procKeyPrefix : "$procKeyPrefix$newNumber" + + if (newNumber > 0) { + log.warn "Key for module '${wfKey}' is duplicated.\n", + "If you run a component multiple times in the same workflow,\n" + + "it's recommended you set a unique key for every call,\n" + + "for example: ${wfKey}.run(key: \"foo\")." + } + + // subset directives and convert to list of tuples + def drctv = workflowArgs.directives + + // TODO: unit test the two commands below + // convert publish array into tags + def valueToStr = { val -> + // ignore closures + if (val instanceof CharSequence) { + if (!val.matches('^[{].*[}]$')) { + '"' + val + '"' + } else { + val + } + } else if (val instanceof List) { + "[" + val.collect{valueToStr(it)}.join(", ") + "]" + } else if (val instanceof Map) { + "[" + val.collect{k, v -> k + ": " + valueToStr(v)}.join(", ") + "]" + } else { + val.inspect() + } + } + + // multiple entries allowed: label, publishdir + def drctvStrs = drctv.collect { key, value -> + if (key in ["label", "publishDir"]) { + value.collect{ val -> + if (val instanceof Map) { + "\n$key " + val.collect{ k, v -> k + ": " + valueToStr(v) }.join(", ") + } else if (val == null) { + "" + } else { + "\n$key " + valueToStr(val) + } + }.join() + } else if (value instanceof Map) { + "\n$key " + value.collect{ k, v -> k + ": " + valueToStr(v) }.join(", ") + } else { + "\n$key " + valueToStr(value) + } + }.join() + + def inputPaths = meta.config.allArguments + .findAll { it.type == "file" && it.direction == "input" } + .collect { ', path(viash_par_' + it.plainName + ', stageAs: "_viash_par/' + it.plainName + '_?/*")' } + .join() + + def outputPaths = meta.config.allArguments + .findAll { it.type == "file" && it.direction == "output" } + .collect { par -> + // insert dummy into every output (see nextflow-io/nextflow#2678) + if (!par.multiple) { + ', path{[".exitcode", args.' + par.plainName + ']}' + } else { + ', path{[".exitcode"] + args.' + par.plainName + '}' + } + } + .join() + + // TODO: move this functionality somewhere else? + if (workflowArgs.auto.transcript) { + outputPaths = outputPaths + ', path{[".exitcode", ".command*"]}' + } else { + outputPaths = outputPaths + ', path{[".exitcode"]}' + } + + // create dirs for output files (based on BashWrapper.createParentFiles) + def createParentStr = meta.config.allArguments + .findAll { it.type == "file" && it.direction == "output" && it.create_parent } + .collect { par -> + def contents = "args[\"${par.plainName}\"] instanceof List ? args[\"${par.plainName}\"].join('\" \"') : args[\"${par.plainName}\"]" + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent '\" + escapeText(${contents}) + \"'\" : \"\" }" + } + .join("\n") + + // construct inputFileExports + def inputFileExports = meta.config.allArguments + .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } + .collect { par -> + def contents = "viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName}" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}='\" + escapeText(${contents}) + \"'\"}" + } + + // NOTE: if using docker, use /tmp instead of tmpDir! + def tmpDir = java.nio.file.Paths.get( + System.getenv('NXF_TEMP') ?: + System.getenv('VIASH_TEMP') ?: + System.getenv('VIASH_TMPDIR') ?: + System.getenv('VIASH_TEMPDIR') ?: + System.getenv('VIASH_TMP') ?: + System.getenv('TEMP') ?: + System.getenv('TMPDIR') ?: + System.getenv('TEMPDIR') ?: + System.getenv('TMP') ?: + '/tmp' + ).toAbsolutePath() + + // construct stub + def stub = meta.config.allArguments + .findAll { it.type == "file" && it.direction == "output" } + .collect { par -> + "\${ args.containsKey(\"${par.plainName}\") ? \"touch2 \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"].replace(\"_*\", \"_0\") : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + } + .join("\n") + + // escape script + def escapedScript = rawScript.replace('\\', '\\\\').replace('$', '\\$').replace('"""', '\\"\\"\\"') + + // publishdir assert + def assertStr = (workflowArgs.auto.publish == true) || workflowArgs.auto.transcript ? + """\nassert task.publishDir.size() > 0: "if auto.publish is true, params.publish_dir needs to be defined.\\n Example: --publish_dir './output/'" """ : + "" + + // generate process string + def procStr = + """nextflow.enable.dsl=2 + | + |def escapeText = { s -> s.toString().replaceAll("'", "'\\\"'\\\"'") } + |process $procKey {$drctvStrs + |input: + | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") + |output: + | tuple val("\$id")$outputPaths, optional: true + |stub: + |\"\"\" + |touch2() { mkdir -p "\\\$(dirname "\\\$1")" && touch "\\\$1" ; } + |$stub + |\"\"\" + |script:$assertStr + |def parInject = args + | .findAll{key, value -> value != null} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}='\${escapeText(value)}'"} + | .join("\\n") + |\"\"\" + |# meta exports + |export VIASH_META_RESOURCES_DIR="\${resourcesDir}" + |export VIASH_META_TEMP_DIR="${['docker', 'podman', 'charliecloud'].any{ it == workflow.containerEngine } ? '/tmp' : tmpDir}" + |export VIASH_META_NAME="${meta.config.name}" + |# export VIASH_META_EXECUTABLE="\\\$VIASH_META_RESOURCES_DIR/\\\$VIASH_META_NAME" + |export VIASH_META_CONFIG="\\\$VIASH_META_RESOURCES_DIR/.config.vsh.yaml" + |\${task.cpus ? "export VIASH_META_CPUS=\$task.cpus" : "" } + |\${task.memory?.bytes != null ? "export VIASH_META_MEMORY_B=\$task.memory.bytes" : "" } + |if [ ! -z \\\${VIASH_META_MEMORY_B+x} ]; then + | export VIASH_META_MEMORY_KB=\\\$(( (\\\$VIASH_META_MEMORY_B+999) / 1000 )) + | export VIASH_META_MEMORY_MB=\\\$(( (\\\$VIASH_META_MEMORY_KB+999) / 1000 )) + | export VIASH_META_MEMORY_GB=\\\$(( (\\\$VIASH_META_MEMORY_MB+999) / 1000 )) + | export VIASH_META_MEMORY_TB=\\\$(( (\\\$VIASH_META_MEMORY_GB+999) / 1000 )) + | export VIASH_META_MEMORY_PB=\\\$(( (\\\$VIASH_META_MEMORY_TB+999) / 1000 )) + | export VIASH_META_MEMORY_KIB=\\\$(( (\\\$VIASH_META_MEMORY_B+1023) / 1024 )) + | export VIASH_META_MEMORY_MIB=\\\$(( (\\\$VIASH_META_MEMORY_KIB+1023) / 1024 )) + | export VIASH_META_MEMORY_GIB=\\\$(( (\\\$VIASH_META_MEMORY_MIB+1023) / 1024 )) + | export VIASH_META_MEMORY_TIB=\\\$(( (\\\$VIASH_META_MEMORY_GIB+1023) / 1024 )) + | export VIASH_META_MEMORY_PIB=\\\$(( (\\\$VIASH_META_MEMORY_TIB+1023) / 1024 )) + |fi + | + |# meta synonyms + |export VIASH_TEMP="\\\$VIASH_META_TEMP_DIR" + |export TEMP_DIR="\\\$VIASH_META_TEMP_DIR" + | + |# create output dirs if need be + |function mkdir_parent { + | for file in "\\\$@"; do + | mkdir -p "\\\$(dirname "\\\$file")" + | done + |} + |$createParentStr + | + |# argument exports${inputFileExports.join()} + |\$parInject + | + |# process script + |${escapedScript} + |\"\"\" + |} + |""".stripMargin() + + // TODO: print on debug + // if (workflowArgs.debug == true) { + // println("######################\n$procStr\n######################") + // } + + // write process to temp file + def tempFile = java.nio.file.Files.createTempFile("viash-process-${procKey}-", ".nf") + addShutdownHook { java.nio.file.Files.deleteIfExists(tempFile) } + tempFile.text = procStr + + // create process from temp file + def binding = new nextflow.script.ScriptBinding([:]) + def session = nextflow.Nextflow.getSession() + def parser = new nextflow.script.ScriptParser(session) + .setModule(true) + .setBinding(binding) + def moduleScript = parser.runScript(tempFile) + .getScript() + + // register module in meta + def module = new nextflow.script.IncludeDef.Module(name: procKey) + scriptMeta.addModule(moduleScript, module.name, module.alias) + + // retrieve and return process from meta + return scriptMeta.getProcess(procKey) +} + +// defaults +meta["defaults"] = [ + // key to be used to trace the process and determine output names + key: null, + + // fixed arguments to be passed to script + args: [:], + + // default directives + directives: readJsonBlob('''{ + "container" : { + "registry" : "images.viash-hub.com", + "image" : "vsh/biobox/bbmap/bbmap_bbsplit", + "tag" : "main" + }, + "tag" : "$id" +}'''), + + // auto settings + auto: readJsonBlob('''{ + "simplifyInput" : true, + "simplifyOutput" : false, + "transcript" : false, + "publish" : false +}'''), + + // Apply a map over the incoming tuple + // Example: `{ tup -> [ tup[0], [input: tup[1].output] ] + tup.drop(2) }` + map: null, + + // Apply a map over the ID element of a tuple (i.e. the first element) + // Example: `{ id -> id + "_foo" }` + mapId: null, + + // Apply a map over the data element of a tuple (i.e. the second element) + // Example: `{ data -> [ input: data.output ] }` + mapData: null, + + // Apply a map over the passthrough elements of a tuple (i.e. the tuple excl. the first two elements) + // Example: `{ pt -> pt.drop(1) }` + mapPassthrough: null, + + // Filter the channel + // Example: `{ tup -> tup[0] == "foo" }` + filter: null, + + // Choose whether or not to run the component on the tuple if the condition is true. + // Otherwise, the tuple will be passed through. + // Example: `{ tup -> tup[0] != "skip_this" }` + runIf: null, + + // Rename keys in the data field of the tuple (i.e. the second element) + // Will likely be deprecated in favour of `fromState`. + // Example: `[ "new_key": "old_key" ]` + renameKeys: null, + + // Fetch data from the state and pass it to the