From db2f4203b81ca8f44af8541bf7ee50813893122e Mon Sep 17 00:00:00 2001 From: CI Date: Tue, 10 Sep 2024 14:11:21 +0000 Subject: [PATCH] Build branch main with version main (c3ba4a7) Build pipeline: viash-hub.biobox.main-n2mwd Source commit: https://github.com/viash-hub/biobox/commit/c3ba4a78497f7518725bb7d3e213b2a9bcee511e Source message: Bcftools annotate (#143) * Initial commit * Update config.vsh.yaml * changes in config file * Update script.sh * Help File * Update script.sh * Update test.sh * bug fixing and adding tests * Update test.sh * Update test.sh * adding 3rd test * More tests * Moreee tests * Update test.sh * small changes * Update CHANGELOG.md * Update config.vsh.yaml * bug fixing on config * Requested changes --------- Co-authored-by: Jakub Majercik <57993790+jakubmajercik@users.noreply.github.com> --- CHANGELOG.md | 2 +- .../bcftools_annotate/config.vsh.yaml | 250 ++ src/bcftools/bcftools_annotate/help.txt | 41 + src/bcftools/bcftools_annotate/script.sh | 54 + 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insertions(+), 276 deletions(-) create mode 100644 src/bcftools/bcftools_annotate/config.vsh.yaml create mode 100644 src/bcftools/bcftools_annotate/help.txt create mode 100644 src/bcftools/bcftools_annotate/script.sh create mode 100644 src/bcftools/bcftools_annotate/test.sh create mode 100644 target/executable/bcftools/bcftools_annotate/.config.vsh.yaml create mode 100755 target/executable/bcftools/bcftools_annotate/bcftools_annotate create mode 100644 target/nextflow/bcftools/bcftools_annotate/.config.vsh.yaml create mode 100644 target/nextflow/bcftools/bcftools_annotate/main.nf create mode 100644 target/nextflow/bcftools/bcftools_annotate/nextflow.config create mode 100644 target/nextflow/bcftools/bcftools_annotate/nextflow_schema.json diff --git a/CHANGELOG.md b/CHANGELOG.md index 2dd152bb..bb640d50 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -42,12 +42,12 @@ * `rsem/rsem_prepare_reference`: Prepare transcript references for RSEM (PR #89). * `bcftools`: + - `bcftools_annotate`: Add or remove annotations from a VCF/BCF file (PR #143). - `bcftools/bcftools_stats`: Parses VCF or BCF and produces a txt stats file which can be plotted using plot-vcfstats (PR #142). - `bcftools/bcftools_sort`: Sorts BCF/VCF files by position and other criteria (PR #141). * `fastqc`: High throughput sequence quality control analysis tool (PR #92). - ## MINOR CHANGES * `busco` components: update BUSCO to `5.7.1` (PR #72). diff --git a/src/bcftools/bcftools_annotate/config.vsh.yaml b/src/bcftools/bcftools_annotate/config.vsh.yaml new file mode 100644 index 00000000..67e8f46e --- /dev/null +++ b/src/bcftools/bcftools_annotate/config.vsh.yaml @@ -0,0 +1,250 @@ +name: bcftools_annotate +namespace: bcftools +description: | + Add or remove annotations from a VCF/BCF file. +keywords: [Annotate, VCF, BCF] +links: + homepage: https://samtools.github.io/bcftools/ + documentation: https://samtools.github.io/bcftools/bcftools.html#annotate + repository: https://github.com/samtools/bcftools + issue_tracker: https://github.com/samtools/bcftools/issues +references: + doi: https://doi.org/10.1093/gigascience/giab008 +license: MIT/Expat, GNU +requirements: + commands: [bcftools] +authors: + - __merge__: /src/_authors/theodoro_gasperin.yaml + roles: [author] + +argument_groups: + - name: Inputs + arguments: + - name: --input + alternatives: -i + type: file + multiple: true + description: Input VCF/BCF file. + required: true + + - name: Outputs + arguments: + - name: --output + alternatives: -o + direction: output + type: file + description: Output annotated file. + required: true + + - name: Options + description: | + For examples on how to use use bcftools annotate see http://samtools.github.io/bcftools/howtos/annotate.html. + For more details on the options see https://samtools.github.io/bcftools/bcftools.html#annotate. + arguments: + + - name: --annotations + alternatives: --a + type: file + description: | + VCF file or tabix-indexed FILE with annotations: CHR\tPOS[\tVALUE]+ . + + - name: --columns + alternatives: --c + type: string + description: | + List of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. + See man page for details. + + - name: --columns_file + alternatives: --C + type: file + description: | + Read -c columns from FILE, one name per row, with optional --merge_logic TYPE: NAME[ TYPE]. + + - name: --exclude + alternatives: --e + type: string + description: | + Exclude sites for which the expression is true. + See https://samtools.github.io/bcftools/bcftools.html#expressions for details. + example: 'QUAL >= 30 && DP >= 10' + + - name: --force + type: boolean_true + description: | + continue even when parsing errors, such as undefined tags, are encountered. + Note this can be an unsafe operation and can result in corrupted BCF files. + If this option is used, make sure to sanity check the result thoroughly. + + - name: --header_line + alternatives: --H + type: string + description: | + Header line which should be appended to the VCF header, can be given multiple times. + + - name: --header_lines + alternatives: --h + type: file + description: | + File with header lines to append to the VCF header. + For example: + ##INFO= + ##INFO= + + - name: --set_id + alternatives: --I + type: string + description: | + Set ID column using a `bcftools query`-like expression, see man page for details. + + - name: --include + type: string + description: | + Select sites for which the expression is true. + See https://samtools.github.io/bcftools/bcftools.html#expressions for details. + example: 'QUAL >= 30 && DP >= 10' + + - name: --keep_sites + alternatives: --k + type: boolean_true + description: | + Leave --include/--exclude sites unchanged instead of discarding them. + + - name: --merge_logic + alternatives: --l + type: string + choices: + description: | + When multiple regions overlap a single record, this option defines how to treat multiple annotation values. + See man page for more details. + + - name: --mark_sites + alternatives: --m + type: string + description: | + Annotate sites which are present ("+") or absent ("-") in the -a file with a new INFO/TAG flag. + + - name: --min_overlap + type: string + description: | + Minimum overlap required as a fraction of the variant in the annotation -a file (ANN), + in the target VCF file (:VCF), or both for reciprocal overlap (ANN:VCF). + By default overlaps of arbitrary length are sufficient. + The option can be used only with the tab-delimited annotation -a file and with BEG and END columns present. + + - name: --no_version + type: boolean_true + description: | + Do not append version and command line information to the output VCF header. + + - name: --output_type + alternatives: --O + type: string + choices: ['u', 'z', 'b', 'v'] + description: | + Output type: + u: uncompressed BCF + z: compressed VCF + b: compressed BCF + v: uncompressed VCF + + - name: --pair_logic + type: string + choices: ['snps', 'indels', 'both', 'all', 'some', 'exact'] + description: | + Controls how to match records from the annotation file to the target VCF. + Effective only when -a is a VCF or BCF file. + The option replaces the former uninuitive --collapse. + See Common Options for more. + + - name: --regions + alternatives: --r + type: string + description: | + Restrict to comma-separated list of regions. + Following formats are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​]. + example: '20:1000000-2000000' + + - name: --regions_file + alternatives: --R + type: file + description: | + Restrict to regions listed in a file. + Regions can be specified either on a VCF, BED, or tab-delimited file (the default). + For more information check manual. + + - name: --regions_overlap + type: string + choices: ['pos', 'record', 'variant', '0', '1', '2'] + description: | + This option controls how overlapping records are determined: + set to 'pos' or '0' if the VCF record has to have POS inside a region (this corresponds to the default behavior of -t/-T); + set to 'record' or '1' if also overlapping records with POS outside a region should be included (this is the default behavior of -r/-R, + and includes indels with POS at the end of a region, which are technically outside the region); + or set to 'variant' or '2' to include only true overlapping variation (compare the full VCF representation "TA>T-" vs the true sequence variation "A>-"). + + - name: --rename_annotations + type: file + description: | + Rename annotations: TYPE/old\tnew, where TYPE is one of FILTER,INFO,FORMAT. + + - name: --rename_chromosomes + type: file + description: | + Rename chromosomes according to the map in file, with "old_name new_name\n" pairs + separated by whitespaces, each on a separate line. + + - name: --samples + type: string + description: | + Subset of samples to annotate. + See also https://samtools.github.io/bcftools/bcftools.html#common_options. + + - name: --samples_file + type: file + description: | + Subset of samples to annotate in file format. + See also https://samtools.github.io/bcftools/bcftools.html#common_options. + + - name: --single_overlaps + type: boolean_true + description: | + Use this option to keep memory requirements low with very large annotation files. + Note, however, that this comes at a cost, only single overlapping intervals are considered in this mode. + This was the default mode until the commit af6f0c9 (Feb 24 2019). + + - name: --remove + alternatives: --x + type: string + description: | + List of annotations to remove. + Use "FILTER" to remove all filters or "FILTER/SomeFilter" to remove a specific filter. + Similarly, "INFO" can be used to remove all INFO tags and "FORMAT" to remove all FORMAT tags except GT. + To remove all INFO tags except "FOO" and "BAR", use "^INFO/FOO,INFO/BAR" (and similarly for FORMAT and FILTER). + "INFO" can be abbreviated to "INF" and "FORMAT" to "FMT". + +resources: + - type: bash_script + path: script.sh + +test_resources: + - type: bash_script + path: test.sh + +engines: + - type: docker + image: debian:stable-slim + setup: + - type: apt + packages: [bcftools, procps] + - type: docker + run: | + echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftools //p')\"" > /var/software_versions.txt + test_setup: + - type: apt + packages: [tabix] + +runners: + - type: executable + - type: nextflow + diff --git a/src/bcftools/bcftools_annotate/help.txt b/src/bcftools/bcftools_annotate/help.txt new file mode 100644 index 00000000..2d1c7807 --- /dev/null +++ b/src/bcftools/bcftools_annotate/help.txt @@ -0,0 +1,41 @@ +``` +bcftools annotate -h +``` + +annotate: option requires an argument -- 'h' + +About: Annotate and edit VCF/BCF files. +Usage: bcftools annotate [options] VCF + +Options: + -a, --annotations FILE VCF file or tabix-indexed FILE with annotations: CHR\tPOS[\tVALUE]+ + -c, --columns LIST List of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. See man page for details + -C, --columns-file FILE Read -c columns from FILE, one name per row, with optional --merge-logic TYPE: NAME[ TYPE] + -e, --exclude EXPR Exclude sites for which the expression is true (see man page for details) + --force Continue despite parsing error (at your own risk!) + -H, --header-line STR Header line which should be appended to the VCF header, can be given multiple times + -h, --header-lines FILE Lines which should be appended to the VCF header + -I, --set-id [+]FORMAT Set ID column using a `bcftools query`-like expression, see man page for details + -i, --include EXPR Select sites for which the expression is true (see man page for details) + -k, --keep-sites Leave -i/-e sites unchanged instead of discarding them + -l, --merge-logic TAG:TYPE Merge logic for multiple overlapping regions (see man page for details), EXPERIMENTAL + -m, --mark-sites [+-]TAG Add INFO/TAG flag to sites which are ("+") or are not ("-") listed in the -a file + --min-overlap ANN:VCF Required overlap as a fraction of variant in the -a file (ANN), the VCF (:VCF), or reciprocal (ANN:VCF) + --no-version Do not append version and command line to the header + -o, --output FILE Write output to a file [standard output] + -O, --output-type u|b|v|z[0-9] u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v] + --pair-logic STR Matching records by , see man page for details [some] + -r, --regions REGION Restrict to comma-separated list of regions + -R, --regions-file FILE Restrict to regions listed in FILE + --regions-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1] + --rename-annots FILE Rename annotations: TYPE/old\tnew, where TYPE is one of FILTER,INFO,FORMAT + --rename-chrs FILE Rename sequences according to the mapping: old\tnew + -s, --samples [^]LIST Comma separated list of samples to annotate (or exclude with "^" prefix) + -S, --samples-file [^]FILE File of samples to annotate (or exclude with "^" prefix) + --single-overlaps Keep memory low by avoiding complexities arising from handling multiple overlapping intervals + -x, --remove LIST List of annotations (e.g. ID,INFO/DP,FORMAT/DP,FILTER) to remove (or keep with "^" prefix). See man page for details + --threads INT Number of extra output compression threads [0] + +Examples: + http://samtools.github.io/bcftools/howtos/annotate.html + diff --git a/src/bcftools/bcftools_annotate/script.sh b/src/bcftools/bcftools_annotate/script.sh new file mode 100644 index 00000000..18137bbf --- /dev/null +++ b/src/bcftools/bcftools_annotate/script.sh @@ -0,0 +1,54 @@ +#!/bin/bash + +## VIASH START +## VIASH END + +# Exit on error +set -eo pipefail + +# Unset parameters +unset_if_false=( + par_force + par_keep_sites + par_no_version + par_single_overlaps +) + +for par in ${unset_if_false[@]}; do + test_val="${!par}" + [[ "$test_val" == "false" ]] && unset $par +done + +# Execute bcftools annotate with the provided arguments +bcftools annotate \ + ${par_annotations:+-a "$par_annotations"} \ + ${par_columns:+-c "$par_columns"} \ + ${par_columns_file:+-C "$par_columns_file"} \ + ${par_exclude:+-e "$par_exclude"} \ + ${par_force:+--force} \ + ${par_header_line:+-H "$par_header_line"} \ + ${par_header_lines:+-h "$par_header_lines"} \ + ${par_set_id:+-I "$par_set_id"} \ + ${par_include:+-i "$par_include"} \ + ${par_keep_sites:+-k} \ + ${par_merge_logic:+-l "$par_merge_logic"} \ + ${par_mark_sites:+-m "$par_mark_sites"} \ + ${par_min_overlap:+--min-overlap "$par_min_overlap"} \ + ${par_no_version:+--no-version} \ + ${par_samples_file:+-S "$par_samples_file"} \ + ${par_output_type:+-O "$par_output_type"} \ + ${par_pair_logic:+--pair-logic "$par_pair_logic"} \ + ${par_regions:+-r "$par_regions"} \ + ${par_regions_file:+-R "$par_regions_file"} \ + ${par_regions_overlap:+--regions-overlap "$par_regions_overlap"} \ + ${par_rename_annotations:+--rename-annots "$par_rename_annotations"} \ + ${par_rename_chromosomes:+--rename-chrs "$par_rename_chromosomes"} \ + ${par_samples:+-s "$par_samples"} \ + ${par_single_overlaps:+--single-overlaps} \ + ${par_threads:+--threads "$par_threads"} \ + ${par_remove:+-x "$par_remove"} \ + -o $par_output \ + $par_input + + + \ No newline at end of file diff --git a/src/bcftools/bcftools_annotate/test.sh b/src/bcftools/bcftools_annotate/test.sh new file mode 100644 index 00000000..39835c82 --- /dev/null +++ b/src/bcftools/bcftools_annotate/test.sh @@ -0,0 +1,305 @@ +#!