module without altering the current state. + // + // `fromState` should be `null`, `List[String]`, `Map[String, String]` or a function. + // + // - If it is `null`, the state will be passed to the module as is. + // - If it is a `List[String]`, the data will be the values of the state at the given keys. + // - If it is a `Map[String, String]`, the data will be the values of the state at the given keys, with the keys renamed according to the map. + // - If it is a function, the tuple (`[id, state]`) in the channel will be passed to the function, and the result will be used as the data. + // + // Example: `{ id, state -> [input: state.fastq_file] }` + // Default: `null` + fromState: null, + + // Determine how the state should be updated after the module has been run. + // + // `toState` should be `null`, `List[String]`, `Map[String, String]` or a function. + // + // - If it is `null`, the state will be replaced with the output of the module. + // - If it is a `List[String]`, the state will be updated with the values of the data at the given keys. + // - If it is a `Map[String, String]`, the state will be updated with the values of the data at the given keys, with the keys renamed according to the map. + // - If it is a function, a tuple (`[id, output, state]`) will be passed to the function, and the result will be used as the new state. + // + // Example: `{ id, output, state -> state + [counts: state.output] }` + // Default: `{ id, output, state -> output }` + toState: null, + + // Whether or not to print debug messages + // Default: `false` + debug: false +] + +// initialise default workflow +meta["workflow"] = workflowFactory([key: meta.config.name], meta.defaults, meta) + +// add workflow to environment +nextflow.script.ScriptMeta.current().addDefinition(meta.workflow) + +// anonymous workflow for running this module as a standalone +workflow { + // add id argument if it's not already in the config + // TODO: deep copy + def newConfig = deepClone(meta.config) + def newParams = deepClone(params) + + def argsContainsId = newConfig.allArguments.any{it.plainName == "id"} + if (!argsContainsId) { + def idArg = [ + 'name': '--id', + 'required': false, + 'type': 'string', + 'description': 'A unique id for every entry.', + 'multiple': false + ] + newConfig.arguments.add(0, idArg) + newConfig = processConfig(newConfig) + } + if (!newParams.containsKey("id")) { + newParams.id = "run" + } + + helpMessage(newConfig) + + channelFromParams(newParams, newConfig) + // make sure id is not in the state if id is not in the args + | map {id, state -> + if (!argsContainsId) { + [id, state.findAll{k, v -> k != "id"}] + } else { + [id, state] + } + } + | meta.workflow.run( + auto: [ publish: "state" ] + ) +} + +// END COMPONENT-SPECIFIC CODE diff --git a/target/nextflow/bbmap/bbmap_bbsplit/nextflow.config b/target/nextflow/bbmap/bbmap_bbsplit/nextflow.config new file mode 100644 index 00000000..4603d2ee --- /dev/null +++ b/target/nextflow/bbmap/bbmap_bbsplit/nextflow.config @@ -0,0 +1,125 @@ +manifest { + name = 'bbmap/bbmap_bbsplit' + mainScript = 'main.nf' + nextflowVersion = '!>=20.12.1-edge' + version = 'main' + description = 'Split sequencing reads by mapping them to multiple references simultaneously.' +} + +process.container = 'nextflow/bash:latest' + +// detect tempdir +tempDir = java.nio.file.Paths.get( + System.getenv('NXF_TEMP') ?: + System.getenv('VIASH_TEMP') ?: + System.getenv('TEMPDIR') ?: + System.getenv('TMPDIR') ?: + '/tmp' +).toAbsolutePath() + +profiles { + no_publish { + process { + withName: '.*' { + publishDir = [ + enabled: false + ] + } + } + } + mount_temp { + docker.temp = tempDir + podman.temp = tempDir + charliecloud.temp = tempDir + } + docker { + docker.enabled = true + // docker.userEmulation = true + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + } + singularity { + singularity.enabled = true + singularity.autoMounts = true + docker.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + } + podman { + podman.enabled = true + docker.enabled = false + singularity.enabled = false + shifter.enabled = false + charliecloud.enabled = false + } + shifter { + shifter.enabled = true + docker.enabled = false + singularity.enabled = false + podman.enabled = false + charliecloud.enabled = false + } + charliecloud { + charliecloud.enabled = true + docker.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + } +} + +process{ + withLabel: mem1gb { memory = 1000000000.B } + withLabel: mem2gb { memory = 2000000000.B } + withLabel: mem5gb { memory = 5000000000.B } + withLabel: mem10gb { memory = 10000000000.B } + withLabel: mem20gb { memory = 20000000000.B } + withLabel: mem50gb { memory = 50000000000.B } + withLabel: mem100gb { memory = 100000000000.B } + withLabel: mem200gb { memory = 200000000000.B } + withLabel: mem500gb { memory = 500000000000.B } + withLabel: mem1tb { memory = 1000000000000.B } + withLabel: mem2tb { memory = 2000000000000.B } + withLabel: mem5tb { memory = 5000000000000.B } + withLabel: mem10tb { memory = 10000000000000.B } + withLabel: mem20tb { memory = 20000000000000.B } + withLabel: mem50tb { memory = 50000000000000.B } + withLabel: mem100tb { memory = 100000000000000.B } + withLabel: mem200tb { memory = 200000000000000.B } + withLabel: mem500tb { memory = 500000000000000.B } + withLabel: mem1gib { memory = 1073741824.B } + withLabel: mem2gib { memory = 2147483648.B } + withLabel: mem4gib { memory = 4294967296.B } + withLabel: mem8gib { memory = 8589934592.B } + withLabel: mem16gib { memory = 17179869184.B } + withLabel: mem32gib { memory = 34359738368.B } + withLabel: mem64gib { memory = 68719476736.B } + withLabel: mem128gib { memory = 137438953472.B } + withLabel: mem256gib { memory = 274877906944.B } + withLabel: mem512gib { memory = 549755813888.B } + withLabel: mem1tib { memory = 1099511627776.B } + withLabel: mem2tib { memory = 2199023255552.B } + withLabel: mem4tib { memory = 4398046511104.B } + withLabel: mem8tib { memory = 8796093022208.B } + withLabel: mem16tib { memory = 17592186044416.B } + withLabel: mem32tib { memory = 35184372088832.B } + withLabel: mem64tib { memory = 70368744177664.B } + withLabel: mem128tib { memory = 140737488355328.B } + withLabel: mem256tib { memory = 281474976710656.B } + withLabel: mem512tib { memory = 562949953421312.B } + withLabel: cpu1 { cpus = 1 } + withLabel: cpu2 { cpus = 2 } + withLabel: cpu5 { cpus = 5 } + withLabel: cpu10 { cpus = 10 } + withLabel: cpu20 { cpus = 20 } + withLabel: cpu50 { cpus = 50 } + withLabel: cpu100 { cpus = 100 } + withLabel: cpu200 { cpus = 200 } + withLabel: cpu500 { cpus = 500 } + withLabel: cpu1000 { cpus = 1000 } +} + + diff --git a/target/nextflow/bbmap/bbmap_bbsplit/nextflow_schema.json b/target/nextflow/bbmap/bbmap_bbsplit/nextflow_schema.json new file mode 100644 index 00000000..f50f6cfc --- /dev/null +++ b/target/nextflow/bbmap/bbmap_bbsplit/nextflow_schema.json @@ -0,0 +1,310 @@ +{ +"$schema": "http://json-schema.org/draft-07/schema", +"title": "bbmap_bbsplit", +"description": "Split sequencing reads by mapping them to multiple references simultaneously.", +"type": "object", +"definitions": { + + + + "input" : { + "title": "Input", + "type": "object", + "description": "No description", + "properties": { + + + "id": { + "type": + "string", + "description": "Type: `string`. Sample ID", + "help_text": "Type: `string`. Sample ID" + + } + + + , + "paired": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Paired fastq files or not?", + "help_text": "Type: `boolean_true`, default: `false`. Paired fastq files or not?" + , + "default": "False" + } + + + , + "input": { + "type": + "string", + "description": "Type: List of `file`, example: `reads.fastq`, multiple_sep: `\";\"`. Input fastq files, either one or two (paired), separated by \";\"", + "help_text": "Type: List of `file`, example: `reads.fastq`, multiple_sep: `\";\"`. Input fastq files, either one or two (paired), separated by \";\"." + + } + + + , + "ref": { + "type": + "string", + "description": "Type: List of `file`, multiple_sep: `\";\"`. Reference FASTA files, separated by \";\"", + "help_text": "Type: List of `file`, multiple_sep: `\";\"`. Reference FASTA files, separated by \";\". The primary reference should be specified first." + + } + + + , + "only_build_index": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. If set, only builds the index", + "help_text": "Type: `boolean_true`, default: `false`. If set, only builds the index. Otherwise, mapping is performed." + , + "default": "False" + } + + + , + "build": { + "type": + "string", + "description": "Type: `string`, example: `1`. Designate index to use", + "help_text": "Type: `string`, example: `1`. Designate index to use. Corresponds to the number specified when building the index.\nIf building the index, this will be the build\u0027s id. If multiple references are indexed\nin the same directory, each needs a unique build ID. Default: 1.\n" + + } + + + , + "qin": { + "type": + "string", + "description": "Type: `string`. Set to 33 or 64 to specify input quality value ASCII offset", + "help_text": "Type: `string`. Set to 33 or 64 to specify input quality value ASCII offset. Automatically detected if\nnot specified.\n" + + } + + + , + "interleaved": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. True forces paired/interleaved input; false forces single-ended mapping", + "help_text": "Type: `boolean_true`, default: `false`. True forces paired/interleaved input; false forces single-ended mapping.\nIf not specified, interleaved status will be autodetected from read names.\n" + , + "default": "False" + } + + + , + "maxindel": { + "type": + "integer", + "description": "Type: `integer`, example: `20`. Don\u0027t look for indels longer than this", + "help_text": "Type: `integer`, example: `20`. Don\u0027t look for indels longer than this. Lower is faster. Set to \u003e=100k for RNA-seq.\n" + + } + + + , + "minratio": { + "type": + "number", + "description": "Type: `double`, example: `0.56`. Fraction of max alignment score required to keep a site", + "help_text": "Type: `double`, example: `0.56`. Fraction of max alignment score required to keep a site. Higher is faster.\n" + + } + + + , + "minhits": { + "type": + "integer", + "description": "Type: `integer`, example: `1`. Minimum number of seed hits required for candidate sites", + "help_text": "Type: `integer`, example: `1`. Minimum number of seed hits required for candidate sites. Higher is faster.\n" + + } + + + , + "ambiguous": { + "type": + "string", + "description": "Type: `string`, example: `best`, choices: ``best`, `toss`, `random`, `all``. Set behavior on ambiguously-mapped reads (with multiple top-scoring mapping locations)", + "help_text": "Type: `string`, example: `best`, choices: ``best`, `toss`, `random`, `all``. 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", + "enum": ["best", "toss", "random", "all"] + + + } + + + , + "ambiguous2": { + "type": + "string", + "description": "Type: `string`, example: `best`, choices: ``best`, `toss`, `all`, `split``. Set behavior only for reads that map ambiguously to multiple different references", + "help_text": "Type: `string`, example: `best`, choices: ``best`, `toss`, `all`, `split``. Set behavior only for reads that map ambiguously to multiple different references.\nNormal \u0027ambiguous=\u0027 controls behavior on all ambiguous reads;\nAmbiguous2 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", + "enum": ["best", "toss", "all", "split"] + + + } + + + , + "qtrim": { + "type": + "string", + "description": "Type: `string`, choices: ``l`, `r`, `lr``. Quality-trim ends to Q5 before mapping", + "help_text": "Type: `string`, choices: ``l`, `r`, `lr``. Quality-trim ends to Q5 before mapping. Options are \u0027l\u0027 (left), \u0027r\u0027 (right), and \u0027lr\u0027 (both).\n", + "enum": ["l", "r", "lr"] + + + } + + + , + "untrim": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Undo trimming after mapping", + "help_text": "Type: `boolean_true`, default: `false`. Undo trimming after mapping. Untrimmed bases will be soft-clipped in cigar strings." + , + "default": "False" + } + + +} +}, + + + "output" : { + "title": "Output", + "type": "object", + "description": "No description", + "properties": { + + + "fastq_1": { + "type": + "string", + "description": "Type: `file`, default: `$id.$key.fastq_1.fastq`, example: `read_out1.fastq`. Output file for read 1", + "help_text": "Type: `file`, default: `$id.$key.fastq_1.fastq`, example: `read_out1.fastq`. Output file for read 1.\n" + , + "default": "$id.$key.fastq_1.fastq" + } + + + , + "fastq_2": { + "type": + "string", + "description": "Type: `file`, default: `$id.$key.fastq_2.fastq`, example: `read_out2.fastq`. Output file for read 2", + "help_text": "Type: `file`, default: `$id.$key.fastq_2.fastq`, example: `read_out2.fastq`. Output file for read 2.\n" + , + "default": "$id.$key.fastq_2.fastq" + } + + + , + "sam2bam": { + "type": + "string", + "description": "Type: `file`, default: `$id.$key.sam2bam.sh`, example: `script.sh`. Write a shell script to \u0027file\u0027 that will turn the sam output into a sorted, indexed bam file", + "help_text": "Type: `file`, default: `$id.$key.sam2bam.sh`, example: `script.sh`. Write a shell script to \u0027file\u0027 that will turn the sam output into a sorted, indexed bam file.\n" + , + "default": "$id.$key.sam2bam.sh" + } + + + , + "scafstats": { + "type": + "string", + "description": "Type: `file`, default: `$id.$key.scafstats.txt`, example: `scaffold_stats.txt`. Write statistics on how many reads mapped to which scaffold to this file", + "help_text": "Type: `file`, default: `$id.$key.scafstats.txt`, example: `scaffold_stats.txt`. Write statistics on how many reads mapped to which scaffold to this file.\n" + , + "default": "$id.$key.scafstats.txt" + } + + + , + "refstats": { + "type": + "string", + "description": "Type: `file`, default: `$id.$key.refstats.txt`, example: `reference_stats.txt`. Write statistics on how many reads were assigned to which reference to this file", + "help_text": "Type: `file`, default: `$id.$key.refstats.txt`, example: `reference_stats.txt`. Write statistics on how many reads were assigned to which reference to this file.\nUnmapped reads whose mate mapped to a reference are considered assigned and will be counted.\n" + , + "default": "$id.$key.refstats.txt" + } + + + , + "nzo": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Only print lines with nonzero coverage", + "help_text": "Type: `boolean_true`, default: `false`. Only print lines with nonzero coverage." + , + "default": "False" + } + + + , + "bbmap_args": { + "type": + "string", + "description": "Type: `string`. Additional arguments from BBMap to pass to BBSplit", + "help_text": "Type: `string`. Additional arguments from BBMap to pass to BBSplit.\n" + + } + + +} +}, + + + "nextflow input-output arguments" : { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + + + "publish_dir": { + "type": + "string", + "description": "Type: `string`, required, example: `output/`. Path to an output directory", + "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." + + } + + + , + "param_list": { + "type": + "string", + "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", + "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", + "hidden": true + + } + + +} +} +}, +"allOf": [ + + { + "$ref": "#/definitions/input" + }, + + { + "$ref": "#/definitions/output" + }, + + { + "$ref": "#/definitions/nextflow input-output arguments" + } +] +} diff --git a/target/nextflow/bcftools/bcftools_annotate/.config.vsh.yaml b/target/nextflow/bcftools/bcftools_annotate/.config.vsh.yaml index abc96b1e..379ee3f3 100644 --- a/target/nextflow/bcftools/bcftools_annotate/.config.vsh.yaml +++ b/target/nextflow/bcftools/bcftools_annotate/.config.vsh.yaml @@ -469,9 +469,9 @@ build_info: output: "target/nextflow/bcftools/bcftools_annotate" executable: "target/nextflow/bcftools/bcftools_annotate/main.nf" 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" diff --git a/target/nextflow/bcftools/bcftools_annotate/main.nf b/target/nextflow/bcftools/bcftools_annotate/main.nf index 85a50724..da22a8f3 100644 --- a/target/nextflow/bcftools/bcftools_annotate/main.nf +++ b/target/nextflow/bcftools/bcftools_annotate/main.nf @@ -3335,9 +3335,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bcftools/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", diff --git a/target/nextflow/bcftools/bcftools_concat/.config.vsh.yaml b/target/nextflow/bcftools/bcftools_concat/.config.vsh.yaml index 052f1a54..e3b85a17 100644 --- a/target/nextflow/bcftools/bcftools_concat/.config.vsh.yaml +++ b/target/nextflow/bcftools/bcftools_concat/.config.vsh.yaml @@ -335,9 +335,9 @@ build_info: output: "target/nextflow/bcftools/bcftools_concat" executable: "target/nextflow/bcftools/bcftools_concat/main.nf" 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" diff --git a/target/nextflow/bcftools/bcftools_concat/main.nf b/target/nextflow/bcftools/bcftools_concat/main.nf index f5826d9b..afbf8c66 100644 --- a/target/nextflow/bcftools/bcftools_concat/main.nf +++ b/target/nextflow/bcftools/bcftools_concat/main.nf @@ -3207,9 +3207,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bcftools/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", diff --git a/target/nextflow/bcftools/bcftools_norm/.config.vsh.yaml b/target/nextflow/bcftools/bcftools_norm/.config.vsh.yaml index 2a115151..baddd32d 100644 --- a/target/nextflow/bcftools/bcftools_norm/.config.vsh.yaml +++ b/target/nextflow/bcftools/bcftools_norm/.config.vsh.yaml @@ -416,9 +416,9 @@ build_info: output: "target/nextflow/bcftools/bcftools_norm" executable: "target/nextflow/bcftools/bcftools_norm/main.nf" 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" diff --git a/target/nextflow/bcftools/bcftools_norm/main.nf b/target/nextflow/bcftools/bcftools_norm/main.nf index 9552c727..025ce250 100644 --- a/target/nextflow/bcftools/bcftools_norm/main.nf +++ b/target/nextflow/bcftools/bcftools_norm/main.nf @@ -3300,9 +3300,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bcftools/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", diff --git a/target/nextflow/bcftools/bcftools_sort/.config.vsh.yaml b/target/nextflow/bcftools/bcftools_sort/.config.vsh.yaml index c0541845..77a85c20 100644 --- a/target/nextflow/bcftools/bcftools_sort/.config.vsh.yaml +++ b/target/nextflow/bcftools/bcftools_sort/.config.vsh.yaml @@ -185,9 +185,9 @@ build_info: output: "target/nextflow/bcftools/bcftools_sort" executable: "target/nextflow/bcftools/bcftools_sort/main.nf" 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" diff --git a/target/nextflow/bcftools/bcftools_sort/main.nf b/target/nextflow/bcftools/bcftools_sort/main.nf index eab6f206..7308be35 100644 --- a/target/nextflow/bcftools/bcftools_sort/main.nf +++ b/target/nextflow/bcftools/bcftools_sort/main.nf @@ -3048,9 +3048,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bcftools/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", diff --git a/target/nextflow/bcftools/bcftools_stats/.config.vsh.yaml b/target/nextflow/bcftools/bcftools_stats/.config.vsh.yaml index b1e8a4ba..2b2da89a 100644 --- a/target/nextflow/bcftools/bcftools_stats/.config.vsh.yaml +++ b/target/nextflow/bcftools/bcftools_stats/.config.vsh.yaml @@ -458,9 +458,9 @@ build_info: output: "target/nextflow/bcftools/bcftools_stats" executable: "target/nextflow/bcftools/bcftools_stats/main.nf" 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" diff --git a/target/nextflow/bcftools/bcftools_stats/main.nf b/target/nextflow/bcftools/bcftools_stats/main.nf index 84e79426..4002ba5f 100644 --- a/target/nextflow/bcftools/bcftools_stats/main.nf +++ b/target/nextflow/bcftools/bcftools_stats/main.nf @@ -3337,9 +3337,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bcftools/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", diff --git a/target/nextflow/bcl_convert/.config.vsh.yaml b/target/nextflow/bcl_convert/.config.vsh.yaml index 07e32490..c31c960b 100644 --- a/target/nextflow/bcl_convert/.config.vsh.yaml +++ b/target/nextflow/bcl_convert/.config.vsh.yaml @@ -418,9 +418,9 @@ build_info: output: "target/nextflow/bcl_convert" executable: "target/nextflow/bcl_convert/main.nf" 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" diff --git a/target/nextflow/bcl_convert/main.nf b/target/nextflow/bcl_convert/main.nf index dcbe43d6..0c40d7bc 100644 --- a/target/nextflow/bcl_convert/main.nf +++ b/target/nextflow/bcl_convert/main.nf @@ -3329,9 +3329,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/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", diff --git a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml index e914cf4d..e587c1a6 100644 --- a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml +++ b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml @@ -274,9 +274,9 @@ build_info: output: "target/nextflow/bd_rhapsody/bd_rhapsody_make_reference" executable: "target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf" viash_version: "0.9.0" - 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" diff --git a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf index 54331ce3..644ddccb 100644 --- a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf +++ b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf @@ -3146,9 +3146,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bd_rhapsody/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", diff --git a/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml b/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml index 9d26d85e..d1268836 100644 --- a/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml +++ b/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml @@ -1115,9 +1115,9 @@ build_info: output: "target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis" executable: "target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/main.nf" 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" diff --git a/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/main.nf b/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/main.nf index 89f2fa26..bc10bd46 100644 --- a/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/main.nf +++ b/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/main.nf @@ -4193,9 +4193,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bd_rhapsody/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", diff --git a/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml index ca2eb1d3..22157bcc 100644 --- a/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml @@ -187,9 +187,9 @@ build_info: output: "target/nextflow/bedtools/bedtools_bamtofastq" executable: "target/nextflow/bedtools/bedtools_bamtofastq/main.nf" 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" diff --git a/target/nextflow/bedtools/bedtools_bamtofastq/main.nf b/target/nextflow/bedtools/bedtools_bamtofastq/main.nf index 2f39872f..25a01e05 100644 --- a/target/nextflow/bedtools/bedtools_bamtofastq/main.nf +++ b/target/nextflow/bedtools/bedtools_bamtofastq/main.nf @@ -3050,9 +3050,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/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", diff --git a/target/nextflow/bedtools/bedtools_bed12tobed6/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_bed12tobed6/.config.vsh.yaml index bf72eeb1..eb7c9e4a 100644 --- a/target/nextflow/bedtools/bedtools_bed12tobed6/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_bed12tobed6/.config.vsh.yaml @@ -176,9 +176,9 @@ build_info: output: "target/nextflow/bedtools/bedtools_bed12tobed6" executable: "target/nextflow/bedtools/bedtools_bed12tobed6/main.nf" 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" diff --git a/target/nextflow/bedtools/bedtools_bed12tobed6/main.nf b/target/nextflow/bedtools/bedtools_bed12tobed6/main.nf index 4b5b16d0..5215a25a 100644 --- a/target/nextflow/bedtools/bedtools_bed12tobed6/main.nf +++ b/target/nextflow/bedtools/bedtools_bed12tobed6/main.nf @@ -3035,9 +3035,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/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", diff --git a/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml index b31a6555..0742849d 100644 --- a/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml @@ -214,9 +214,9 @@ build_info: output: "target/nextflow/bedtools/bedtools_bedtobam" executable: "target/nextflow/bedtools/bedtools_bedtobam/main.nf" 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" diff --git a/target/nextflow/bedtools/bedtools_bedtobam/main.nf b/target/nextflow/bedtools/bedtools_bedtobam/main.nf index a0ede177..152115e8 100644 --- a/target/nextflow/bedtools/bedtools_bedtobam/main.nf +++ b/target/nextflow/bedtools/bedtools_bedtobam/main.nf @@ -3083,9 +3083,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/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", diff --git a/target/nextflow/bedtools/bedtools_genomecov/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_genomecov/.config.vsh.yaml index 76de6d8a..388dda09 100644 --- a/target/nextflow/bedtools/bedtools_genomecov/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_genomecov/.config.vsh.yaml @@ -337,9 +337,9 @@ build_info: output: "target/nextflow/bedtools/bedtools_genomecov" executable: "target/nextflow/bedtools/bedtools_genomecov/main.nf" 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" diff --git a/target/nextflow/bedtools/bedtools_genomecov/main.nf b/target/nextflow/bedtools/bedtools_genomecov/main.nf index b21a6beb..4465e475 100644 --- a/target/nextflow/bedtools/bedtools_genomecov/main.nf +++ b/target/nextflow/bedtools/bedtools_genomecov/main.nf @@ -3207,9 +3207,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/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", diff --git a/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml index a9619037..1953409e 100644 --- a/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml @@ -232,9 +232,9 @@ build_info: output: "target/nextflow/bedtools/bedtools_getfasta" executable: "target/nextflow/bedtools/bedtools_getfasta/main.nf" 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" diff --git a/target/nextflow/bedtools/bedtools_getfasta/main.nf b/target/nextflow/bedtools/bedtools_getfasta/main.nf index 40c0995e..0a9bc296 100644 --- a/target/nextflow/bedtools/bedtools_getfasta/main.nf +++ b/target/nextflow/bedtools/bedtools_getfasta/main.nf @@ -3086,9 +3086,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/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", diff --git a/target/nextflow/bedtools/bedtools_groupby/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_groupby/.config.vsh.yaml index 4195bdb3..615b9e99 100644 --- a/target/nextflow/bedtools/bedtools_groupby/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_groupby/.config.vsh.yaml @@ -273,9 +273,9 @@ build_info: output: "target/nextflow/bedtools/bedtools_groupby" executable: "target/nextflow/bedtools/bedtools_groupby/main.nf" 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" diff --git a/target/nextflow/bedtools/bedtools_groupby/main.nf b/target/nextflow/bedtools/bedtools_groupby/main.nf index 55e57c50..8cbba9ee 100644 --- a/target/nextflow/bedtools/bedtools_groupby/main.nf +++ b/target/nextflow/bedtools/bedtools_groupby/main.nf @@ -3130,9 +3130,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/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", diff --git a/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml index f6bad6ab..5ff83713 100644 --- a/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml @@ -410,9 +410,9 @@ build_info: output: "target/nextflow/bedtools/bedtools_intersect" executable: "target/nextflow/bedtools/bedtools_intersect/main.nf" 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" diff --git a/target/nextflow/bedtools/bedtools_intersect/main.nf b/target/nextflow/bedtools/bedtools_intersect/main.nf index 35da9226..d3c63bc5 100644 --- a/target/nextflow/bedtools/bedtools_intersect/main.nf +++ b/target/nextflow/bedtools/bedtools_intersect/main.nf @@ -3282,9 +3282,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/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", diff --git a/target/nextflow/bedtools/bedtools_links/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_links/.config.vsh.yaml index 0543e51c..57ae0020 100644 --- a/target/nextflow/bedtools/bedtools_links/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_links/.config.vsh.yaml @@ -210,9 +210,9 @@ build_info: output: "target/nextflow/bedtools/bedtools_links" executable: "target/nextflow/bedtools/bedtools_links/main.nf" 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" diff --git a/target/nextflow/bedtools/bedtools_links/main.nf b/target/nextflow/bedtools/bedtools_links/main.nf index 4c1003e7..cbb2bd88 100644 --- a/target/nextflow/bedtools/bedtools_links/main.nf +++ b/target/nextflow/bedtools/bedtools_links/main.nf @@ -3073,9 +3073,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/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", diff --git a/target/nextflow/bedtools/bedtools_merge/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_merge/.config.vsh.yaml index e88e4115..8bc8a017 100644 --- a/target/nextflow/bedtools/bedtools_merge/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_merge/.config.vsh.yaml @@ -279,9 +279,9 @@ build_info: output: "target/nextflow/bedtools/bedtools_merge" executable: "target/nextflow/bedtools/bedtools_merge/main.nf" 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" diff --git a/target/nextflow/bedtools/bedtools_merge/main.nf b/target/nextflow/bedtools/bedtools_merge/main.nf index e746dcf1..3af70cc8 100644 --- a/target/nextflow/bedtools/bedtools_merge/main.nf +++ b/target/nextflow/bedtools/bedtools_merge/main.nf @@ -3134,9 +3134,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/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", diff --git a/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml index c2ddabe6..af9a1914 100644 --- a/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml @@ -222,9 +222,9 @@ build_info: output: "target/nextflow/bedtools/bedtools_sort" executable: "target/nextflow/bedtools/bedtools_sort/main.nf" 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" diff --git a/target/nextflow/bedtools/bedtools_sort/main.nf b/target/nextflow/bedtools/bedtools_sort/main.nf index 97b9304e..8143c3ca 100644 --- a/target/nextflow/bedtools/bedtools_sort/main.nf +++ b/target/nextflow/bedtools/bedtools_sort/main.nf @@ -3092,9 +3092,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/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", diff --git a/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml b/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml index 590c158d..a9c6652d 100644 --- a/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml +++ b/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml @@ -158,9 +158,9 @@ build_info: output: "target/nextflow/busco/busco_download_datasets" executable: "target/nextflow/busco/busco_download_datasets/main.nf" 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" diff --git a/target/nextflow/busco/busco_download_datasets/main.nf b/target/nextflow/busco/busco_download_datasets/main.nf index e3239b39..67e931bd 100644 --- a/target/nextflow/busco/busco_download_datasets/main.nf +++ b/target/nextflow/busco/busco_download_datasets/main.nf @@ -3011,9 +3011,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/busco/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", diff --git a/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml b/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml index 2df647b2..fff6266d 100644 --- a/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml +++ b/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml @@ -145,9 +145,9 @@ build_info: output: "target/nextflow/busco/busco_list_datasets" executable: "target/nextflow/busco/busco_list_datasets/main.nf" 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" diff --git a/target/nextflow/busco/busco_list_datasets/main.nf b/target/nextflow/busco/busco_list_datasets/main.nf index d252e8f8..ab9732d6 100644 --- a/target/nextflow/busco/busco_list_datasets/main.nf +++ b/target/nextflow/busco/busco_list_datasets/main.nf @@ -2997,9 +2997,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/busco/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", diff --git a/target/nextflow/busco/busco_run/.config.vsh.yaml b/target/nextflow/busco/busco_run/.config.vsh.yaml index a9ae8837..533fcba3 100644 --- a/target/nextflow/busco/busco_run/.config.vsh.yaml +++ b/target/nextflow/busco/busco_run/.config.vsh.yaml @@ -423,9 +423,9 @@ build_info: output: "target/nextflow/busco/busco_run" executable: "target/nextflow/busco/busco_run/main.nf" 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" diff --git a/target/nextflow/busco/busco_run/main.nf b/target/nextflow/busco/busco_run/main.nf index 3c10af5a..72a46f2c 100644 --- a/target/nextflow/busco/busco_run/main.nf +++ b/target/nextflow/busco/busco_run/main.nf @@ -3309,9 +3309,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/busco/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", diff --git a/target/nextflow/cutadapt/.config.vsh.yaml b/target/nextflow/cutadapt/.config.vsh.yaml index 8788cb7e..d61ba10b 100644 --- a/target/nextflow/cutadapt/.config.vsh.yaml +++ b/target/nextflow/cutadapt/.config.vsh.yaml @@ -740,9 +740,9 @@ build_info: output: "target/nextflow/cutadapt" executable: "target/nextflow/cutadapt/main.nf" 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" diff --git a/target/nextflow/cutadapt/main.nf b/target/nextflow/cutadapt/main.nf index c38f7055..07efa1c9 100644 --- a/target/nextflow/cutadapt/main.nf +++ b/target/nextflow/cutadapt/main.nf @@ -3619,9 +3619,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/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", diff --git a/target/nextflow/falco/.config.vsh.yaml b/target/nextflow/falco/.config.vsh.yaml index c01f5044..4a545338 100644 --- a/target/nextflow/falco/.config.vsh.yaml +++ b/target/nextflow/falco/.config.vsh.yaml @@ -317,9 +317,9 @@ build_info: output: "target/nextflow/falco" executable: "target/nextflow/falco/main.nf" 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" diff --git a/target/nextflow/falco/main.nf b/target/nextflow/falco/main.nf index e270c472..4df81cc0 100644 --- a/target/nextflow/falco/main.nf +++ b/target/nextflow/falco/main.nf @@ -3170,9 +3170,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/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", diff --git a/target/nextflow/fastp/.config.vsh.yaml b/target/nextflow/fastp/.config.vsh.yaml index fa1eabc2..7c4cda3b 100644 --- a/target/nextflow/fastp/.config.vsh.yaml +++ b/target/nextflow/fastp/.config.vsh.yaml @@ -1083,9 +1083,9 @@ build_info: output: "target/nextflow/fastp" executable: "target/nextflow/fastp/main.nf" 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" diff --git a/target/nextflow/fastp/main.nf b/target/nextflow/fastp/main.nf index b635e7da..b50efecf 100644 --- a/target/nextflow/fastp/main.nf +++ b/target/nextflow/fastp/main.nf @@ -4023,9 +4023,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/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", diff --git a/target/nextflow/fastqc/.config.vsh.yaml b/target/nextflow/fastqc/.config.vsh.yaml index 84103af1..a8995745 100644 --- a/target/nextflow/fastqc/.config.vsh.yaml +++ b/target/nextflow/fastqc/.config.vsh.yaml @@ -340,9 +340,9 @@ build_info: output: "target/nextflow/fastqc" executable: "target/nextflow/fastqc/main.nf" 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" diff --git a/target/nextflow/fastqc/main.nf b/target/nextflow/fastqc/main.nf index ff664c21..a09aa5a6 100644 --- a/target/nextflow/fastqc/main.nf +++ b/target/nextflow/fastqc/main.nf @@ -3182,9 +3182,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/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", diff --git a/target/nextflow/featurecounts/.config.vsh.yaml b/target/nextflow/featurecounts/.config.vsh.yaml index 0dfc492a..a542225a 100644 --- a/target/nextflow/featurecounts/.config.vsh.yaml +++ b/target/nextflow/featurecounts/.config.vsh.yaml @@ -645,9 +645,9 @@ build_info: output: "target/nextflow/featurecounts" executable: "target/nextflow/featurecounts/main.nf" 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" diff --git a/target/nextflow/featurecounts/main.nf b/target/nextflow/featurecounts/main.nf index bf8a1f4c..667c27d2 100644 --- a/target/nextflow/featurecounts/main.nf +++ b/target/nextflow/featurecounts/main.nf @@ -3549,9 +3549,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/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", diff --git a/target/nextflow/fq_subsample/.config.vsh.yaml