/bin/bash + +## VIASH START +## VIASH END + +# Exit on error +set -eo pipefail + +#test_data="$meta_resources_dir/test_data" + +############################################# +# helper functions +assert_file_exists() { + [ -f "$1" ] || { echo "File '$1' does not exist" && exit 1; } +} +assert_file_not_empty() { + [ -s "$1" ] || { echo "File '$1' is empty but shouldn't be" && exit 1; } +} +assert_file_contains() { + grep -q "$2" "$1" || { echo "File '$1' does not contain '$2'" && exit 1; } +} +assert_identical_content() { + diff -a "$2" "$1" \ + || (echo "Files are not identical!" && exit 1) +} +############################################# + +# Create directories for tests +echo "Creating Test Data..." +TMPDIR=$(mktemp -d "$meta_temp_dir/XXXXXX") +function clean_up { + [[ -d "$TMPDIR" ]] && rm -r "$TMPDIR" +} +trap clean_up EXIT + +# Create test data +cat < "$TMPDIR/example.vcf" +##fileformat=VCFv4.1 +##contig= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE1 +1 752567 llama A C . . . . . +1 752722 . G A . . . . . +EOF + +bgzip -c $TMPDIR/example.vcf > $TMPDIR/example.vcf.gz +tabix -p vcf $TMPDIR/example.vcf.gz + +cat < "$TMPDIR/annots.tsv" +1 752567 752567 FooValue1 12345 +1 752722 752722 FooValue2 67890 +EOF + +cat < "$TMPDIR/rename.tsv" +INFO/. Luigi +EOF + +bgzip $TMPDIR/annots.tsv +tabix -s1 -b2 -e3 $TMPDIR/annots.tsv.gz + +cat < "$TMPDIR/header.hdr" +##FORMAT= +##INFO= +EOF + +cat < "$TMPDIR/rename_chrm.tsv" +1 chr1 +2 chr2 +EOF + +# Test 1: Remove ID annotations +mkdir "$TMPDIR/test1" && pushd "$TMPDIR/test1" > /dev/null + +echo "> Run bcftools_annotate remove annotations" +"$meta_executable" \ + --input "../example.vcf" \ + --output "annotated.vcf" \ + --remove "ID" \ + +# checks +assert_file_exists "annotated.vcf" +assert_file_not_empty "annotated.vcf" +assert_file_contains "annotated.vcf" "1 752567 . A C" +echo "- test1 succeeded -" + +popd > /dev/null + +# Test 2: Annotate with -a, -c and -h options +mkdir "$TMPDIR/test2" && pushd "$TMPDIR/test2" > /dev/null + +echo "> Run bcftools_annotate with -a, -c and -h options" +"$meta_executable" \ + --input "../example.vcf" \ + --output "annotated.vcf" \ + --annotations "../annots.tsv.gz" \ + --header_lines "../header.hdr" \ + --columns "CHROM,FROM,TO,FMT/FOO,BAR" \ + --mark_sites "BAR" \ + +# checks +assert_file_exists "annotated.vcf" +assert_file_not_empty "annotated.vcf" +assert_file_contains "annotated.vcf" $(echo -e "1\t752567\tllama\tA\tC\t.\t.\tBAR=12345\tFOO\tFooValue1") +echo "- test2 succeeded -" + +popd > /dev/null + +# Test 3: +mkdir "$TMPDIR/test3" && pushd "$TMPDIR/test3" > /dev/null + +echo "> Run bcftools_annotate with --set_id option" +"$meta_executable" \ + --input "../example.vcf" \ + --output "annotated.vcf" \ + --set_id "+'%CHROM\_%POS\_%REF\_%FIRST_ALT'" \ + +# checks +assert_file_exists "annotated.vcf" +assert_file_not_empty "annotated.vcf" +assert_file_contains "annotated.vcf" "'1_752722_G_A'" +echo "- test3 succeeded -" + +popd > /dev/null + +# Test 4: +mkdir "$TMPDIR/test4" && pushd "$TMPDIR/test4" > /dev/null + +echo "> Run bcftools_annotate with --rename-annotations option" +"$meta_executable" \ + --input "../example.vcf" \ + --output "annotated.vcf" \ + --rename_annotations "../rename.tsv" + +# checks +assert_file_exists "annotated.vcf" +assert_file_not_empty "annotated.vcf" +assert_file_contains "annotated.vcf" "##bcftools_annotateCommand=annotate --rename-annots ../rename.tsv -o annotated.vcf" +echo "- test4 succeeded -" + +popd > /dev/null + +# Test 5: Rename chromosomes +mkdir "$TMPDIR/test5" && pushd "$TMPDIR/test5" > /dev/null + +echo "> Run bcftools_annotate with --rename-chromosomes option" +"$meta_executable" \ + --input "../example.vcf" \ + --output "annotated.vcf" \ + --rename_chromosomes "../rename_chrm.tsv" + +# checks +assert_file_exists "annotated.vcf" +assert_file_not_empty "annotated.vcf" +assert_file_contains "annotated.vcf" "chr1" +echo "- test5 succeeded -" + +popd > /dev/null + +# Test 6: Sample option +mkdir "$TMPDIR/test6" && pushd "$TMPDIR/test6" > /dev/null + +echo "> Run bcftools_annotate with -s option" +"$meta_executable" \ + --input "../example.vcf" \ + --output "annotated.vcf" \ + --samples "SAMPLE1" + +# checks +assert_file_exists "annotated.vcf" +assert_file_not_empty "annotated.vcf" +assert_file_contains "annotated.vcf" "##bcftools_annotateCommand=annotate -s SAMPLE1 -o annotated.vcf ../example.vcf" +echo "- test6 succeeded -" + +popd > /dev/null + +# Test 7: Single overlaps +mkdir "$TMPDIR/test7" && pushd "$TMPDIR/test7" > /dev/null + +echo "> Run bcftools_annotate with --single-overlaps option" +"$meta_executable" \ + --input "../example.vcf" \ + --output "annotated.vcf" \ + --single_overlaps \ + --keep_sites \ + +# checks +assert_file_exists "annotated.vcf" +assert_file_not_empty "annotated.vcf" +assert_file_contains "annotated.vcf" "annotate -k --single-overlaps -o annotated.vcf ../example.vcf" +echo "- test7 succeeded -" + +popd > /dev/null + +# Test 8: Min overlap +mkdir "$TMPDIR/test8" && pushd "$TMPDIR/test8" > /dev/null + +echo "> Run bcftools_annotate with --min-overlap option" +"$meta_executable" \ + --input "../example.vcf" \ + --output "annotated.vcf" \ + --annotations "../annots.tsv.gz" \ + --columns "CHROM,FROM,TO,FMT/FOO,BAR" \ + --header_lines "../header.hdr" \ + --min_overlap "1" + +# checks +assert_file_exists "annotated.vcf" +assert_file_not_empty "annotated.vcf" +assert_file_contains "annotated.vcf" "annotate -a ../annots.tsv.gz -c CHROM,FROM,TO,FMT/FOO,BAR -h ../header.hdr --min-overlap 1 -o annotated.vcf ../example.vcf" +echo "- test8 succeeded -" + +popd > /dev/null + +# Test 9: Regions +mkdir "$TMPDIR/test9" && pushd "$TMPDIR/test9" > /dev/null + +echo "> Run bcftools_annotate with -r option" +"$meta_executable" \ + --input "../example.vcf.gz" \ + --output "annotated.vcf" \ + --regions "1:752567-752722" + +# checks +assert_file_exists "annotated.vcf" +assert_file_not_empty "annotated.vcf" +assert_file_contains "annotated.vcf" "annotate -r 1:752567-752722 -o annotated.vcf ../example.vcf.gz" +echo "- test9 succeeded -" + +popd > /dev/null + +# Test 10: pair-logic +mkdir "$TMPDIR/test10" && pushd "$TMPDIR/test10" > /dev/null + +echo "> Run bcftools_annotate with --pair-logic option" +"$meta_executable" \ + --input "../example.vcf" \ + --output "annotated.vcf" \ + --pair_logic "all" + +# checks +assert_file_exists "annotated.vcf" +assert_file_not_empty "annotated.vcf" +assert_file_contains "annotated.vcf" "annotate --pair-logic all -o annotated.vcf ../example.vcf" +echo "- test10 succeeded -" + +popd > /dev/null + +# Test 11: regions-overlap +mkdir "$TMPDIR/test11" && pushd "$TMPDIR/test11" > /dev/null + +echo "> Run bcftools_annotate with --regions-overlap option" +"$meta_executable" \ + --input "../example.vcf" \ + --output "annotated.vcf" \ + --regions_overlap "1" + +# checks +assert_file_exists "annotated.vcf" +assert_file_not_empty "annotated.vcf" +assert_file_contains "annotated.vcf" "annotate --regions-overlap 1 -o annotated.vcf ../example.vcf" +echo "- test11 succeeded -" + +popd > /dev/null + +# Test 12: include +mkdir "$TMPDIR/test12" && pushd "$TMPDIR/test12" > /dev/null + +echo "> Run bcftools_annotate with -i option" +"$meta_executable" \ + --input "../example.vcf" \ + --output "annotated.vcf" \ + --include "FILTER='PASS'" \ + +# checks +assert_file_exists "annotated.vcf" +assert_file_not_empty "annotated.vcf" +assert_file_contains "annotated.vcf" "annotate -i FILTER='PASS' -o annotated.vcf ../example.vcf" +echo "- test12 succeeded -" + +popd > /dev/null + +# Test 13: exclude +mkdir "$TMPDIR/test13" && pushd "$TMPDIR/test13" > /dev/null + +echo "> Run bcftools_annotate with -e option" +"$meta_executable" \ + --annotations "../annots.tsv.gz" \ + --input "../example.vcf" \ + --output "annotated.vcf" \ + --exclude "FILTER='PASS'" \ + --header_lines "../header.hdr" \ + --columns "CHROM,FROM,TO,FMT/FOO,BAR" \ + --merge_logic "FOO:first" \ + +# checks +assert_file_exists "annotated.vcf" +assert_file_not_empty "annotated.vcf" +assert_file_contains "annotated.vcf" "annotate -a ../annots.tsv.gz -c CHROM,FROM,TO,FMT/FOO,BAR -e FILTER='PASS' -h ../header.hdr -l FOO:first -o annotated.vcf ../example.vcf" +echo "- test13 succeeded -" + +popd > /dev/null + + +echo "---- All tests succeeded! ----" +exit 0 + diff --git a/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml b/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml index b5c9c010..0f432b52 100644 --- a/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml +++ b/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml @@ -235,7 +235,7 @@ build_info: output: "target/executable/agat/agat_convert_bed2gff" executable: "target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff b/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff index 146a65df..59f6ea69 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="2024-09-10T13:55:49Z" +LABEL org.opencontainers.image.created="2024-09-10T13:57:09Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" 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 f1853d8d..bce29f7f 100644 --- a/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml +++ b/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml @@ -225,7 +225,7 @@ build_info: output: "target/executable/agat/agat_convert_embl2gff" executable: "target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff b/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff index 426fe661..947172a5 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="2024-09-10T13:55:49Z" +LABEL org.opencontainers.image.created="2024-09-10T13:57:09Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" 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 07da2c28..e8ca3f5d 100644 --- a/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml +++ b/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml @@ -228,7 +228,7 @@ build_info: output: "target/executable/agat/agat_convert_sp_gff2gtf" executable: "target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf b/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf index dc5f2994..fc88d699 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="2024-09-10T13:55:50Z" +LABEL org.opencontainers.image.created="2024-09-10T13:57:09Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" 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 362aadbe..a6715948 100644 --- a/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml +++ b/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml @@ -188,7 +188,7 @@ build_info: output: "target/executable/agat/agat_convert_sp_gff2tsv" executable: "target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv b/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv index e4b8739e..7bd8fa5a 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="2024-09-10T13:55:49Z" +LABEL org.opencontainers.image.created="2024-09-10T13:57:08Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" 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 2fafb70b..3e2bf612 100644 --- a/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml +++ b/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml @@ -195,7 +195,7 @@ build_info: output: "target/executable/agat/agat_convert_sp_gxf2gxf" executable: "target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf b/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf index 295ed3ad..43c5c42e 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="2024-09-10T13:55:48Z" +LABEL org.opencontainers.image.created="2024-09-10T13:57:08Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/arriba/.config.vsh.yaml b/target/executable/arriba/.config.vsh.yaml index fc6d156b..54b226f4 100644 --- a/target/executable/arriba/.config.vsh.yaml +++ b/target/executable/arriba/.config.vsh.yaml @@ -706,7 +706,7 @@ build_info: output: "target/executable/arriba" executable: "target/executable/arriba/arriba" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/arriba/arriba b/target/executable/arriba/arriba index 27f2397d..26b99f0e 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="2024-09-10T13:55:51Z" +LABEL org.opencontainers.image.created="2024-09-10T13:57:11Z" LABEL org.opencontainers.image.source="https://github.com/suhrig/arriba" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bcftools/bcftools_annotate/.config.vsh.yaml b/target/executable/bcftools/bcftools_annotate/.config.vsh.yaml new file mode 100644 index 00000000..70d4d712 --- /dev/null +++ b/target/executable/bcftools/bcftools_annotate/.config.vsh.yaml @@ -0,0 +1,495 @@ +name: "bcftools_annotate" +namespace: "bcftools" +version: "main" +authors: +- name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatician" +argument_groups: +- name: "Inputs" + arguments: + - type: "file" + name: "--input" + alternatives: + - "-i" + description: "Input VCF/BCF file." + info: null + must_exist: true + create_parent: true + required: true + direction: "input" + multiple: true + multiple_sep: ";" +- name: "Outputs" + arguments: + - type: "file" + name: "--output" + alternatives: + - "-o" + description: "Output annotated file." + info: null + must_exist: true + create_parent: true + required: true + direction: "output" + multiple: false + multiple_sep: ";" +- name: "Options" + description: "For examples on how to use use bcftools annotate see http://samtools.github.io/bcftools/howtos/annotate.html.\n\ + For more details on the options see https://samtools.github.io/bcftools/bcftools.html#annotate.\n" + arguments: + - type: "file" + name: "--annotations" + alternatives: + - "--a" + description: "VCF file or tabix-indexed FILE with annotations: CHR\\tPOS[\\tVALUE]+\ + \ . \n" + info: null + must_exist: true + create_parent: true + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "string" + name: "--columns" + alternatives: + - "--c" + description: "List of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG.\ + \ \nSee man page for details.\n" + info: null + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "file" + name: "--columns_file" + alternatives: + - "--C" + description: "Read -c columns from FILE, one name per row, with optional --merge_logic\ + \ TYPE: NAME[ TYPE].\n" + info: null + must_exist: true + create_parent: true + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "string" + name: "--exclude" + alternatives: + - "--e" + description: "Exclude sites for which the expression is true.\nSee https://samtools.github.io/bcftools/bcftools.html#expressions\ + \ for details.\n" + info: null + example: + - "QUAL >= 30 && DP >= 10" + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "boolean_true" + name: "--force" + description: "continue even when parsing errors, such as undefined tags, are encountered.\ + \ \nNote this can be an unsafe operation and can result in corrupted BCF files.\ + \ \nIf this option is used, make sure to sanity check the result thoroughly.\n" + info: null + direction: "input" + - type: "string" + name: "--header_line" + alternatives: + - "--H" + description: "Header line which should be appended to the VCF header, can be given\ + \ multiple times.\n" + info: null + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "file" + name: "--header_lines" + alternatives: + - "--h" + description: "File with header lines to append to the VCF header.\nFor example:\n\ + \ ##INFO=\n ##INFO=\n" + info: null + must_exist: true + create_parent: true + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "string" + name: "--set_id" + alternatives: + - "--I" + description: "Set ID column using a `bcftools query`-like expression, see man\ + \ page for details.\n" + info: null + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "string" + name: "--include" + description: "Select sites for which the expression is true.\nSee https://samtools.github.io/bcftools/bcftools.html#expressions\ + \ for details.\n" + info: null + example: + - "QUAL >= 30 && DP >= 10" + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "boolean_true" + name: "--keep_sites" + alternatives: + - "--k" + description: "Leave --include/--exclude sites unchanged instead of discarding\ + \ them.\n" + info: null + direction: "input" + - type: "string" + name: "--merge_logic" + alternatives: + - "--l" + description: "When multiple regions overlap a single record, this option defines\ + \ how to treat multiple annotation values.\nSee man page for more details.\n" + info: null + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "string" + name: "--mark_sites" + alternatives: + - "--m" + description: "Annotate sites which are present (\"+\") or absent (\"-\") in the\ + \ -a file with a new INFO/TAG flag.