b/target/nextflow/fq_subsample/.config.vsh.yaml index a8cd153b..85d0415d 100644 --- a/target/nextflow/fq_subsample/.config.vsh.yaml +++ b/target/nextflow/fq_subsample/.config.vsh.yaml @@ -190,9 +190,9 @@ build_info: output: "target/nextflow/fq_subsample" executable: "target/nextflow/fq_subsample/main.nf" 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" diff --git a/target/nextflow/fq_subsample/main.nf b/target/nextflow/fq_subsample/main.nf index a6f286fd..11bb5fa5 100644 --- a/target/nextflow/fq_subsample/main.nf +++ b/target/nextflow/fq_subsample/main.nf @@ -3032,9 +3032,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/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", diff --git a/target/nextflow/gffread/.config.vsh.yaml b/target/nextflow/gffread/.config.vsh.yaml index 6f92dc7e..aa089675 100644 --- a/target/nextflow/gffread/.config.vsh.yaml +++ b/target/nextflow/gffread/.config.vsh.yaml @@ -685,9 +685,9 @@ build_info: output: "target/nextflow/gffread" executable: "target/nextflow/gffread/main.nf" 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" diff --git a/target/nextflow/gffread/main.nf b/target/nextflow/gffread/main.nf index c755ff35..739241da 100644 --- a/target/nextflow/gffread/main.nf +++ b/target/nextflow/gffread/main.nf @@ -3606,9 +3606,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/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", diff --git a/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml b/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml index 6bfc974a..3e42f876 100644 --- a/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml +++ b/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml @@ -218,9 +218,9 @@ build_info: output: "target/nextflow/kallisto/kallisto_index" executable: "target/nextflow/kallisto/kallisto_index/main.nf" 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" diff --git a/target/nextflow/kallisto/kallisto_index/main.nf b/target/nextflow/kallisto/kallisto_index/main.nf index aea87359..ac8cf864 100644 --- a/target/nextflow/kallisto/kallisto_index/main.nf +++ b/target/nextflow/kallisto/kallisto_index/main.nf @@ -3071,9 +3071,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/kallisto/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", diff --git a/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml b/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml index 839799ca..296430a3 100644 --- a/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml +++ b/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml @@ -234,9 +234,9 @@ build_info: output: "target/nextflow/kallisto/kallisto_quant" executable: "target/nextflow/kallisto/kallisto_quant/main.nf" 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" diff --git a/target/nextflow/kallisto/kallisto_quant/main.nf b/target/nextflow/kallisto/kallisto_quant/main.nf index fd9ce0c1..ffa97552 100644 --- a/target/nextflow/kallisto/kallisto_quant/main.nf +++ b/target/nextflow/kallisto/kallisto_quant/main.nf @@ -3092,9 +3092,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/kallisto/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", diff --git a/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml b/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml index ab1aa412..614fd3e1 100644 --- a/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml +++ b/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml @@ -507,9 +507,9 @@ build_info: output: "target/nextflow/lofreq/lofreq_call" executable: "target/nextflow/lofreq/lofreq_call/main.nf" 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" diff --git a/target/nextflow/lofreq/lofreq_call/main.nf b/target/nextflow/lofreq/lofreq_call/main.nf index c338dab8..1dc0f1da 100644 --- a/target/nextflow/lofreq/lofreq_call/main.nf +++ b/target/nextflow/lofreq/lofreq_call/main.nf @@ -3414,9 +3414,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/lofreq/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", diff --git a/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml b/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml index 51c27db0..b13e457d 100644 --- a/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml +++ b/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml @@ -215,9 +215,9 @@ build_info: output: "target/nextflow/lofreq/lofreq_indelqual" executable: "target/nextflow/lofreq/lofreq_indelqual/main.nf" 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" diff --git a/target/nextflow/lofreq/lofreq_indelqual/main.nf b/target/nextflow/lofreq/lofreq_indelqual/main.nf index 0f675132..78745c21 100644 --- a/target/nextflow/lofreq/lofreq_indelqual/main.nf +++ b/target/nextflow/lofreq/lofreq_indelqual/main.nf @@ -3077,9 +3077,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/lofreq/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", diff --git a/target/nextflow/multiqc/.config.vsh.yaml b/target/nextflow/multiqc/.config.vsh.yaml index bf23523e..0ec1371e 100644 --- a/target/nextflow/multiqc/.config.vsh.yaml +++ b/target/nextflow/multiqc/.config.vsh.yaml @@ -456,9 +456,9 @@ build_info: output: "target/nextflow/multiqc" executable: "target/nextflow/multiqc/main.nf" 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" diff --git a/target/nextflow/multiqc/main.nf b/target/nextflow/multiqc/main.nf index a9054271..49798d21 100644 --- a/target/nextflow/multiqc/main.nf +++ b/target/nextflow/multiqc/main.nf @@ -3366,9 +3366,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/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", diff --git a/target/nextflow/pear/.config.vsh.yaml b/target/nextflow/pear/.config.vsh.yaml index aba23d95..8b8903d6 100644 --- a/target/nextflow/pear/.config.vsh.yaml +++ b/target/nextflow/pear/.config.vsh.yaml @@ -398,9 +398,9 @@ build_info: output: "target/nextflow/pear" executable: "target/nextflow/pear/main.nf" 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" diff --git a/target/nextflow/pear/main.nf b/target/nextflow/pear/main.nf index 6164f1a7..7448ed85 100644 --- a/target/nextflow/pear/main.nf +++ b/target/nextflow/pear/main.nf @@ -3259,9 +3259,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/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", diff --git a/target/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml b/target/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml index b8a36d54..b387ad01 100644 --- a/target/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml +++ b/target/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml @@ -264,9 +264,9 @@ build_info: output: "target/nextflow/qualimap/qualimap_rnaseq" executable: "target/nextflow/qualimap/qualimap_rnaseq/main.nf" 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" diff --git a/target/nextflow/qualimap/qualimap_rnaseq/main.nf b/target/nextflow/qualimap/qualimap_rnaseq/main.nf index b7715bbe..5821f0f4 100644 --- a/target/nextflow/qualimap/qualimap_rnaseq/main.nf +++ b/target/nextflow/qualimap/qualimap_rnaseq/main.nf @@ -3129,9 +3129,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/qualimap/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", diff --git a/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml b/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml index c48ca0fd..7ad9c97d 100644 --- a/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml +++ b/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml @@ -852,9 +852,9 @@ build_info: output: "target/nextflow/rsem/rsem_calculate_expression" executable: "target/nextflow/rsem/rsem_calculate_expression/main.nf" 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" diff --git a/target/nextflow/rsem/rsem_calculate_expression/main.nf b/target/nextflow/rsem/rsem_calculate_expression/main.nf index da70dfa4..6483607d 100644 --- a/target/nextflow/rsem/rsem_calculate_expression/main.nf +++ b/target/nextflow/rsem/rsem_calculate_expression/main.nf @@ -3661,9 +3661,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/rsem/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", diff --git a/target/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml b/target/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml index 654ff7d4..69add8ad 100644 --- a/target/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml +++ b/target/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml @@ -416,9 +416,9 @@ build_info: output: "target/nextflow/rsem/rsem_prepare_reference" executable: "target/nextflow/rsem/rsem_prepare_reference/main.nf" 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" diff --git a/target/nextflow/rsem/rsem_prepare_reference/main.nf b/target/nextflow/rsem/rsem_prepare_reference/main.nf index eac4db68..6ff7f8e8 100644 --- a/target/nextflow/rsem/rsem_prepare_reference/main.nf +++ b/target/nextflow/rsem/rsem_prepare_reference/main.nf @@ -3245,9 +3245,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/rsem/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", diff --git a/target/nextflow/salmon/salmon_index/.config.vsh.yaml b/target/nextflow/salmon/salmon_index/.config.vsh.yaml index a292ffd0..d1ae7541 100644 --- a/target/nextflow/salmon/salmon_index/.config.vsh.yaml +++ b/target/nextflow/salmon/salmon_index/.config.vsh.yaml @@ -277,9 +277,9 @@ build_info: output: "target/nextflow/salmon/salmon_index" executable: "target/nextflow/salmon/salmon_index/main.nf" 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" diff --git a/target/nextflow/salmon/salmon_index/main.nf b/target/nextflow/salmon/salmon_index/main.nf index 460fc9ee..c7ba9c96 100644 --- a/target/nextflow/salmon/salmon_index/main.nf +++ b/target/nextflow/salmon/salmon_index/main.nf @@ -3129,9 +3129,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/salmon/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", diff --git a/target/nextflow/salmon/salmon_quant/.config.vsh.yaml b/target/nextflow/salmon/salmon_quant/.config.vsh.yaml index 402f23a7..3058d9db 100644 --- a/target/nextflow/salmon/salmon_quant/.config.vsh.yaml +++ b/target/nextflow/salmon/salmon_quant/.config.vsh.yaml @@ -1173,9 +1173,9 @@ build_info: output: "target/nextflow/salmon/salmon_quant" executable: "target/nextflow/salmon/salmon_quant/main.nf" 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" diff --git a/target/nextflow/salmon/salmon_quant/main.nf b/target/nextflow/salmon/salmon_quant/main.nf index a31b55bc..a4770222 100644 --- a/target/nextflow/salmon/salmon_quant/main.nf +++ b/target/nextflow/salmon/salmon_quant/main.nf @@ -3964,9 +3964,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/salmon/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", diff --git a/target/nextflow/samtools/samtools_collate/.config.vsh.yaml b/target/nextflow/samtools/samtools_collate/.config.vsh.yaml index 882861ce..a08c0d60 100644 --- a/target/nextflow/samtools/samtools_collate/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_collate/.config.vsh.yaml @@ -264,9 +264,9 @@ build_info: output: "target/nextflow/samtools/samtools_collate" executable: "target/nextflow/samtools/samtools_collate/main.nf" 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" diff --git a/target/nextflow/samtools/samtools_collate/main.nf b/target/nextflow/samtools/samtools_collate/main.nf index 4cc53544..0395fca8 100644 --- a/target/nextflow/samtools/samtools_collate/main.nf +++ b/target/nextflow/samtools/samtools_collate/main.nf @@ -3140,9 +3140,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/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", diff --git a/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml b/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml index e17166c1..255a9cb3 100644 --- a/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml @@ -243,9 +243,9 @@ build_info: output: "target/nextflow/samtools/samtools_faidx" executable: "target/nextflow/samtools/samtools_faidx/main.nf" 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" diff --git a/target/nextflow/samtools/samtools_faidx/main.nf b/target/nextflow/samtools/samtools_faidx/main.nf index 8ec4710b..65104b00 100644 --- a/target/nextflow/samtools/samtools_faidx/main.nf +++ b/target/nextflow/samtools/samtools_faidx/main.nf @@ -3112,9 +3112,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_faidx", "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", diff --git a/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml b/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml index 72a5850f..7fc79d34 100644 --- a/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml @@ -433,9 +433,9 @@ build_info: output: "target/nextflow/samtools/samtools_fasta" executable: "target/nextflow/samtools/samtools_fasta/main.nf" 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" diff --git a/target/nextflow/samtools/samtools_fasta/main.nf b/target/nextflow/samtools/samtools_fasta/main.nf index 72023b00..a6c0c293 100644 --- a/target/nextflow/samtools/samtools_fasta/main.nf +++ b/target/nextflow/samtools/samtools_fasta/main.nf @@ -3304,9 +3304,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_fasta", "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", diff --git a/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml b/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml index e854e46a..75a7061f 100644 --- a/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml @@ -433,9 +433,9 @@ build_info: output: "target/nextflow/samtools/samtools_fastq" executable: "target/nextflow/samtools/samtools_fastq/main.nf" 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" diff --git a/target/nextflow/samtools/samtools_fastq/main.nf b/target/nextflow/samtools/samtools_fastq/main.nf index 2e92324b..96eef9b7 100644 --- a/target/nextflow/samtools/samtools_fastq/main.nf +++ b/target/nextflow/samtools/samtools_fastq/main.nf @@ -3304,9 +3304,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_fastq", "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", diff --git a/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml b/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml index 8479a4bb..0bd3ec4e 100644 --- a/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml @@ -173,9 +173,9 @@ build_info: output: "target/nextflow/samtools/samtools_flagstat" executable: "target/nextflow/samtools/samtools_flagstat/main.nf" 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" diff --git a/target/nextflow/samtools/samtools_flagstat/main.nf b/target/nextflow/samtools/samtools_flagstat/main.nf index 1ac4f606..a16f5f52 100644 --- a/target/nextflow/samtools/samtools_flagstat/main.nf +++ b/target/nextflow/samtools/samtools_flagstat/main.nf @@ -3028,9 +3028,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_flagstat", "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", diff --git a/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml b/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml index 15ba27df..ea9b52fd 100644 --- a/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml @@ -183,9 +183,9 @@ build_info: output: "target/nextflow/samtools/samtools_idxstats" executable: "target/nextflow/samtools/samtools_idxstats/main.nf" 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" diff --git a/target/nextflow/samtools/samtools_idxstats/main.nf b/target/nextflow/samtools/samtools_idxstats/main.nf index b47f344d..7d4ff1d1 100644 --- a/target/nextflow/samtools/samtools_idxstats/main.nf +++ b/target/nextflow/samtools/samtools_idxstats/main.nf @@ -3040,9 +3040,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_idxstats", "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", diff --git a/target/nextflow/samtools/samtools_index/.config.vsh.yaml b/target/nextflow/samtools/samtools_index/.config.vsh.yaml index 8aa94a39..35952019 100644 --- a/target/nextflow/samtools/samtools_index/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_index/.config.vsh.yaml @@ -189,9 +189,9 @@ build_info: output: "target/nextflow/samtools/samtools_index" executable: "target/nextflow/samtools/samtools_index/main.nf" 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" diff --git a/target/nextflow/samtools/samtools_index/main.nf b/target/nextflow/samtools/samtools_index/main.nf index f3446818..9a1210d9 100644 --- a/target/nextflow/samtools/samtools_index/main.nf +++ b/target/nextflow/samtools/samtools_index/main.nf @@ -3053,9 +3053,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_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", diff --git a/target/nextflow/samtools/samtools_sort/.config.vsh.yaml b/target/nextflow/samtools/samtools_sort/.config.vsh.yaml index 10adadca..2c6bfe2c 100644 --- a/target/nextflow/samtools/samtools_sort/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_sort/.config.vsh.yaml @@ -332,9 +332,9 @@ build_info: output: "target/nextflow/samtools/samtools_sort" executable: "target/nextflow/samtools/samtools_sort/main.nf" 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" diff --git a/target/nextflow/samtools/samtools_sort/main.nf b/target/nextflow/samtools/samtools_sort/main.nf index 07562f31..5355dd3a 100644 --- a/target/nextflow/samtools/samtools_sort/main.nf +++ b/target/nextflow/samtools/samtools_sort/main.nf @@ -3225,9 +3225,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_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", diff --git a/target/nextflow/samtools/samtools_stats/.config.vsh.yaml b/target/nextflow/samtools/samtools_stats/.config.vsh.yaml index b4e83892..43ff922c 100644 --- a/target/nextflow/samtools/samtools_stats/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_stats/.config.vsh.yaml @@ -401,9 +401,9 @@ build_info: output: "target/nextflow/samtools/samtools_stats" executable: "target/nextflow/samtools/samtools_stats/main.nf" 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" diff --git a/target/nextflow/samtools/samtools_stats/main.nf b/target/nextflow/samtools/samtools_stats/main.nf index 3d8db615..b8fa1065 100644 --- a/target/nextflow/samtools/samtools_stats/main.nf +++ b/target/nextflow/samtools/samtools_stats/main.nf @@ -3295,9 +3295,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_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", diff --git a/target/nextflow/samtools/samtools_view/.config.vsh.yaml b/target/nextflow/samtools/samtools_view/.config.vsh.yaml index 211392a0..73bf77ca 100644 --- a/target/nextflow/samtools/samtools_view/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_view/.config.vsh.yaml @@ -665,9 +665,9 @@ build_info: output: "target/nextflow/samtools/samtools_view" executable: "target/nextflow/samtools/samtools_view/main.nf" 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" diff --git a/target/nextflow/samtools/samtools_view/main.nf b/target/nextflow/samtools/samtools_view/main.nf index e0f32bdc..8224a44c 100644 --- a/target/nextflow/samtools/samtools_view/main.nf +++ b/target/nextflow/samtools/samtools_view/main.nf @@ -3476,9 +3476,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_view", "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", diff --git a/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml b/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml index 30a6103b..fb6a77ea 100644 --- a/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml +++ b/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml @@ -173,9 +173,9 @@ build_info: output: "target/nextflow/seqtk/seqtk_sample" executable: "target/nextflow/seqtk/seqtk_sample/main.nf" 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" diff --git a/target/nextflow/seqtk/seqtk_sample/main.nf b/target/nextflow/seqtk/seqtk_sample/main.nf index 822b4131..01b0c2dc 100644 --- a/target/nextflow/seqtk/seqtk_sample/main.nf +++ b/target/nextflow/seqtk/seqtk_sample/main.nf @@ -3030,9 +3030,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/seqtk/seqtk_sample", "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", diff --git a/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml b/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml index d9196184..5b6cac3c 100644 --- a/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml +++ b/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml @@ -196,9 +196,9 @@ build_info: output: "target/nextflow/seqtk/seqtk_subseq" executable: "target/nextflow/seqtk/seqtk_subseq/main.nf" 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" diff --git a/target/nextflow/seqtk/seqtk_subseq/main.nf b/target/nextflow/seqtk/seqtk_subseq/main.nf index 79f6377f..9b903621 100644 --- a/target/nextflow/seqtk/seqtk_subseq/main.nf +++ b/target/nextflow/seqtk/seqtk_subseq/main.nf @@ -3060,9 +3060,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/seqtk/seqtk_subseq", "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", diff --git a/target/nextflow/snpeff/.config.vsh.yaml b/target/nextflow/snpeff/.config.vsh.yaml index f66226cb..7cc29048 100644 --- a/target/nextflow/snpeff/.config.vsh.yaml +++ b/target/nextflow/snpeff/.config.vsh.yaml @@ -628,9 +628,9 @@ build_info: output: "target/nextflow/snpeff" executable: "target/nextflow/snpeff/main.nf" 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" diff --git a/target/nextflow/snpeff/main.nf b/target/nextflow/snpeff/main.nf index c8a7fb42..3a78177a 100644 --- a/target/nextflow/snpeff/main.nf +++ b/target/nextflow/snpeff/main.nf @@ -3555,9 +3555,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/snpeff", "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", diff --git a/target/nextflow/sortmerna/.config.vsh.yaml b/target/nextflow/sortmerna/.config.vsh.yaml index cb8f61c3..89a75786 100644 --- a/target/nextflow/sortmerna/.config.vsh.yaml +++ b/target/nextflow/sortmerna/.config.vsh.yaml @@ -591,9 +591,9 @@ build_info: output: "target/nextflow/sortmerna" executable: "target/nextflow/sortmerna/main.nf" 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" diff --git a/target/nextflow/sortmerna/main.nf b/target/nextflow/sortmerna/main.nf index 33809318..af095f24 100644 --- a/target/nextflow/sortmerna/main.nf +++ b/target/nextflow/sortmerna/main.nf @@ -3456,9 +3456,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/sortmerna", "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", diff --git a/target/nextflow/star/star_align_reads/.config.vsh.yaml b/target/nextflow/star/star_align_reads/.config.vsh.yaml index 76e1411f..5dac6c12 100644 --- a/target/nextflow/star/star_align_reads/.config.vsh.yaml +++ b/target/nextflow/star/star_align_reads/.config.vsh.yaml @@ -2663,9 +2663,9 @@ build_info: output: "target/nextflow/star/star_align_reads" executable: "target/nextflow/star/star_align_reads/main.nf" 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" diff --git a/target/nextflow/star/star_align_reads/main.nf b/target/nextflow/star/star_align_reads/main.nf index 7b80abea..bfda8f22 100644 --- a/target/nextflow/star/star_align_reads/main.nf +++ b/target/nextflow/star/star_align_reads/main.nf @@ -5943,9 +5943,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/star/star_align_reads", "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", diff --git a/target/nextflow/star/star_genome_generate/.config.vsh.yaml b/target/nextflow/star/star_genome_generate/.config.vsh.yaml index 5047fd80..47b25204 100644 --- a/target/nextflow/star/star_genome_generate/.config.vsh.yaml +++ b/target/nextflow/star/star_genome_generate/.config.vsh.yaml @@ -333,9 +333,9 @@ build_info: output: "target/nextflow/star/star_genome_generate" executable: "target/nextflow/star/star_genome_generate/main.nf" 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" diff --git a/target/nextflow/star/star_genome_generate/main.nf b/target/nextflow/star/star_genome_generate/main.nf index 313240c2..07933cda 100644 --- a/target/nextflow/star/star_genome_generate/main.nf +++ b/target/nextflow/star/star_genome_generate/main.nf @@ -3195,9 +3195,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/star/star_genome_generate", "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", diff --git a/target/nextflow/trimgalore/.config.vsh.yaml b/target/nextflow/trimgalore/.config.vsh.yaml index 3183912e..e58a4070 100644 --- a/target/nextflow/trimgalore/.config.vsh.yaml +++ b/target/nextflow/trimgalore/.config.vsh.yaml @@ -770,9 +770,9 @@ build_info: output: "target/nextflow/trimgalore" executable: "target/nextflow/trimgalore/main.nf" 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" diff --git a/target/nextflow/trimgalore/main.nf b/target/nextflow/trimgalore/main.nf index a05d22e2..69d67589 100644 --- a/target/nextflow/trimgalore/main.nf +++ b/target/nextflow/trimgalore/main.nf @@ -3560,9 +3560,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/trimgalore", "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", diff --git a/target/nextflow/umi_tools/umi_tools_dedup/.config.vsh.yaml b/target/nextflow/umi_tools/umi_tools_dedup/.config.vsh.yaml index 4941dc3f..f421b88b 100644 --- a/target/nextflow/umi_tools/umi_tools_dedup/.config.vsh.yaml +++ b/target/nextflow/umi_tools/umi_tools_dedup/.config.vsh.yaml @@ -611,9 +611,9 @@ build_info: output: "target/nextflow/umi_tools/umi_tools_dedup" executable: "target/nextflow/umi_tools/umi_tools_dedup/main.nf" viash_version: "0.9.0" - 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" diff --git a/target/nextflow/umi_tools/umi_tools_dedup/main.nf b/target/nextflow/umi_tools/umi_tools_dedup/main.nf index 2ca61a0b..fce3cbc9 100644 --- a/target/nextflow/umi_tools/umi_tools_dedup/main.nf +++ b/target/nextflow/umi_tools/umi_tools_dedup/main.nf @@ -3487,9 +3487,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/umi_tools/umi_tools_dedup", "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", diff --git a/target/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml b/target/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml index 4a4a6397..6b26b479 100644 --- a/target/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml +++ b/target/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml @@ -449,9 +449,9 @@ build_info: output: "target/nextflow/umi_tools/umi_tools_extract" executable: "target/nextflow/umi_tools/umi_tools_extract/main.nf" viash_version: "0.9.0" - 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" diff --git a/target/nextflow/umi_tools/umi_tools_extract/main.nf b/target/nextflow/umi_tools/umi_tools_extract/main.nf index 2cccd244..48f436f3 100644 --- a/target/nextflow/umi_tools/umi_tools_extract/main.nf +++ b/target/nextflow/umi_tools/umi_tools_extract/main.nf @@ -3316,9 +3316,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/umi_tools/umi_tools_extract", "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", diff --git a/target/nextflow/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml b/target/nextflow/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml index e86d7b36..7674b2c6 100644 --- a/target/nextflow/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml +++ b/target/nextflow/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml @@ -256,9 +256,9 @@ build_info: output: "target/nextflow/umi_tools/umi_tools_prepareforrsem" executable: "target/nextflow/umi_tools/umi_tools_prepareforrsem/main.nf" 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" diff --git a/target/nextflow/umi_tools/umi_tools_prepareforrsem/main.nf b/target/nextflow/umi_tools/umi_tools_prepareforrsem/main.nf index 58d48b70..0937572e 100644 --- a/target/nextflow/umi_tools/umi_tools_prepareforrsem/main.nf +++ b/target/nextflow/umi_tools/umi_tools_prepareforrsem/main.nf @@ -3121,9 +3121,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/umi_tools/umi_tools_prepareforrsem", "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",