\n" + info: null + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "string" + name: "--min_overlap" + description: "Minimum overlap required as a fraction of the variant in the annotation\ + \ -a file (ANN), \nin the target VCF file (:VCF), or both for reciprocal overlap\ + \ (ANN:VCF). \nBy default overlaps of arbitrary length are sufficient. \nThe\ + \ option can be used only with the tab-delimited annotation -a file and with\ + \ BEG and END columns present.\n" + info: null + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "boolean_true" + name: "--no_version" + description: "Do not append version and command line information to the output\ + \ VCF header.\n" + info: null + direction: "input" + - type: "string" + name: "--output_type" + alternatives: + - "--O" + description: "Output type:\n u: uncompressed BCF\n z: compressed VCF\n b: compressed\ + \ BCF\n v: uncompressed VCF\n" + info: null + required: false + choices: + - "u" + - "z" + - "b" + - "v" + direction: "input" + multiple: false + multiple_sep: ";" + - type: "string" + name: "--pair_logic" + description: "Controls how to match records from the annotation file to the target\ + \ VCF. \nEffective only when -a is a VCF or BCF file. \nThe option replaces\ + \ the former uninuitive --collapse. \nSee Common Options for more.\n" + info: null + required: false + choices: + - "snps" + - "indels" + - "both" + - "all" + - "some" + - "exact" + direction: "input" + multiple: false + multiple_sep: ";" + - type: "string" + name: "--regions" + alternatives: + - "--r" + description: "Restrict to comma-separated list of regions. \nFollowing formats\ + \ are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​].\n" + info: null + example: + - "20:1000000-2000000" + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "file" + name: "--regions_file" + alternatives: + - "--R" + description: "Restrict to regions listed in a file. \nRegions can be specified\ + \ either on a VCF, BED, or tab-delimited file (the default). \nFor more information\ + \ check manual.\n" + info: null + must_exist: true + create_parent: true + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "string" + name: "--regions_overlap" + description: "This option controls how overlapping records are determined: \n\ + set to 'pos' or '0' if the VCF record has to have POS inside a region (this\ + \ corresponds to the default behavior of -t/-T); \nset to 'record' or '1' if\ + \ also overlapping records with POS outside a region should be included (this\ + \ is the default behavior of -r/-R, \nand includes indels with POS at the end\ + \ of a region, which are technically outside the region); \nor set to 'variant'\ + \ or '2' to include only true overlapping variation (compare the full VCF representation\ + \ \"TA>T-\" vs the true sequence variation \"A>-\").\n" + info: null + required: false + choices: + - "pos" + - "record" + - "variant" + - "0" + - "1" + - "2" + direction: "input" + multiple: false + multiple_sep: ";" + - type: "file" + name: "--rename_annotations" + description: "Rename annotations: TYPE/old\\tnew, where TYPE is one of FILTER,INFO,FORMAT.\n" + info: null + must_exist: true + create_parent: true + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "file" + name: "--rename_chromosomes" + description: "Rename chromosomes according to the map in file, with \"old_name\ + \ new_name\\n\" pairs \nseparated by whitespaces, each on a separate line.\n" + info: null + must_exist: true + create_parent: true + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "string" + name: "--samples" + description: "Subset of samples to annotate.\nSee also https://samtools.github.io/bcftools/bcftools.html#common_options.\n" + info: null + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "file" + name: "--samples_file" + description: "Subset of samples to annotate in file format.\nSee also https://samtools.github.io/bcftools/bcftools.html#common_options.\n" + info: null + must_exist: true + create_parent: true + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "boolean_true" + name: "--single_overlaps" + description: "Use this option to keep memory requirements low with very large\ + \ annotation files. \nNote, however, that this comes at a cost, only single\ + \ overlapping intervals are considered in this mode. \nThis was the default\ + \ mode until the commit af6f0c9 (Feb 24 2019).\n" + info: null + direction: "input" + - type: "string" + name: "--remove" + alternatives: + - "--x" + description: "List of annotations to remove. \nUse \"FILTER\" to remove all filters\ + \ or \"FILTER/SomeFilter\" to remove a specific filter. \nSimilarly, \"INFO\"\ + \ can be used to remove all INFO tags and \"FORMAT\" to remove all FORMAT tags\ + \ except GT. \nTo remove all INFO tags except \"FOO\" and \"BAR\", use \"^INFO/FOO,INFO/BAR\"\ + \ (and similarly for FORMAT and FILTER). \n\"INFO\" can be abbreviated to \"\ + INF\" and \"FORMAT\" to \"FMT\".\n" + info: null + required: false + direction: "input" + multiple: false + multiple_sep: ";" +resources: +- type: "bash_script" + path: "script.sh" + is_executable: true +description: "Add or remove annotations from a VCF/BCF file.\n" +test_resources: +- type: "bash_script" + path: "test.sh" + is_executable: true +info: null +status: "enabled" +requirements: + commands: + - "ps" +keywords: +- "Annotate" +- "VCF" +- "BCF" +license: "MIT/Expat, GNU" +references: + doi: + - "https://doi.org/10.1093/gigascience/giab008" +links: + repository: "https://github.com/samtools/bcftools" + homepage: "https://samtools.github.io/bcftools/" + documentation: "https://samtools.github.io/bcftools/bcftools.html#annotate" + issue_tracker: "https://github.com/samtools/bcftools/issues" +runners: +- type: "executable" + id: "executable" + docker_setup_strategy: "ifneedbepullelsecachedbuild" +- type: "nextflow" + id: "nextflow" + directives: + tag: "$id" + auto: + simplifyInput: true + simplifyOutput: false + transcript: false + publish: false + config: + labels: + mem1gb: "memory = 1000000000.B" + mem2gb: "memory = 2000000000.B" + mem5gb: "memory = 5000000000.B" + mem10gb: "memory = 10000000000.B" + mem20gb: "memory = 20000000000.B" + mem50gb: "memory = 50000000000.B" + mem100gb: "memory = 100000000000.B" + mem200gb: "memory = 200000000000.B" + mem500gb: "memory = 500000000000.B" + mem1tb: "memory = 1000000000000.B" + mem2tb: "memory = 2000000000000.B" + mem5tb: "memory = 5000000000000.B" + mem10tb: "memory = 10000000000000.B" + mem20tb: "memory = 20000000000000.B" + mem50tb: "memory = 50000000000000.B" + mem100tb: "memory = 100000000000000.B" + mem200tb: "memory = 200000000000000.B" + mem500tb: "memory = 500000000000000.B" + mem1gib: "memory = 1073741824.B" + mem2gib: "memory = 2147483648.B" + mem4gib: "memory = 4294967296.B" + mem8gib: "memory = 8589934592.B" + mem16gib: "memory = 17179869184.B" + mem32gib: "memory = 34359738368.B" + mem64gib: "memory = 68719476736.B" + mem128gib: "memory = 137438953472.B" + mem256gib: "memory = 274877906944.B" + mem512gib: "memory = 549755813888.B" + mem1tib: "memory = 1099511627776.B" + mem2tib: "memory = 2199023255552.B" + mem4tib: "memory = 4398046511104.B" + mem8tib: "memory = 8796093022208.B" + mem16tib: "memory = 17592186044416.B" + mem32tib: "memory = 35184372088832.B" + mem64tib: "memory = 70368744177664.B" + mem128tib: "memory = 140737488355328.B" + mem256tib: "memory = 281474976710656.B" + mem512tib: "memory = 562949953421312.B" + cpu1: "cpus = 1" + cpu2: "cpus = 2" + cpu5: "cpus = 5" + cpu10: "cpus = 10" + cpu20: "cpus = 20" + cpu50: "cpus = 50" + cpu100: "cpus = 100" + cpu200: "cpus = 200" + cpu500: "cpus = 500" + cpu1000: "cpus = 1000" + debug: false + container: "docker" +engines: +- type: "docker" + id: "docker" + image: "debian:stable-slim" + target_registry: "images.viash-hub.com" + target_tag: "main" + namespace_separator: "/" + setup: + - type: "apt" + packages: + - "bcftools" + - "procps" + interactive: false + - type: "docker" + run: + - "echo \"bcftools: \\\"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftools\ + \ //p')\\\"\" > /var/software_versions.txt\n" + test_setup: + - type: "apt" + packages: + - "tabix" + interactive: false + entrypoint: [] + cmd: null +- type: "native" + id: "native" +build_info: + config: "src/bcftools/bcftools_annotate/config.vsh.yaml" + runner: "executable" + engine: "docker|native" + output: "target/executable/bcftools/bcftools_annotate" + executable: "target/executable/bcftools/bcftools_annotate/bcftools_annotate" + viash_version: "0.9.0-RC7" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" + git_remote: "https://github.com/viash-hub/biobox" +package_config: + name: "biobox" + version: "main" + description: "A collection of bioinformatics tools for working with sequence data.\n" + info: null + viash_version: "0.9.0-RC7" + source: "src" + target: "target" + config_mods: + - ".requirements.commands := ['ps']\n" + - ".engines += { type: \"native\" }" + - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" + - ".engines[.type == 'docker'].target_tag := 'main'" + keywords: + - "bioinformatics" + - "modules" + - "sequencing" + license: "MIT" + organization: "vsh" + links: + repository: "https://github.com/viash-hub/biobox" + issue_tracker: "https://github.com/viash-hub/biobox/issues" diff --git a/target/executable/bcftools/bcftools_annotate/bcftools_annotate b/target/executable/bcftools/bcftools_annotate/bcftools_annotate new file mode 100755 index 00000000..79ad7e6a --- /dev/null +++ b/target/executable/bcftools/bcftools_annotate/bcftools_annotate @@ -0,0 +1,1866 @@ +#!/usr/bin/env bash + +# bcftools_annotate main +# +# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a +# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from +# Data Intuitive. +# +# The component may contain files which fall under a different license. The +# authors of this component should specify the license in the header of such +# files, or include a separate license file detailing the licenses of all included +# files. +# +# Component authors: +# * Theodoro Gasperin Terra Camargo (author) + +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 $VIASH_META_RESOURCES_DIR` + +# define meta fields +VIASH_META_NAME="bcftools_annotate" +VIASH_META_FUNCTIONALITY_NAME="bcftools_annotate" +VIASH_META_EXECUTABLE="$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 "bcftools_annotate main" + echo "" + echo "Add or remove annotations from a VCF/BCF file." + echo "" + echo "Inputs:" + echo " -i, --input" + echo " type: file, required parameter, multiple values allowed, file must exist" + echo " Input VCF/BCF file." + echo "" + echo "Outputs:" + echo " -o, --output" + echo " type: file, required parameter, output, file must exist" + echo " Output annotated file." + echo "" + echo "Options:" + echo " For examples on how to use use bcftools annotate see" + echo " http://samtools.github.io/bcftools/howtos/annotate.html." + echo " For more details on the options see" + echo " https://samtools.github.io/bcftools/bcftools.html#annotate." + echo "" + echo " --a, --annotations" + echo " type: file, file must exist" + echo " VCF file or tabix-indexed FILE with annotations: CHR\\tPOS[\\tVALUE]+ ." + echo "" + echo " --c, --columns" + echo " type: string" + echo " List of columns in the annotation file, e.g." + echo " CHROM,POS,REF,ALT,-,INFO/TAG." + echo " See man page for details." + echo "" + echo " --C, --columns_file" + echo " type: file, file must exist" + echo " Read -c columns from FILE, one name per row, with optional --merge_logic" + echo " TYPE: NAME[ TYPE]." + echo "" + echo " --e, --exclude" + echo " type: string" + echo " example: QUAL >= 30 && DP >= 10" + echo " Exclude sites for which the expression is true." + echo " See https://samtools.github.io/bcftools/bcftools.html#expressions for" + echo " details." + echo "" + echo " --force" + echo " type: boolean_true" + echo " continue even when parsing errors, such as undefined tags, are" + echo " encountered." + echo " Note this can be an unsafe operation and can result in corrupted BCF" + echo " files." + echo " If this option is used, make sure to sanity check the result thoroughly." + echo "" + echo " --H, --header_line" + echo " type: string" + echo " Header line which should be appended to the VCF header, can be given" + echo " multiple times." + echo "" + echo " --h, --header_lines" + echo " type: file, file must exist" + echo " File with header lines to append to the VCF header." + echo " For example:" + echo " ##INFO=" + echo " ##INFO=" + echo "" + echo " --I, --set_id" + echo " type: string" + echo " Set ID column using a \`bcftools query\`-like expression, see man page for" + echo " details." + echo "" + echo " --include" + echo " type: string" + echo " example: QUAL >= 30 && DP >= 10" + echo " Select sites for which the expression is true." + echo " See https://samtools.github.io/bcftools/bcftools.html#expressions for" + echo " details." + echo "" + echo " --k, --keep_sites" + echo " type: boolean_true" + echo " Leave --include/--exclude sites unchanged instead of discarding them." + echo "" + echo " --l, --merge_logic" + echo " type: string" + echo " When multiple regions overlap a single record, this option defines how" + echo " to treat multiple annotation values." + echo " See man page for more details." + echo "" + echo " --m, --mark_sites" + echo " type: string" + echo " Annotate sites which are present (\"+\") or absent (\"-\") in the -a file" + echo " with a new INFO/TAG flag." + echo "" + echo " --min_overlap" + echo " type: string" + echo " Minimum overlap required as a fraction of the variant in the annotation" + echo " -a file (ANN)," + echo " in the target VCF file (:VCF), or both for reciprocal overlap (ANN:VCF)." + echo " By default overlaps of arbitrary length are sufficient." + echo " The option can be used only with the tab-delimited annotation -a file" + echo " and with BEG and END columns present." + echo "" + echo " --no_version" + echo " type: boolean_true" + echo " Do not append version and command line information to the output VCF" + echo " header." + echo "" + echo " --O, --output_type" + echo " type: string" + echo " choices: [ u, z, b, v ]" + echo " Output type:" + echo " u: uncompressed BCF" + echo " z: compressed VCF" + echo " b: compressed BCF" + echo " v: uncompressed VCF" + echo "" + echo " --pair_logic" + echo " type: string" + echo " choices: [ snps, indels, both, all, some, exact ]" + echo " Controls how to match records from the annotation file to the target" + echo " VCF." + echo " Effective only when -a is a VCF or BCF file." + echo " The option replaces the former uninuitive --collapse." + echo " See Common Options for more." + echo "" + echo " --r, --regions" + echo " type: string" + echo " example: 20:1000000-2000000" + echo " Restrict to comma-separated list of regions." + echo " Following formats are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​]." + echo "" + echo " --R, --regions_file" + echo " type: file, file must exist" + echo " Restrict to regions listed in a file." + echo " Regions can be specified either on a VCF, BED, or tab-delimited file" + echo " (the default)." + echo " For more information check manual." + echo "" + echo " --regions_overlap" + echo " type: string" + echo " choices: [ pos, record, variant, 0, 1, 2 ]" + echo " This option controls how overlapping records are determined:" + echo " set to 'pos' or '0' if the VCF record has to have POS inside a region" + echo " (this corresponds to the default behavior of -t/-T);" + echo " set to 'record' or '1' if also overlapping records with POS outside a" + echo " region should be included (this is the default behavior of -r/-R," + echo " and includes indels with POS at the end of a region, which are" + echo " technically outside the region);" + echo " or set to 'variant' or '2' to include only true overlapping variation" + echo " (compare the full VCF representation \"TA>T-\" vs the true sequence" + echo " variation \"A>-\")." + echo "" + echo " --rename_annotations" + echo " type: file, file must exist" + echo " Rename annotations: TYPE/old\\tnew, where TYPE is one of" + echo " FILTER,INFO,FORMAT." + echo "" + echo " --rename_chromosomes" + echo " type: file, file must exist" + echo " Rename chromosomes according to the map in file, with \"old_name" + echo " new_name\\n\" pairs" + echo " separated by whitespaces, each on a separate line." + echo "" + echo " --samples" + echo " type: string" + echo " Subset of samples to annotate." + echo " See also" + echo " https://samtools.github.io/bcftools/bcftools.html#common_options." + echo "" + echo " --samples_file" + echo " type: file, file must exist" + echo " Subset of samples to annotate in file format." + echo " See also" + echo " https://samtools.github.io/bcftools/bcftools.html#common_options." + echo "" + echo " --single_overlaps" + echo " type: boolean_true" + echo " Use this option to keep memory requirements low with very large" + echo " annotation files." + echo " Note, however, that this comes at a cost, only single overlapping" + echo " intervals are considered in this mode." + echo " This was the default mode until the commit af6f0c9 (Feb 24 2019)." + echo "" + echo " --x, --remove" + echo " type: string" + echo " List of annotations to remove." + echo " Use \"FILTER\" to remove all filters or \"FILTER/SomeFilter\" to remove a" + echo " specific filter." + echo " Similarly, \"INFO\" can be used to remove all INFO tags and \"FORMAT\" to" + echo " remove all FORMAT tags except GT." + echo " To remove all INFO tags except \"FOO\" and \"BAR\", use \"^INFO/FOO,INFO/BAR\"" + echo " (and similarly for FORMAT and FILTER)." + echo " \"INFO\" can be abbreviated to \"INF\" and \"FORMAT\" to \"FMT\"." +} + +# 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 debian:stable-slim +ENTRYPOINT [] +RUN apt-get update && \ + DEBIAN_FRONTEND=noninteractive apt-get install -y bcftools procps && \ + rm -rf /var/lib/apt/lists/* + +RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftools //p')\"" > /var/software_versions.txt + +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="2024-09-10T13:57:04Z" +LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" +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 "$1")" + shift 1 + ;; + --version) + echo "bcftools_annotate main" + exit + ;; + --input) + if [ -z "$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 "$1") + fi + shift 1 + ;; + -i) + if [ -z "$VIASH_PAR_INPUT" ]; then + VIASH_PAR_INPUT="$2" + else + VIASH_PAR_INPUT="$VIASH_PAR_INPUT;""$2" + fi + [ $# -lt 2 ] && ViashError Not enough arguments passed to -i. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --output) + [ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'--output\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_OUTPUT="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --output. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --output=*) + [ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'--output=*\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_OUTPUT=$(ViashRemoveFlags "$1") + shift 1 + ;; + -o) + [ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'-o\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_OUTPUT="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to -o. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --annotations) + [ -n "$VIASH_PAR_ANNOTATIONS" ] && ViashError Bad arguments for option \'--annotations\': \'$VIASH_PAR_ANNOTATIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_ANNOTATIONS="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --annotations. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --annotations=*) + [ -n "$VIASH_PAR_ANNOTATIONS" ] && ViashError Bad arguments for option \'--annotations=*\': \'$VIASH_PAR_ANNOTATIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_ANNOTATIONS=$(ViashRemoveFlags "$1") + shift 1 + ;; + --a) + [ -n "$VIASH_PAR_ANNOTATIONS" ] && ViashError Bad arguments for option \'--a\': \'$VIASH_PAR_ANNOTATIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_ANNOTATIONS="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --a. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --columns) + [ -n "$VIASH_PAR_COLUMNS" ] && ViashError Bad arguments for option \'--columns\': \'$VIASH_PAR_COLUMNS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_COLUMNS="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --columns. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --columns=*) + [ -n "$VIASH_PAR_COLUMNS" ] && ViashError Bad arguments for option \'--columns=*\': \'$VIASH_PAR_COLUMNS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_COLUMNS=$(ViashRemoveFlags "$1") + shift 1 + ;; + --c) + [ -n "$VIASH_PAR_COLUMNS" ] && ViashError Bad arguments for option \'--c\': \'$VIASH_PAR_COLUMNS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_COLUMNS="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --c. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --columns_file) + [ -n "$VIASH_PAR_COLUMNS_FILE" ] && ViashError Bad arguments for option \'--columns_file\': \'$VIASH_PAR_COLUMNS_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_COLUMNS_FILE="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --columns_file. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --columns_file=*) + [ -n "$VIASH_PAR_COLUMNS_FILE" ] && ViashError Bad arguments for option \'--columns_file=*\': \'$VIASH_PAR_COLUMNS_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_COLUMNS_FILE=$(ViashRemoveFlags "$1") + shift 1 + ;; + --C) + [ -n "$VIASH_PAR_COLUMNS_FILE" ] && ViashError Bad arguments for option \'--C\': \'$VIASH_PAR_COLUMNS_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_COLUMNS_FILE="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --C. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --exclude) + [ -n "$VIASH_PAR_EXCLUDE" ] && ViashError Bad arguments for option \'--exclude\': \'$VIASH_PAR_EXCLUDE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_EXCLUDE="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --exclude. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --exclude=*) + [ -n "$VIASH_PAR_EXCLUDE" ] && ViashError Bad arguments for option \'--exclude=*\': \'$VIASH_PAR_EXCLUDE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_EXCLUDE=$(ViashRemoveFlags "$1") + shift 1 + ;; + --e) + [ -n "$VIASH_PAR_EXCLUDE" ] && ViashError Bad arguments for option \'--e\': \'$VIASH_PAR_EXCLUDE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_EXCLUDE="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --e. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --force) + [ -n "$VIASH_PAR_FORCE" ] && ViashError Bad arguments for option \'--force\': \'$VIASH_PAR_FORCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_FORCE=true + shift 1 + ;; + --header_line) + [ -n "$VIASH_PAR_HEADER_LINE" ] && ViashError Bad arguments for option \'--header_line\': \'$VIASH_PAR_HEADER_LINE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_HEADER_LINE="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --header_line. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --header_line=*) + [ -n "$VIASH_PAR_HEADER_LINE" ] && ViashError Bad arguments for option \'--header_line=*\': \'$VIASH_PAR_HEADER_LINE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_HEADER_LINE=$(ViashRemoveFlags "$1") + shift 1 + ;; + --H) + [ -n "$VIASH_PAR_HEADER_LINE" ] && ViashError Bad arguments for option \'--H\': \'$VIASH_PAR_HEADER_LINE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_HEADER_LINE="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --H. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --header_lines) + [ -n "$VIASH_PAR_HEADER_LINES" ] && ViashError Bad arguments for option \'--header_lines\': \'$VIASH_PAR_HEADER_LINES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_HEADER_LINES="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --header_lines. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --header_lines=*) + [ -n "$VIASH_PAR_HEADER_LINES" ] && ViashError Bad arguments for option \'--header_lines=*\': \'$VIASH_PAR_HEADER_LINES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_HEADER_LINES=$(ViashRemoveFlags "$1") + shift 1 + ;; + --h) + [ -n "$VIASH_PAR_HEADER_LINES" ] && ViashError Bad arguments for option \'--h\': \'$VIASH_PAR_HEADER_LINES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_HEADER_LINES="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --h. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --set_id) + [ -n "$VIASH_PAR_SET_ID" ] && ViashError Bad arguments for option \'--set_id\': \'$VIASH_PAR_SET_ID\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_SET_ID="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --set_id. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --set_id=*) + [ -n "$VIASH_PAR_SET_ID" ] && ViashError Bad arguments for option \'--set_id=*\': \'$VIASH_PAR_SET_ID\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_SET_ID=$(ViashRemoveFlags "$1") + shift 1 + ;; + --I) + [ -n "$VIASH_PAR_SET_ID" ] && ViashError Bad arguments for option \'--I\': \'$VIASH_PAR_SET_ID\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_SET_ID="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --I. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --include) + [ -n "$VIASH_PAR_INCLUDE" ] && ViashError Bad arguments for option \'--include\': \'$VIASH_PAR_INCLUDE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_INCLUDE="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --include. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --include=*) + [ -n "$VIASH_PAR_INCLUDE" ] && ViashError Bad arguments for option \'--include=*\': \'$VIASH_PAR_INCLUDE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_INCLUDE=$(ViashRemoveFlags "$1") + shift 1 + ;; + --keep_sites) + [ -n "$VIASH_PAR_KEEP_SITES" ] && ViashError Bad arguments for option \'--keep_sites\': \'$VIASH_PAR_KEEP_SITES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_KEEP_SITES=true + shift 1 + ;; + --k) + [ -n "$VIASH_PAR_KEEP_SITES" ] && ViashError Bad arguments for option \'--k\': \'$VIASH_PAR_KEEP_SITES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_KEEP_SITES=true + shift 1 + ;; + --merge_logic) + [ -n "$VIASH_PAR_MERGE_LOGIC" ] && ViashError Bad arguments for option \'--merge_logic\': \'$VIASH_PAR_MERGE_LOGIC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_MERGE_LOGIC="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --merge_logic. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --merge_logic=*) + [ -n "$VIASH_PAR_MERGE_LOGIC" ] && ViashError Bad arguments for option \'--merge_logic=*\': \'$VIASH_PAR_MERGE_LOGIC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_MERGE_LOGIC=$(ViashRemoveFlags "$1") + shift 1 + ;; + --l) + [ -n "$VIASH_PAR_MERGE_LOGIC" ] && ViashError Bad arguments for option \'--l\': \'$VIASH_PAR_MERGE_LOGIC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_MERGE_LOGIC="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --l. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --mark_sites) + [ -n "$VIASH_PAR_MARK_SITES" ] && ViashError Bad arguments for option \'--mark_sites\': \'$VIASH_PAR_MARK_SITES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_MARK_SITES="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --mark_sites. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --mark_sites=*) + [ -n "$VIASH_PAR_MARK_SITES" ] && ViashError Bad arguments for option \'--mark_sites=*\': \'$VIASH_PAR_MARK_SITES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_MARK_SITES=$(ViashRemoveFlags "$1") + shift 1 + ;; + --m) + [ -n "$VIASH_PAR_MARK_SITES" ] && ViashError Bad arguments for option \'--m\': \'$VIASH_PAR_MARK_SITES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_MARK_SITES="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --m. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --min_overlap) + [ -n "$VIASH_PAR_MIN_OVERLAP" ] && ViashError Bad arguments for option \'--min_overlap\': \'$VIASH_PAR_MIN_OVERLAP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_MIN_OVERLAP="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --min_overlap. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --min_overlap=*) + [ -n "$VIASH_PAR_MIN_OVERLAP" ] && ViashError Bad arguments for option \'--min_overlap=*\': \'$VIASH_PAR_MIN_OVERLAP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_MIN_OVERLAP=$(ViashRemoveFlags "$1") + shift 1 + ;; + --no_version) + [ -n "$VIASH_PAR_NO_VERSION" ] && ViashError Bad arguments for option \'--no_version\': \'$VIASH_PAR_NO_VERSION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_NO_VERSION=true + shift 1 + ;; + --output_type) + [ -n "$VIASH_PAR_OUTPUT_TYPE" ] && ViashError Bad arguments for option \'--output_type\': \'$VIASH_PAR_OUTPUT_TYPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_OUTPUT_TYPE="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --output_type. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --output_type=*) + [ -n "$VIASH_PAR_OUTPUT_TYPE" ] && ViashError Bad arguments for option \'--output_type=*\': \'$VIASH_PAR_OUTPUT_TYPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_OUTPUT_TYPE=$(ViashRemoveFlags "$1") + shift 1 + ;; + --O) + [ -n "$VIASH_PAR_OUTPUT_TYPE" ] && ViashError Bad arguments for option \'--O\': \'$VIASH_PAR_OUTPUT_TYPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_OUTPUT_TYPE="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --O. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --pair_logic) + [ -n "$VIASH_PAR_PAIR_LOGIC" ] && ViashError Bad arguments for option \'--pair_logic\': \'$VIASH_PAR_PAIR_LOGIC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_PAIR_LOGIC="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --pair_logic. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --pair_logic=*) + [ -n "$VIASH_PAR_PAIR_LOGIC" ] && ViashError Bad arguments for option \'--pair_logic=*\': \'$VIASH_PAR_PAIR_LOGIC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_PAIR_LOGIC=$(ViashRemoveFlags "$1") + shift 1 + ;; + --regions) + [ -n "$VIASH_PAR_REGIONS" ] && ViashError Bad arguments for option \'--regions\': \'$VIASH_PAR_REGIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_REGIONS="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --regions. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --regions=*) + [ -n "$VIASH_PAR_REGIONS" ] && ViashError Bad arguments for option \'--regions=*\': \'$VIASH_PAR_REGIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_REGIONS=$(ViashRemoveFlags "$1") + shift 1 + ;; + --r) + [ -n "$VIASH_PAR_REGIONS" ] && ViashError Bad arguments for option \'--r\': \'$VIASH_PAR_REGIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_REGIONS="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --r. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --regions_file) + [ -n "$VIASH_PAR_REGIONS_FILE" ] && ViashError Bad arguments for option \'--regions_file\': \'$VIASH_PAR_REGIONS_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_REGIONS_FILE="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --regions_file. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --regions_file=*) + [ -n "$VIASH_PAR_REGIONS_FILE" ] && ViashError Bad arguments for option \'--regions_file=*\': \'$VIASH_PAR_REGIONS_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_REGIONS_FILE=$(ViashRemoveFlags "$1") + shift 1 + ;; + --R) + [ -n "$VIASH_PAR_REGIONS_FILE" ] && ViashError Bad arguments for option \'--R\': \'$VIASH_PAR_REGIONS_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_REGIONS_FILE="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --R. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --regions_overlap) + [ -n "$VIASH_PAR_REGIONS_OVERLAP" ] && ViashError Bad arguments for option \'--regions_overlap\': \'$VIASH_PAR_REGIONS_OVERLAP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_REGIONS_OVERLAP="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --regions_overlap. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --regions_overlap=*) + [ -n "$VIASH_PAR_REGIONS_OVERLAP" ] && ViashError Bad arguments for option \'--regions_overlap=*\': \'$VIASH_PAR_REGIONS_OVERLAP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_REGIONS_OVERLAP=$(ViashRemoveFlags "$1") + shift 1 + ;; + --rename_annotations) + [ -n "$VIASH_PAR_RENAME_ANNOTATIONS" ] && ViashError Bad arguments for option \'--rename_annotations\': \'$VIASH_PAR_RENAME_ANNOTATIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_RENAME_ANNOTATIONS="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --rename_annotations. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --rename_annotations=*) + [ -n "$VIASH_PAR_RENAME_ANNOTATIONS" ] && ViashError Bad arguments for option \'--rename_annotations=*\': \'$VIASH_PAR_RENAME_ANNOTATIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_RENAME_ANNOTATIONS=$(ViashRemoveFlags "$1") + shift 1 + ;; + --rename_chromosomes) + [ -n "$VIASH_PAR_RENAME_CHROMOSOMES" ] && ViashError Bad arguments for option \'--rename_chromosomes\': \'$VIASH_PAR_RENAME_CHROMOSOMES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_RENAME_CHROMOSOMES="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --rename_chromosomes. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --rename_chromosomes=*) + [ -n "$VIASH_PAR_RENAME_CHROMOSOMES" ] && ViashError Bad arguments for option \'--rename_chromosomes=*\': \'$VIASH_PAR_RENAME_CHROMOSOMES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_RENAME_CHROMOSOMES=$(ViashRemoveFlags "$1") + shift 1 + ;; + --samples) + [ -n "$VIASH_PAR_SAMPLES" ] && ViashError Bad arguments for option \'--samples\': \'$VIASH_PAR_SAMPLES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_SAMPLES="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --samples. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --samples=*) + [ -n "$VIASH_PAR_SAMPLES" ] && ViashError Bad arguments for option \'--samples=*\': \'$VIASH_PAR_SAMPLES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_SAMPLES=$(ViashRemoveFlags "$1") + shift 1 + ;; + --samples_file) + [ -n "$VIASH_PAR_SAMPLES_FILE" ] && ViashError Bad arguments for option \'--samples_file\': \'$VIASH_PAR_SAMPLES_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_SAMPLES_FILE="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --samples_file. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --samples_file=*) + [ -n "$VIASH_PAR_SAMPLES_FILE" ] && ViashError Bad arguments for option \'--samples_file=*\': \'$VIASH_PAR_SAMPLES_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_SAMPLES_FILE=$(ViashRemoveFlags "$1") + shift 1 + ;; + --single_overlaps) + [ -n "$VIASH_PAR_SINGLE_OVERLAPS" ] && ViashError Bad arguments for option \'--single_overlaps\': \'$VIASH_PAR_SINGLE_OVERLAPS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_SINGLE_OVERLAPS=true + shift 1 + ;; + --remove) + [ -n "$VIASH_PAR_REMOVE" ] && ViashError Bad arguments for option \'--remove\': \'$VIASH_PAR_REMOVE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_REMOVE="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --remove. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --remove=*) + [ -n "$VIASH_PAR_REMOVE" ] && ViashError Bad arguments for option \'--remove=*\': \'$VIASH_PAR_REMOVE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_REMOVE=$(ViashRemoveFlags "$1") + shift 1 + ;; + --x) + [ -n "$VIASH_PAR_REMOVE" ] && ViashError Bad arguments for option \'--x\': \'$VIASH_PAR_REMOVE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_REMOVE="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --x. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + ---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/bcftools/bcftools_annotate: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_PAR_INPUT+x} ]; then + ViashError '--input' is a required argument. Use "--help" to get more information on the parameters. + exit 1 +fi +if [ -z ${VIASH_PAR_OUTPUT+x} ]; then + ViashError '--output' is a required argument. Use "--help" to get more information on the parameters. + exit 1 +fi +if [ -z ${VIASH_META_NAME+x} ]; then + ViashError 'name' is a required argument. Use "--help" to get more information on the parameters. + exit 1 +fi +if [ -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then + ViashError 'functionality_name' is a required argument. Use "--help" to get more information on the parameters. + exit 1 +fi +if [ -z ${VIASH_META_RESOURCES_DIR+x} ]; then + ViashError 'resources_dir' is a required argument. Use "--help" to get more information on the parameters. + exit 1 +fi +if [ -z ${VIASH_META_EXECUTABLE+x} ]; then + ViashError 'executable' is a required argument. Use "--help" to get more information on the parameters. + exit 1 +fi +if [ -z ${VIASH_META_CONFIG+x} ]; then + ViashError 'config' is a required argument. Use "--help" to get more information on the parameters. + exit 1 +fi +if [ -z ${VIASH_META_TEMP_DIR+x} ]; then + ViashError 'temp_dir' is a required argument. Use "--help" to get more information on the parameters. + exit 1 +fi + +# filling in defaults +if [ -z ${VIASH_PAR_FORCE+x} ]; then + VIASH_PAR_FORCE="false" +fi +if [ -z ${VIASH_PAR_KEEP_SITES+x} ]; then + VIASH_PAR_KEEP_SITES="false" +fi +if [ -z ${VIASH_PAR_NO_VERSION+x} ]; then + VIASH_PAR_NO_VERSION="false" +fi +if [ -z ${VIASH_PAR_SINGLE_OVERLAPS+x} ]; then + VIASH_PAR_SINGLE_OVERLAPS="false" +fi + +# check whether required files exist +if [ ! -z "$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_ANNOTATIONS" ] && [ ! -e "$VIASH_PAR_ANNOTATIONS" ]; then + ViashError "Input file '$VIASH_PAR_ANNOTATIONS' does not exist." + exit 1 +fi +if [ ! -z "$VIASH_PAR_COLUMNS_FILE" ] && [ ! -e "$VIASH_PAR_COLUMNS_FILE" ]; then + ViashError "Input file '$VIASH_PAR_COLUMNS_FILE' does not exist." + exit 1 +fi +if [ ! -z "$VIASH_PAR_HEADER_LINES" ] && [ ! -e "$VIASH_PAR_HEADER_LINES" ]; then + ViashError "Input file '$VIASH_PAR_HEADER_LINES' does not exist." + exit 1 +fi +if [ ! -z "$VIASH_PAR_REGIONS_FILE" ] && [ ! -e "$VIASH_PAR_REGIONS_FILE" ]; then + ViashError "Input file '$VIASH_PAR_REGIONS_FILE' does not exist." + exit 1 +fi +if [ ! -z "$VIASH_PAR_RENAME_ANNOTATIONS" ] && [ ! -e "$VIASH_PAR_RENAME_ANNOTATIONS" ]; then + ViashError "Input file '$VIASH_PAR_RENAME_ANNOTATIONS' does not exist." + exit 1 +fi +if [ ! -z "$VIASH_PAR_RENAME_CHROMOSOMES" ] && [ ! -e "$VIASH_PAR_RENAME_CHROMOSOMES" ]; then + ViashError "Input file '$VIASH_PAR_RENAME_CHROMOSOMES' does not exist." + exit 1 +fi +if [ ! -z "$VIASH_PAR_SAMPLES_FILE" ] && [ ! -e "$VIASH_PAR_SAMPLES_FILE" ]; then + ViashError "Input file '$VIASH_PAR_SAMPLES_FILE' does not exist." + exit 1 +fi + +# check whether parameters values are of the right type +if [[ -n "$VIASH_PAR_FORCE" ]]; then + if ! [[ "$VIASH_PAR_FORCE" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then + ViashError '--force' has to be a boolean_true. Use "--help" to get more information on the parameters. + exit 1 + fi +fi +if [[ -n "$VIASH_PAR_KEEP_SITES" ]]; then + if ! [[ "$VIASH_PAR_KEEP_SITES" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then + ViashError '--keep_sites' has to be a boolean_true. Use "--help" to get more information on the parameters. + exit 1 + fi +fi +if [[ -n "$VIASH_PAR_NO_VERSION" ]]; then + if ! [[ "$VIASH_PAR_NO_VERSION" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then + ViashError '--no_version' has to be a boolean_true. Use "--help" to get more information on the parameters. + exit 1 + fi +fi +if [[ -n "$VIASH_PAR_SINGLE_OVERLAPS" ]]; then + if ! [[ "$VIASH_PAR_SINGLE_OVERLAPS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then + ViashError '--single_overlaps' 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 "$VIASH_PAR_OUTPUT_TYPE" ]; then + VIASH_PAR_OUTPUT_TYPE_CHOICES=("u;z;b;v") + IFS=';' + set -f + if ! [[ ";${VIASH_PAR_OUTPUT_TYPE_CHOICES[*]};" =~ ";$VIASH_PAR_OUTPUT_TYPE;" ]]; then + ViashError '--output_type' specified value of \'$VIASH_PAR_OUTPUT_TYPE\' 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 "$VIASH_PAR_PAIR_LOGIC" ]; then + VIASH_PAR_PAIR_LOGIC_CHOICES=("snps;indels;both;all;some;exact") + IFS=';' + set -f + if ! [[ ";${VIASH_PAR_PAIR_LOGIC_CHOICES[*]};" =~ ";$VIASH_PAR_PAIR_LOGIC;" ]]; then + ViashError '--pair_logic' specified value of \'$VIASH_PAR_PAIR_LOGIC\' 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 "$VIASH_PAR_REGIONS_OVERLAP" ]; then + VIASH_PAR_REGIONS_OVERLAP_CHOICES=("pos;record;variant;0;1;2") + IFS=';' + set -f + if ! [[ ";${VIASH_PAR_REGIONS_OVERLAP_CHOICES[*]};" =~ ";$VIASH_PAR_REGIONS_OVERLAP;" ]]; then + ViashError '--regions_overlap' specified value of \'$VIASH_PAR_REGIONS_OVERLAP\' 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 "$VIASH_PAR_OUTPUT" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT")" ]; then + mkdir -p "$(dirname "$VIASH_PAR_OUTPUT")" +fi + +if [ "$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 "$VIASH_PAR_OUTPUT" ]; then + VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT")" ) + VIASH_PAR_OUTPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT") + VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT" ) +fi +if [ ! -z "$VIASH_PAR_ANNOTATIONS" ]; then + VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_ANNOTATIONS")" ) + VIASH_PAR_ANNOTATIONS=$(ViashDockerAutodetectMount "$VIASH_PAR_ANNOTATIONS") +fi +if [ ! -z "$VIASH_PAR_COLUMNS_FILE" ]; then + VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_COLUMNS_FILE")" ) + VIASH_PAR_COLUMNS_FILE=$(ViashDockerAutodetectMount "$VIASH_PAR_COLUMNS_FILE") +fi +if [ ! -z "$VIASH_PAR_HEADER_LINES" ]; then + VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_HEADER_LINES")" ) + VIASH_PAR_HEADER_LINES=$(ViashDockerAutodetectMount "$VIASH_PAR_HEADER_LINES") +fi +if [ ! -z "$VIASH_PAR_REGIONS_FILE" ]; then + VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_REGIONS_FILE")" ) + VIASH_PAR_REGIONS_FILE=$(ViashDockerAutodetectMount "$VIASH_PAR_REGIONS_FILE") +fi +if [ ! -z "$VIASH_PAR_RENAME_ANNOTATIONS" ]; then + VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_RENAME_ANNOTATIONS")" ) + VIASH_PAR_RENAME_ANNOTATIONS=$(ViashDockerAutodetectMount "$VIASH_PAR_RENAME_ANNOTATIONS") +fi +if [ ! -z "$VIASH_PAR_RENAME_CHROMOSOMES" ]; then + VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_RENAME_CHROMOSOMES")" ) + VIASH_PAR_RENAME_CHROMOSOMES=$(ViashDockerAutodetectMount "$VIASH_PAR_RENAME_CHROMOSOMES") +fi +if [ ! -z "$VIASH_PAR_SAMPLES_FILE" ]; then + VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_SAMPLES_FILE")" ) + VIASH_PAR_SAMPLES_FILE=$(ViashDockerAutodetectMount "$VIASH_PAR_SAMPLES_FILE") +fi +if [ ! -z "$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-bcftools_annotate-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 ${VIASH_PAR_INPUT+x} ]; then echo "${VIASH_PAR_INPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_input='&'#" ; else echo "# par_input="; fi ) +$( if [ ! -z ${VIASH_PAR_OUTPUT+x} ]; then echo "${VIASH_PAR_OUTPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_output='&'#" ; else echo "# par_output="; fi ) +$( if [ ! -z ${VIASH_PAR_ANNOTATIONS+x} ]; then echo "${VIASH_PAR_ANNOTATIONS}" | sed "s#'#'\"'\"'#g;s#.*#par_annotations='&'#" ; else echo "# par_annotations="; fi ) +$( if [ ! -z ${VIASH_PAR_COLUMNS+x} ]; then echo "${VIASH_PAR_COLUMNS}" | sed "s#'#'\"'\"'#g;s#.*#par_columns='&'#" ; else echo "# par_columns="; fi ) +$( if [ ! -z ${VIASH_PAR_COLUMNS_FILE+x} ]; then echo "${VIASH_PAR_COLUMNS_FILE}" | sed "s#'#'\"'\"'#g;s#.*#par_columns_file='&'#" ; else echo "# par_columns_file="; fi ) +$( if [ ! -z ${VIASH_PAR_EXCLUDE+x} ]; then echo "${VIASH_PAR_EXCLUDE}" | sed "s#'#'\"'\"'#g;s#.*#par_exclude='&'#" ; else echo "# par_exclude="; fi ) +$( if [ ! -z ${VIASH_PAR_FORCE+x} ]; then echo "${VIASH_PAR_FORCE}" | sed "s#'#'\"'\"'#g;s#.*#par_force='&'#" ; else echo "# par_force="; fi ) +$( if [ ! -z ${VIASH_PAR_HEADER_LINE+x} ]; then echo "${VIASH_PAR_HEADER_LINE}" | sed "s#'#'\"'\"'#g;s#.*#par_header_line='&'#" ; else echo "# par_header_line="; fi ) +$( if [ ! -z ${VIASH_PAR_HEADER_LINES+x} ]; then echo "${VIASH_PAR_HEADER_LINES}" | sed "s#'#'\"'\"'#g;s#.*#par_header_lines='&'#" ; else echo "# par_header_lines="; fi ) +$( if [ ! -z ${VIASH_PAR_SET_ID+x} ]; then echo "${VIASH_PAR_SET_ID}" | sed "s#'#'\"'\"'#g;s#.*#par_set_id='&'#" ; else echo "# par_set_id="; fi ) +$( if [ ! -z ${VIASH_PAR_INCLUDE+x} ]; then echo "${VIASH_PAR_INCLUDE}" | sed "s#'#'\"'\"'#g;s#.*#par_include='&'#" ; else echo "# par_include="; fi ) +$( if [ ! -z ${VIASH_PAR_KEEP_SITES+x} ]; then echo "${VIASH_PAR_KEEP_SITES}" | sed "s#'#'\"'\"'#g;s#.*#par_keep_sites='&'#" ; else echo "# par_keep_sites="; fi ) +$( if [ ! -z ${VIASH_PAR_MERGE_LOGIC+x} ]; then echo "${VIASH_PAR_MERGE_LOGIC}" | sed "s#'#'\"'\"'#g;s#.*#par_merge_logic='&'#" ; else echo "# par_merge_logic="; fi ) +$( if [ ! -z ${VIASH_PAR_MARK_SITES+x} ]; then echo "${VIASH_PAR_MARK_SITES}" | sed "s#'#'\"'\"'#g;s#.*#par_mark_sites='&'#" ; else echo "# par_mark_sites="; fi ) +$( if [ ! -z ${VIASH_PAR_MIN_OVERLAP+x} ]; then echo "${VIASH_PAR_MIN_OVERLAP}" | sed "s#'#'\"'\"'#g;s#.*#par_min_overlap='&'#" ; else echo "# par_min_overlap="; fi ) +$( if [ ! -z ${VIASH_PAR_NO_VERSION+x} ]; then echo "${VIASH_PAR_NO_VERSION}" | sed "s#'#'\"'\"'#g;s#.*#par_no_version='&'#" ; else echo "# par_no_version="; fi ) +$( if [ ! -z ${VIASH_PAR_OUTPUT_TYPE+x} ]; then echo "${VIASH_PAR_OUTPUT_TYPE}" | sed "s#'#'\"'\"'#g;s#.*#par_output_type='&'#" ; else echo "# par_output_type="; fi ) +$( if [ ! -z ${VIASH_PAR_PAIR_LOGIC+x} ]; then echo "${VIASH_PAR_PAIR_LOGIC}" | sed "s#'#'\"'\"'#g;s#.*#par_pair_logic='&'#" ; else echo "# par_pair_logic="; fi ) +$( if [ ! -z ${VIASH_PAR_REGIONS+x} ]; then echo "${VIASH_PAR_REGIONS}" | sed "s#'#'\"'\"'#g;s#.*#par_regions='&'#" ; else echo "# par_regions="; fi ) +$( if [ ! -z ${VIASH_PAR_REGIONS_FILE+x} ]; then echo "${VIASH_PAR_REGIONS_FILE}" | sed "s#'#'\"'\"'#g;s#.*#par_regions_file='&'#" ; else echo "# par_regions_file="; fi ) +$( if [ ! -z ${VIASH_PAR_REGIONS_OVERLAP+x} ]; then echo "${VIASH_PAR_REGIONS_OVERLAP}" | sed "s#'#'\"'\"'#g;s#.*#par_regions_overlap='&'#" ; else echo "# par_regions_overlap="; fi ) +$( if [ ! -z ${VIASH_PAR_RENAME_ANNOTATIONS+x} ]; then echo "${VIASH_PAR_RENAME_ANNOTATIONS}" | sed "s#'#'\"'\"'#g;s#.*#par_rename_annotations='&'#" ; else echo "# par_rename_annotations="; fi ) +$( if [ ! -z ${VIASH_PAR_RENAME_CHROMOSOMES+x} ]; then echo "${VIASH_PAR_RENAME_CHROMOSOMES}" | sed "s#'#'\"'\"'#g;s#.*#par_rename_chromosomes='&'#" ; else echo "# par_rename_chromosomes="; fi ) +$( if [ ! -z ${VIASH_PAR_SAMPLES+x} ]; then echo "${VIASH_PAR_SAMPLES}" | sed "s#'#'\"'\"'#g;s#.*#par_samples='&'#" ; else echo "# par_samples="; fi ) +$( if [ ! -z ${VIASH_PAR_SAMPLES_FILE+x} ]; then echo "${VIASH_PAR_SAMPLES_FILE}" | sed "s#'#'\"'\"'#g;s#.*#par_samples_file='&'#" ; else echo "# par_samples_file="; fi ) +$( if [ ! -z ${VIASH_PAR_SINGLE_OVERLAPS+x} ]; then echo "${VIASH_PAR_SINGLE_OVERLAPS}" | sed "s#'#'\"'\"'#g;s#.*#par_single_overlaps='&'#" ; else echo "# par_single_overlaps="; fi ) +$( if [ ! -z ${VIASH_PAR_REMOVE+x} ]; then echo "${VIASH_PAR_REMOVE}" | sed "s#'#'\"'\"'#g;s#.*#par_remove='&'#" ; else echo "# par_remove="; 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 + +# Exit on error +set -eo pipefail + +# Unset parameters +unset_if_false=( + par_force + par_keep_sites + par_no_version + par_single_overlaps +) + +for par in \${unset_if_false[@]}; do + test_val="\${!par}" + [[ "\$test_val" == "false" ]] && unset \$par +done + +# Execute bcftools annotate with the provided arguments +bcftools annotate \\ + \${par_annotations:+-a "\$par_annotations"} \\ + \${par_columns:+-c "\$par_columns"} \\ + \${par_columns_file:+-C "\$par_columns_file"} \\ + \${par_exclude:+-e "\$par_exclude"} \\ + \${par_force:+--force} \\ + \${par_header_line:+-H "\$par_header_line"} \\ + \${par_header_lines:+-h "\$par_header_lines"} \\ + \${par_set_id:+-I "\$par_set_id"} \\ + \${par_include:+-i "\$par_include"} \\ + \${par_keep_sites:+-k} \\ + \${par_merge_logic:+-l "\$par_merge_logic"} \\ + \${par_mark_sites:+-m "\$par_mark_sites"} \\ + \${par_min_overlap:+--min-overlap "\$par_min_overlap"} \\ + \${par_no_version:+--no-version} \\ + \${par_samples_file:+-S "\$par_samples_file"} \\ + \${par_output_type:+-O "\$par_output_type"} \\ + \${par_pair_logic:+--pair-logic "\$par_pair_logic"} \\ + \${par_regions:+-r "\$par_regions"} \\ + \${par_regions_file:+-R "\$par_regions_file"} \\ + \${par_regions_overlap:+--regions-overlap "\$par_regions_overlap"} \\ + \${par_rename_annotations:+--rename-annots "\$par_rename_annotations"} \\ + \${par_rename_chromosomes:+--rename-chrs "\$par_rename_chromosomes"} \\ + \${par_samples:+-s "\$par_samples"} \\ + \${par_single_overlaps:+--single-overlaps} \\ + \${par_threads:+--threads "\$par_threads"} \\ + \${par_remove:+-x "\$par_remove"} \\ + -o \$par_output \\ + \$par_input + + + +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 "$VIASH_PAR_OUTPUT" ]; then + VIASH_PAR_OUTPUT=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT") + fi + if [ ! -z "$VIASH_PAR_ANNOTATIONS" ]; then + VIASH_PAR_ANNOTATIONS=$(ViashDockerStripAutomount "$VIASH_PAR_ANNOTATIONS") + fi + if [ ! -z "$VIASH_PAR_COLUMNS_FILE" ]; then + VIASH_PAR_COLUMNS_FILE=$(ViashDockerStripAutomount "$VIASH_PAR_COLUMNS_FILE") + fi + if [ ! -z "$VIASH_PAR_HEADER_LINES" ]; then + VIASH_PAR_HEADER_LINES=$(ViashDockerStripAutomount "$VIASH_PAR_HEADER_LINES") + fi + if [ ! -z "$VIASH_PAR_REGIONS_FILE" ]; then + VIASH_PAR_REGIONS_FILE=$(ViashDockerStripAutomount "$VIASH_PAR_REGIONS_FILE") + fi + if [ ! -z "$VIASH_PAR_RENAME_ANNOTATIONS" ]; then + VIASH_PAR_RENAME_ANNOTATIONS=$(ViashDockerStripAutomount "$VIASH_PAR_RENAME_ANNOTATIONS") + fi + if [ ! -z "$VIASH_PAR_RENAME_CHROMOSOMES" ]; then + VIASH_PAR_RENAME_CHROMOSOMES=$(ViashDockerStripAutomount "$VIASH_PAR_RENAME_CHROMOSOMES") + fi + if [ ! -z "$VIASH_PAR_SAMPLES_FILE" ]; then + VIASH_PAR_SAMPLES_FILE=$(ViashDockerStripAutomount "$VIASH_PAR_SAMPLES_FILE") + 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 "$VIASH_PAR_OUTPUT" ] && [ ! -e "$VIASH_PAR_OUTPUT" ]; then + ViashError "Output file '$VIASH_PAR_OUTPUT' does not exist." + exit 1 +fi + + +exit 0 diff --git a/target/executable/bcftools/bcftools_sort/.config.vsh.yaml b/target/executable/bcftools/bcftools_sort/.config.vsh.yaml index 1deea226..67f324c0 100644 --- a/target/executable/bcftools/bcftools_sort/.config.vsh.yaml +++ b/target/executable/bcftools/bcftools_sort/.config.vsh.yaml @@ -185,7 +185,7 @@ build_info: output: "target/executable/bcftools/bcftools_sort" executable: "target/executable/bcftools/bcftools_sort/bcftools_sort" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/bcftools/bcftools_sort/bcftools_sort b/target/executable/bcftools/bcftools_sort/bcftools_sort index 720ef7d2..d860794f 100755 --- a/target/executable/bcftools/bcftools_sort/bcftools_sort +++ b/target/executable/bcftools/bcftools_sort/bcftools_sort @@ -483,9 +483,9 @@ RUN echo "bcftools: \"$(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="2024-09-10T13:55:44Z" +LABEL org.opencontainers.image.created="2024-09-10T13:57:03Z" LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" 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 b79a55ee..e674b5b7 100644 --- a/target/executable/bcftools/bcftools_stats/.config.vsh.yaml +++ b/target/executable/bcftools/bcftools_stats/.config.vsh.yaml @@ -458,7 +458,7 @@ build_info: output: "target/executable/bcftools/bcftools_stats" executable: "target/executable/bcftools/bcftools_stats/bcftools_stats" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/bcftools/bcftools_stats/bcftools_stats b/target/executable/bcftools/bcftools_stats/bcftools_stats index 3bae890b..70111391 100755 --- a/target/executable/bcftools/bcftools_stats/bcftools_stats +++ b/target/executable/bcftools/bcftools_stats/bcftools_stats @@ -626,9 +626,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_stats" -LABEL org.opencontainers.image.created="2024-09-10T13:55:44Z" +LABEL org.opencontainers.image.created="2024-09-10T13:57:04Z" LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bcl_convert/.config.vsh.yaml b/target/executable/bcl_convert/.config.vsh.yaml index 31f49ca0..278ced0d 100644 --- a/target/executable/bcl_convert/.config.vsh.yaml +++ b/target/executable/bcl_convert/.config.vsh.yaml @@ -418,7 +418,7 @@ build_info: output: "target/executable/bcl_convert" executable: "target/executable/bcl_convert/bcl_convert" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/bcl_convert/bcl_convert b/target/executable/bcl_convert/bcl_convert index a2ec3278..f71379fc 100755 --- a/target/executable/bcl_convert/bcl_convert +++ b/target/executable/bcl_convert/bcl_convert @@ -599,9 +599,9 @@ RUN echo "bcl-convert: \"$(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="2024-09-10T13:55:50Z" +LABEL org.opencontainers.image.created="2024-09-10T13:57:10Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" 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 9e2cb5a2..ad0471dd 100644 --- a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml +++ b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml @@ -270,7 +270,7 @@ build_info: output: "target/executable/bd_rhapsody/bd_rhapsody_make_reference" executable: "target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference index 2057cc00..cc1efc70 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 @@ -549,9 +549,9 @@ RUN echo "bdgenomics/rhapsody: 2.2.1" > /var/software_versions.txt LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Weiwei Schultz" LABEL org.opencontainers.image.description="Companion container for running component bd_rhapsody bd_rhapsody_make_reference" -LABEL org.opencontainers.image.created="2024-09-10T13:55:54Z" +LABEL org.opencontainers.image.created="2024-09-10T13:57:13Z" LABEL org.opencontainers.image.source="https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1/Extra_Utilities/" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" 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 267e315c..9a61a0b3 100644 --- a/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml @@ -187,7 +187,7 @@ build_info: output: "target/executable/bedtools/bedtools_bamtofastq" executable: "target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq b/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq index 5b6810ac..6d398830 100755 --- a/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq +++ b/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq @@ -483,9 +483,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bamtofastq" -LABEL org.opencontainers.image.created="2024-09-10T13:55:37Z" +LABEL org.opencontainers.image.created="2024-09-10T13:56:57Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml b/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml index 7ca4fce6..68af3ca3 100644 --- a/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml @@ -176,7 +176,7 @@ build_info: output: "target/executable/bedtools/bedtools_bed12tobed6" executable: "target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6 b/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6 index 1820e9d2..af10d403 100755 --- a/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6 +++ b/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6 @@ -480,9 +480,9 @@ RUN echo "bedtools: \"$(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="2024-09-10T13:55:36Z" +LABEL org.opencontainers.image.created="2024-09-10T13:56:55Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" 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 a2fdfd32..271c9cb1 100644 --- a/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml @@ -214,7 +214,7 @@ build_info: output: "target/executable/bedtools/bedtools_bedtobam" executable: "target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam b/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam index acd5f8f1..2404fb07 100755 --- a/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam +++ b/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam @@ -496,9 +496,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bedtobam" -LABEL org.opencontainers.image.created="2024-09-10T13:55:38Z" +LABEL org.opencontainers.image.created="2024-09-10T13:56:58Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bedtools/bedtools_genomecov/.config.vsh.yaml b/target/executable/bedtools/bedtools_genomecov/.config.vsh.yaml index 184fbfda..9daf2352 100644 --- a/target/executable/bedtools/bedtools_genomecov/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_genomecov/.config.vsh.yaml @@ -337,7 +337,7 @@ build_info: output: "target/executable/bedtools/bedtools_genomecov" executable: "target/executable/bedtools/bedtools_genomecov/bedtools_genomecov" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/bedtools/bedtools_genomecov/bedtools_genomecov b/target/executable/bedtools/bedtools_genomecov/bedtools_genomecov index 9604c113..36b4ef84 100755 --- a/target/executable/bedtools/bedtools_genomecov/bedtools_genomecov +++ b/target/executable/bedtools/bedtools_genomecov/bedtools_genomecov @@ -591,9 +591,9 @@ RUN echo "bedtools: \"$(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="2024-09-10T13:55:36Z" +LABEL org.opencontainers.image.created="2024-09-10T13:56:55Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" 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 c97d6fd4..112a8b4e 100644 --- a/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml @@ -232,7 +232,7 @@ build_info: output: "target/executable/bedtools/bedtools_getfasta" executable: "target/executable/bedtools/bedtools_getfasta/bedtools_getfasta" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta b/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta index 826d0764..dc6f4a36 100755 --- a/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta +++ b/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta @@ -526,9 +526,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_getfasta" -LABEL org.opencontainers.image.created="2024-09-10T13:55:36Z" +LABEL org.opencontainers.image.created="2024-09-10T13:56:56Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml b/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml index 76d16300..38f2ab48 100644 --- a/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml @@ -273,7 +273,7 @@ build_info: output: "target/executable/bedtools/bedtools_groupby" executable: "target/executable/bedtools/bedtools_groupby/bedtools_groupby" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/bedtools/bedtools_groupby/bedtools_groupby b/target/executable/bedtools/bedtools_groupby/bedtools_groupby index 55b68c40..8d210031 100755 --- a/target/executable/bedtools/bedtools_groupby/bedtools_groupby +++ b/target/executable/bedtools/bedtools_groupby/bedtools_groupby @@ -552,9 +552,9 @@ RUN echo "bedtools: \"$(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="2024-09-10T13:55:38Z" +LABEL org.opencontainers.image.created="2024-09-10T13:56:57Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" 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 bd8b9a7c..52b8eb3d 100644 --- a/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml @@ -410,7 +410,7 @@ build_info: output: "target/executable/bedtools/bedtools_intersect" executable: "target/executable/bedtools/bedtools_intersect/bedtools_intersect" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/bedtools/bedtools_intersect/bedtools_intersect b/target/executable/bedtools/bedtools_intersect/bedtools_intersect index f95457e3..8ef4f9f9 100755 --- a/target/executable/bedtools/bedtools_intersect/bedtools_intersect +++ b/target/executable/bedtools/bedtools_intersect/bedtools_intersect @@ -633,9 +633,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_intersect" -LABEL org.opencontainers.image.created="2024-09-10T13:55:37Z" +LABEL org.opencontainers.image.created="2024-09-10T13:56:56Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bedtools/bedtools_links/.config.vsh.yaml b/target/executable/bedtools/bedtools_links/.config.vsh.yaml index 5ce3edd0..be82d4d0 100644 --- a/target/executable/bedtools/bedtools_links/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_links/.config.vsh.yaml @@ -210,7 +210,7 @@ build_info: output: "target/executable/bedtools/bedtools_links" executable: "target/executable/bedtools/bedtools_links/bedtools_links" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/bedtools/bedtools_links/bedtools_links b/target/executable/bedtools/bedtools_links/bedtools_links index 2f7cf4ca..b5983b83 100755 --- a/target/executable/bedtools/bedtools_links/bedtools_links +++ b/target/executable/bedtools/bedtools_links/bedtools_links @@ -500,9 +500,9 @@ RUN echo "bedtools: \"$(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="2024-09-10T13:55:37Z" +LABEL org.opencontainers.image.created="2024-09-10T13:56:56Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" 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 3ee52602..c75eca7b 100644 --- a/target/executable/bedtools/bedtools_merge/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_merge/.config.vsh.yaml @@ -279,7 +279,7 @@ build_info: output: "target/executable/bedtools/bedtools_merge" executable: "target/executable/bedtools/bedtools_merge/bedtools_merge" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/bedtools/bedtools_merge/bedtools_merge b/target/executable/bedtools/bedtools_merge/bedtools_merge index f5ae6476..81eaebe7 100755 --- a/target/executable/bedtools/bedtools_merge/bedtools_merge +++ b/target/executable/bedtools/bedtools_merge/bedtools_merge @@ -558,9 +558,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_merge" -LABEL org.opencontainers.image.created="2024-09-10T13:55:35Z" +LABEL org.opencontainers.image.created="2024-09-10T13:56:55Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bedtools/bedtools_sort/.config.vsh.yaml b/target/executable/bedtools/bedtools_sort/.config.vsh.yaml index 14304ae1..c154490f 100644 --- a/target/executable/bedtools/bedtools_sort/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_sort/.config.vsh.yaml @@ -222,7 +222,7 @@ build_info: output: "target/executable/bedtools/bedtools_sort" executable: "target/executable/bedtools/bedtools_sort/bedtools_sort" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/bedtools/bedtools_sort/bedtools_sort b/target/executable/bedtools/bedtools_sort/bedtools_sort index bd318425..b9c4741e 100755 --- a/target/executable/bedtools/bedtools_sort/bedtools_sort +++ b/target/executable/bedtools/bedtools_sort/bedtools_sort @@ -509,9 +509,9 @@ RUN echo "bedtools: \"$(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="2024-09-10T13:55:38Z" +LABEL org.opencontainers.image.created="2024-09-10T13:56:57Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" 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 bcd4ec51..f5ca7f7b 100644 --- a/target/executable/busco/busco_download_datasets/.config.vsh.yaml +++ b/target/executable/busco/busco_download_datasets/.config.vsh.yaml @@ -158,7 +158,7 @@ build_info: output: "target/executable/busco/busco_download_datasets" executable: "target/executable/busco/busco_download_datasets/busco_download_datasets" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/busco/busco_download_datasets/busco_download_datasets b/target/executable/busco/busco_download_datasets/busco_download_datasets index 94884e73..a6a303bc 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="2024-09-10T13:55:47Z" +LABEL org.opencontainers.image.created="2024-09-10T13:57:07Z" LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" 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 7a5844ad..faa4d666 100644 --- a/target/executable/busco/busco_list_datasets/.config.vsh.yaml +++ b/target/executable/busco/busco_list_datasets/.config.vsh.yaml @@ -145,7 +145,7 @@ build_info: output: "target/executable/busco/busco_list_datasets" executable: "target/executable/busco/busco_list_datasets/busco_list_datasets" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/busco/busco_list_datasets/busco_list_datasets b/target/executable/busco/busco_list_datasets/busco_list_datasets index ca3d6537..ef72b817 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="2024-09-10T13:55:47Z" +LABEL org.opencontainers.image.created="2024-09-10T13:57:07Z" LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" 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 b20fa795..73b5b34b 100644 --- a/target/executable/busco/busco_run/.config.vsh.yaml +++ b/target/executable/busco/busco_run/.config.vsh.yaml @@ -423,7 +423,7 @@ build_info: output: "target/executable/busco/busco_run" executable: "target/executable/busco/busco_run/busco_run" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/busco/busco_run/busco_run b/target/executable/busco/busco_run/busco_run index e264ae37..b539568e 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="2024-09-10T13:55:48Z" +LABEL org.opencontainers.image.created="2024-09-10T13:57:07Z" LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/cutadapt/.config.vsh.yaml b/target/executable/cutadapt/.config.vsh.yaml index afed51f3..f2e9eb16 100644 --- a/target/executable/cutadapt/.config.vsh.yaml +++ b/target/executable/cutadapt/.config.vsh.yaml @@ -740,7 +740,7 @@ build_info: output: "target/executable/cutadapt" executable: "target/executable/cutadapt/cutadapt" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/cutadapt/cutadapt b/target/executable/cutadapt/cutadapt index 95834c34..29855542 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="2024-09-10T13:55:53Z" +LABEL org.opencontainers.image.created="2024-09-10T13:57:12Z" LABEL org.opencontainers.image.source="https://github.com/marcelm/cutadapt" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/falco/.config.vsh.yaml b/target/executable/falco/.config.vsh.yaml index 16525d14..353b6a50 100644 --- a/target/executable/falco/.config.vsh.yaml +++ b/target/executable/falco/.config.vsh.yaml @@ -317,7 +317,7 @@ build_info: output: "target/executable/falco" executable: "target/executable/falco/falco" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/falco/falco b/target/executable/falco/falco index 6b5ee665..3c6a46aa 100755 --- a/target/executable/falco/falco +++ b/target/executable/falco/falco @@ -589,9 +589,9 @@ RUN echo "falco: \"$(falco -v | sed -n 's/^falco //p')\"" > /var/software_versio LABEL org.opencontainers.image.authors="Toni Verbeiren" LABEL org.opencontainers.image.description="Companion container for running component falco" -LABEL org.opencontainers.image.created="2024-09-10T13:55:53Z" +LABEL org.opencontainers.image.created="2024-09-10T13:57:13Z" LABEL org.opencontainers.image.source="https://github.com/smithlabcode/falco" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/fastp/.config.vsh.yaml b/target/executable/fastp/.config.vsh.yaml index c455571f..cf7ce5dc 100644 --- a/target/executable/fastp/.config.vsh.yaml +++ b/target/executable/fastp/.config.vsh.yaml @@ -1083,7 +1083,7 @@ build_info: output: "target/executable/fastp" executable: "target/executable/fastp/fastp" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/fastp/fastp b/target/executable/fastp/fastp index 3c849009..6bae1ef3 100755 --- a/target/executable/fastp/fastp +++ b/target/executable/fastp/fastp @@ -1028,9 +1028,9 @@ RUN fastp --version 2>&1 | sed 's# #: "#;s#$#"#' > /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="2024-09-10T13:55:50Z" +LABEL org.opencontainers.image.created="2024-09-10T13:57:10Z" LABEL org.opencontainers.image.source="https://github.com/OpenGene/fastp" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/fastqc/.config.vsh.yaml b/target/executable/fastqc/.config.vsh.yaml index ad30ebd7..8e458b8e 100644 --- a/target/executable/fastqc/.config.vsh.yaml +++ b/target/executable/fastqc/.config.vsh.yaml @@ -340,7 +340,7 @@ build_info: output: "target/executable/fastqc" executable: "target/executable/fastqc/fastqc" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/fastqc/fastqc b/target/executable/fastqc/fastqc index 52b2723c..5549b02e 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="2024-09-10T13:55:43Z" +LABEL org.opencontainers.image.created="2024-09-10T13:57:02Z" LABEL org.opencontainers.image.source="https://github.com/s-andrews/FastQC" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/featurecounts/.config.vsh.yaml b/target/executable/featurecounts/.config.vsh.yaml index c7741a7d..13d1285f 100644 --- a/target/executable/featurecounts/.config.vsh.yaml +++ b/target/executable/featurecounts/.config.vsh.yaml @@ -645,7 +645,7 @@ build_info: output: "target/executable/featurecounts" executable: "target/executable/featurecounts/featurecounts" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/featurecounts/featurecounts b/target/executable/featurecounts/featurecounts index 1eb1ed1f..711d0583 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="2024-09-10T13:55:45Z" +LABEL org.opencontainers.image.created="2024-09-10T13:57:05Z" LABEL org.opencontainers.image.source="https://github.com/ShiLab-Bioinformatics/subread" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" 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 d26d1e51..6e5073e0 100644 --- a/target/executable/fq_subsample/.config.vsh.yaml +++ b/target/executable/fq_subsample/.config.vsh.yaml @@ -190,7 +190,7 @@ build_info: output: "target/executable/fq_subsample" executable: "target/executable/fq_subsample/fq_subsample" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/fq_subsample/fq_subsample b/target/executable/fq_subsample/fq_subsample index a87c1dd7..e86f9ead 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="2024-09-10T13:55:43Z" +LABEL org.opencontainers.image.created="2024-09-10T13:57:02Z" LABEL org.opencontainers.image.source="https://github.com/stjude-rust-labs/fq" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/gffread/.config.vsh.yaml b/target/executable/gffread/.config.vsh.yaml index 0c4c93c6..42eac61e 100644 --- a/target/executable/gffread/.config.vsh.yaml +++ b/target/executable/gffread/.config.vsh.yaml @@ -685,7 +685,7 @@ build_info: output: "target/executable/gffread" executable: "target/executable/gffread/gffread" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/gffread/gffread b/target/executable/gffread/gffread index e72c9a72..167333b8 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="2024-09-10T13:55:35Z" +LABEL org.opencontainers.image.created="2024-09-10T13:56:54Z" LABEL org.opencontainers.image.source="https://github.com/gpertea/gffread" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" 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 dcf07c65..6b0a81db 100644 --- a/target/executable/lofreq/lofreq_call/.config.vsh.yaml +++ b/target/executable/lofreq/lofreq_call/.config.vsh.yaml @@ -507,7 +507,7 @@ build_info: output: "target/executable/lofreq/lofreq_call" executable: "target/executable/lofreq/lofreq_call/lofreq_call" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/lofreq/lofreq_call/lofreq_call b/target/executable/lofreq/lofreq_call/lofreq_call index 540cb24b..a3b190a8 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="2024-09-10T13:55:45Z" +LABEL org.opencontainers.image.created="2024-09-10T13:57:05Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" 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 94f89b13..a36d46ac 100644 --- a/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml +++ b/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml @@ -215,7 +215,7 @@ build_info: output: "target/executable/lofreq/lofreq_indelqual" executable: "target/executable/lofreq/lofreq_indelqual/lofreq_indelqual" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual b/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual index 9c216a75..dbbba126 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="2024-09-10T13:55:45Z" +LABEL org.opencontainers.image.created="2024-09-10T13:57:04Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/multiqc/.config.vsh.yaml b/target/executable/multiqc/.config.vsh.yaml index 660b04a2..c077a457 100644 --- a/target/executable/multiqc/.config.vsh.yaml +++ b/target/executable/multiqc/.config.vsh.yaml @@ -456,7 +456,7 @@ build_info: output: "target/executable/multiqc" executable: "target/executable/multiqc/multiqc" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/multiqc/multiqc b/target/executable/multiqc/multiqc index 5a19cc1e..0b7bdd55 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="2024-09-10T13:55:53Z" +LABEL org.opencontainers.image.created="2024-09-10T13:57:13Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/pear/.config.vsh.yaml b/target/executable/pear/.config.vsh.yaml index 874f60b3..b953cdff 100644 --- a/target/executable/pear/.config.vsh.yaml +++ b/target/executable/pear/.config.vsh.yaml @@ -398,7 +398,7 @@ build_info: output: "target/executable/pear" executable: "target/executable/pear/pear" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/pear/pear b/target/executable/pear/pear index 6c0da657..ad532d5b 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="2024-09-10T13:55:39Z" +LABEL org.opencontainers.image.created="2024-09-10T13:56:58Z" LABEL org.opencontainers.image.source="https://github.com/tseemann/PEAR" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" 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 fae11c56..ef9512da 100644 --- a/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml +++ b/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml @@ -264,7 +264,7 @@ build_info: output: "target/executable/qualimap/qualimap_rnaseq" executable: "target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq b/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq index 188e6285..d7ed56ac 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="2024-09-10T13:55:42Z" +LABEL org.opencontainers.image.created="2024-09-10T13:57:02Z" LABEL org.opencontainers.image.source="https://bitbucket.org/kokonech/qualimap/commits/branch/master" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" 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 77d13fd1..a16d37f4 100644 --- a/target/executable/rsem/rsem_prepare_reference/.config.vsh.yaml +++ b/target/executable/rsem/rsem_prepare_reference/.config.vsh.yaml @@ -416,7 +416,7 @@ build_info: output: "target/executable/rsem/rsem_prepare_reference" executable: "target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference b/target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference index 88e5bfdc..1203afee 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="2024-09-10T13:55:48Z" +LABEL org.opencontainers.image.created="2024-09-10T13:57:08Z" LABEL org.opencontainers.image.source="https://github.com/deweylab/RSEM" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" 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 660898c3..7b7b6729 100644 --- a/target/executable/salmon/salmon_index/.config.vsh.yaml +++ b/target/executable/salmon/salmon_index/.config.vsh.yaml @@ -277,7 +277,7 @@ build_info: output: "target/executable/salmon/salmon_index" executable: "target/executable/salmon/salmon_index/salmon_index" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/salmon/salmon_index/salmon_index b/target/executable/salmon/salmon_index/salmon_index index bbdcd9a8..347d0152 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="2024-09-10T13:55:52Z" +LABEL org.opencontainers.image.created="2024-09-10T13:57:11Z" LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" 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 fecac65a..e31132fb 100644 --- a/target/executable/salmon/salmon_quant/.config.vsh.yaml +++ b/target/executable/salmon/salmon_quant/.config.vsh.yaml @@ -1173,7 +1173,7 @@ build_info: output: "target/executable/salmon/salmon_quant" executable: "target/executable/salmon/salmon_quant/salmon_quant" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/salmon/salmon_quant/salmon_quant b/target/executable/salmon/salmon_quant/salmon_quant index d1c78cdc..1666e353 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="2024-09-10T13:55:52Z" +LABEL org.opencontainers.image.created="2024-09-10T13:57:12Z" LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" 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 7107f65d..baeac2b1 100644 --- a/target/executable/samtools/samtools_collate/.config.vsh.yaml +++ b/target/executable/samtools/samtools_collate/.config.vsh.yaml @@ -264,7 +264,7 @@ build_info: output: "target/executable/samtools/samtools_collate" executable: "target/executable/samtools/samtools_collate/samtools_collate" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/samtools/samtools_collate/samtools_collate b/target/executable/samtools/samtools_collate/samtools_collate index e0fbe002..b25662c5 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="2024-09-10T13:55:41Z" +LABEL org.opencontainers.image.created="2024-09-10T13:57:00Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" 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 8ffeceea..bcb9e452 100644 --- a/target/executable/samtools/samtools_faidx/.config.vsh.yaml +++ b/target/executable/samtools/samtools_faidx/.config.vsh.yaml @@ -243,7 +243,7 @@ build_info: output: "target/executable/samtools/samtools_faidx" executable: "target/executable/samtools/samtools_faidx/samtools_faidx" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/samtools/samtools_faidx/samtools_faidx b/target/executable/samtools/samtools_faidx/samtools_faidx index 4f5e1bbb..01438ede 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="2024-09-10T13:55:41Z" +LABEL org.opencontainers.image.created="2024-09-10T13:57:00Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" 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 d2523582..5dc448ff 100644 --- a/target/executable/samtools/samtools_fasta/.config.vsh.yaml +++ b/target/executable/samtools/samtools_fasta/.config.vsh.yaml @@ -433,7 +433,7 @@ build_info: output: "target/executable/samtools/samtools_fasta" executable: "target/executable/samtools/samtools_fasta/samtools_fasta" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/samtools/samtools_fasta/samtools_fasta b/target/executable/samtools/samtools_fasta/samtools_fasta index 4a36ca19..00a946e7 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="2024-09-10T13:55:41Z" +LABEL org.opencontainers.image.created="2024-09-10T13:57:01Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" 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 23bb71d9..0742843e 100644 --- a/target/executable/samtools/samtools_fastq/.config.vsh.yaml +++ b/target/executable/samtools/samtools_fastq/.config.vsh.yaml @@ -433,7 +433,7 @@ build_info: output: "target/executable/samtools/samtools_fastq" executable: "target/executable/samtools/samtools_fastq/samtools_fastq" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/samtools/samtools_fastq/samtools_fastq b/target/executable/samtools/samtools_fastq/samtools_fastq index bd342fef..3d0e1286 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="2024-09-10T13:55:40Z" +LABEL org.opencontainers.image.created="2024-09-10T13:57:00Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" 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 2f1527df..896a2f4d 100644 --- a/target/executable/samtools/samtools_flagstat/.config.vsh.yaml +++ b/target/executable/samtools/samtools_flagstat/.config.vsh.yaml @@ -173,7 +173,7 @@ build_info: output: "target/executable/samtools/samtools_flagstat" executable: "target/executable/samtools/samtools_flagstat/samtools_flagstat" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/samtools/samtools_flagstat/samtools_flagstat b/target/executable/samtools/samtools_flagstat/samtools_flagstat index f6d74ccd..e317a8c8 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="2024-09-10T13:55:40Z" +LABEL org.opencontainers.image.created="2024-09-10T13:56:59Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" 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 47547163..69afcaaa 100644 --- a/target/executable/samtools/samtools_idxstats/.config.vsh.yaml +++ b/target/executable/samtools/samtools_idxstats/.config.vsh.yaml @@ -183,7 +183,7 @@ build_info: output: "target/executable/samtools/samtools_idxstats" executable: "target/executable/samtools/samtools_idxstats/samtools_idxstats" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/samtools/samtools_idxstats/samtools_idxstats b/target/executable/samtools/samtools_idxstats/samtools_idxstats index bbcfeade..9baf5701 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="2024-09-10T13:55:39Z" +LABEL org.opencontainers.image.created="2024-09-10T13:56:59Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" 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 7dde978e..8302d4e2 100644 --- a/target/executable/samtools/samtools_index/.config.vsh.yaml +++ b/target/executable/samtools/samtools_index/.config.vsh.yaml @@ -189,7 +189,7 @@ build_info: output: "target/executable/samtools/samtools_index" executable: "target/executable/samtools/samtools_index/samtools_index" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/samtools/samtools_index/samtools_index b/target/executable/samtools/samtools_index/samtools_index index 270323e7..1fda2ede 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="2024-09-10T13:55:39Z" +LABEL org.opencontainers.image.created="2024-09-10T13:56:58Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" 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 f985b59b..d62f71e3 100644 --- a/target/executable/samtools/samtools_sort/.config.vsh.yaml +++ b/target/executable/samtools/samtools_sort/.config.vsh.yaml @@ -332,7 +332,7 @@ build_info: output: "target/executable/samtools/samtools_sort" executable: "target/executable/samtools/samtools_sort/samtools_sort" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/samtools/samtools_sort/samtools_sort b/target/executable/samtools/samtools_sort/samtools_sort index 1aaf3c76..4c0f3d10 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="2024-09-10T13:55:42Z" +LABEL org.opencontainers.image.created="2024-09-10T13:57:01Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" 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 907d931b..98d03659 100644 --- a/target/executable/samtools/samtools_stats/.config.vsh.yaml +++ b/target/executable/samtools/samtools_stats/.config.vsh.yaml @@ -401,7 +401,7 @@ build_info: output: "target/executable/samtools/samtools_stats" executable: "target/executable/samtools/samtools_stats/samtools_stats" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/samtools/samtools_stats/samtools_stats b/target/executable/samtools/samtools_stats/samtools_stats index b4fb5a93..9bba90d7 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="2024-09-10T13:55:42Z" +LABEL org.opencontainers.image.created="2024-09-10T13:57:01Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" 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 7bd5cc40..57b9c780 100644 --- a/target/executable/samtools/samtools_view/.config.vsh.yaml +++ b/target/executable/samtools/samtools_view/.config.vsh.yaml @@ -665,7 +665,7 @@ build_info: output: "target/executable/samtools/samtools_view" executable: "target/executable/samtools/samtools_view/samtools_view" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/samtools/samtools_view/samtools_view b/target/executable/samtools/samtools_view/samtools_view index 8e52eb31..7ef55e93 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="2024-09-10T13:55:40Z" +LABEL org.opencontainers.image.created="2024-09-10T13:56:59Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" 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 80170287..73a0667d 100644 --- a/target/executable/seqtk/seqtk_sample/.config.vsh.yaml +++ b/target/executable/seqtk/seqtk_sample/.config.vsh.yaml @@ -173,7 +173,7 @@ build_info: output: "target/executable/seqtk/seqtk_sample" executable: "target/executable/seqtk/seqtk_sample/seqtk_sample" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/seqtk/seqtk_sample/seqtk_sample b/target/executable/seqtk/seqtk_sample/seqtk_sample index de115b1f..30c40f14 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="2024-09-10T13:55:54Z" +LABEL org.opencontainers.image.created="2024-09-10T13:57:14Z" LABEL org.opencontainers.image.source="https://github.com/lh3/seqtk/tree/v1.4" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" 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 01d90bec..2aa9b3dc 100644 --- a/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml +++ b/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml @@ -196,7 +196,7 @@ build_info: output: "target/executable/seqtk/seqtk_subseq" executable: "target/executable/seqtk/seqtk_subseq/seqtk_subseq" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/seqtk/seqtk_subseq/seqtk_subseq b/target/executable/seqtk/seqtk_subseq/seqtk_subseq index 0192c53e..15adbc1f 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="2024-09-10T13:55:54Z" +LABEL org.opencontainers.image.created="2024-09-10T13:57:14Z" LABEL org.opencontainers.image.source="https://github.com/lh3/seqtk/tree/v1.4" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/sortmerna/.config.vsh.yaml b/target/executable/sortmerna/.config.vsh.yaml index d5f3b7bd..dd4cdb89 100644 --- a/target/executable/sortmerna/.config.vsh.yaml +++ b/target/executable/sortmerna/.config.vsh.yaml @@ -591,7 +591,7 @@ build_info: output: "target/executable/sortmerna" executable: "target/executable/sortmerna/sortmerna" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/sortmerna/sortmerna b/target/executable/sortmerna/sortmerna index 2e6d89b5..b08b8dc3 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="2024-09-10T13:55:51Z" +LABEL org.opencontainers.image.created="2024-09-10T13:57:11Z" LABEL org.opencontainers.image.source="https://github.com/sortmerna/sortmerna" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" 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 fd557223..f25eb9b1 100644 --- a/target/executable/star/star_align_reads/.config.vsh.yaml +++ b/target/executable/star/star_align_reads/.config.vsh.yaml @@ -2663,7 +2663,7 @@ build_info: output: "target/executable/star/star_align_reads" executable: "target/executable/star/star_align_reads/star_align_reads" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/star/star_align_reads/star_align_reads b/target/executable/star/star_align_reads/star_align_reads index 44f93d98..25bce711 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="2024-09-10T13:55:46Z" +LABEL org.opencontainers.image.created="2024-09-10T13:57:06Z" LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" 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 5f3d26da..37eeae8e 100644 --- a/target/executable/star/star_genome_generate/.config.vsh.yaml +++ b/target/executable/star/star_genome_generate/.config.vsh.yaml @@ -333,7 +333,7 @@ build_info: output: "target/executable/star/star_genome_generate" executable: "target/executable/star/star_genome_generate/star_genome_generate" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/star/star_genome_generate/star_genome_generate b/target/executable/star/star_genome_generate/star_genome_generate index 7afb016a..7179877c 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="2024-09-10T13:55:46Z" +LABEL org.opencontainers.image.created="2024-09-10T13:57:06Z" LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" 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 65c8f8d7..a738d92d 100644 --- a/target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml +++ b/target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml @@ -611,7 +611,7 @@ build_info: output: "target/executable/umi_tools/umi_tools_dedup" executable: "target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup b/target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup index 27c3ce64..d2114f36 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="2024-09-10T13:55:44Z" +LABEL org.opencontainers.image.created="2024-09-10T13:57:03Z" LABEL org.opencontainers.image.source="https://github.com/CGATOxford/UMI-tools" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" 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 97f6a1b3..4c4e5c9f 100644 --- a/target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml +++ b/target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml @@ -449,7 +449,7 @@ build_info: output: "target/executable/umi_tools/umi_tools_extract" executable: "target/executable/umi_tools/umi_tools_extract/umi_tools_extract" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/umi_tools/umi_tools_extract/umi_tools_extract b/target/executable/umi_tools/umi_tools_extract/umi_tools_extract index 7f67d4f8..671c0883 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="2024-09-10T13:55:43Z" +LABEL org.opencontainers.image.created="2024-09-10T13:57:03Z" LABEL org.opencontainers.image.source="https://github.com/CGATOxford/UMI-tools" -LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" +LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e" 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 f861932f..ed2bec6e 100644 --- a/target/nextflow/agat/agat_convert_bed2gff/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_bed2gff/.config.vsh.yaml @@ -235,7 +235,7 @@ build_info: output: "target/nextflow/agat/agat_convert_bed2gff" executable: "target/nextflow/agat/agat_convert_bed2gff/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/agat/agat_convert_bed2gff/main.nf b/target/nextflow/agat/agat_convert_bed2gff/main.nf index 3258e5c4..5197ade9 100644 --- a/target/nextflow/agat/agat_convert_bed2gff/main.nf +++ b/target/nextflow/agat/agat_convert_bed2gff/main.nf @@ -3086,7 +3086,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_convert_bed2gff", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml b/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml index a60875f9..6dfcb278 100644 --- a/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml @@ -225,7 +225,7 @@ build_info: output: "target/nextflow/agat/agat_convert_embl2gff" executable: "target/nextflow/agat/agat_convert_embl2gff/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/agat/agat_convert_embl2gff/main.nf b/target/nextflow/agat/agat_convert_embl2gff/main.nf index 53664218..806cce8b 100644 --- a/target/nextflow/agat/agat_convert_embl2gff/main.nf +++ b/target/nextflow/agat/agat_convert_embl2gff/main.nf @@ -3079,7 +3079,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_convert_embl2gff", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml b/target/nextflow/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml index d30e6042..35b0e877 100644 --- a/target/nextflow/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml @@ -228,7 +228,7 @@ build_info: output: "target/nextflow/agat/agat_convert_sp_gff2gtf" executable: "target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf b/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf index f7dc61fd..19b5fbb0 100644 --- a/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf +++ b/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf @@ -3062,7 +3062,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_convert_sp_gff2gtf", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml b/target/nextflow/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml index beb434de..918aeccd 100644 --- a/target/nextflow/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml @@ -188,7 +188,7 @@ build_info: output: "target/nextflow/agat/agat_convert_sp_gff2tsv" executable: "target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf b/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf index b9642498..3806711b 100644 --- a/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf +++ b/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf @@ -3040,7 +3040,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_convert_sp_gff2tsv", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml b/target/nextflow/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml index ef46cbb4..2e70d754 100644 --- a/target/nextflow/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml @@ -195,7 +195,7 @@ build_info: output: "target/nextflow/agat/agat_convert_sp_gxf2gxf" executable: "target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf b/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf index e017ac9d..d58ade1c 100644 --- a/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf +++ b/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf @@ -3040,7 +3040,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_convert_sp_gxf2gxf", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/arriba/.config.vsh.yaml b/target/nextflow/arriba/.config.vsh.yaml index 951109a3..c0616f58 100644 --- a/target/nextflow/arriba/.config.vsh.yaml +++ b/target/nextflow/arriba/.config.vsh.yaml @@ -706,7 +706,7 @@ build_info: output: "target/nextflow/arriba" executable: "target/nextflow/arriba/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/arriba/main.nf b/target/nextflow/arriba/main.nf index f8391478..074f8521 100644 --- a/target/nextflow/arriba/main.nf +++ b/target/nextflow/arriba/main.nf @@ -3586,7 +3586,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/arriba", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/bcftools/bcftools_annotate/.config.vsh.yaml b/target/nextflow/bcftools/bcftools_annotate/.config.vsh.yaml new file mode 100644 index 00000000..7ddd2260 --- /dev/null +++ b/target/nextflow/bcftools/bcftools_annotate/.config.vsh.yaml @@ -0,0 +1,495 @@ +name: "bcftools_annotate" +namespace: "bcftools" +version: "main" +authors: +- name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatician" +argument_groups: +- name: "Inputs" + arguments: + - type: "file" + name: "--input" + alternatives: + - "-i" + description: "Input VCF/BCF file." + info: null + must_exist: true + create_parent: true + required: true + direction: "input" + multiple: true + multiple_sep: ";" +- name: "Outputs" + arguments: + - type: "file" + name: "--output" + alternatives: + - "-o" + description: "Output annotated file." + info: null + must_exist: true + create_parent: true + required: true + direction: "output" + multiple: false + multiple_sep: ";" +- name: "Options" + description: "For examples on how to use use bcftools annotate see http://samtools.github.io/bcftools/howtos/annotate.html.\n\ + For more details on the options see https://samtools.github.io/bcftools/bcftools.html#annotate.\n" + arguments: + - type: "file" + name: "--annotations" + alternatives: + - "--a" + description: "VCF file or tabix-indexed FILE with annotations: CHR\\tPOS[\\tVALUE]+\ + \ . \n" + info: null + must_exist: true + create_parent: true + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "string" + name: "--columns" + alternatives: + - "--c" + description: "List of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG.\ + \ \nSee man page for details.\n" + info: null + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "file" + name: "--columns_file" + alternatives: + - "--C" + description: "Read -c columns from FILE, one name per row, with optional --merge_logic\ + \ TYPE: NAME[ TYPE].\n" + info: null + must_exist: true + create_parent: true + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "string" + name: "--exclude" + alternatives: + - "--e" + description: "Exclude sites for which the expression is true.\nSee https://samtools.github.io/bcftools/bcftools.html#expressions\ + \ for details.\n" + info: null + example: + - "QUAL >= 30 && DP >= 10" + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "boolean_true" + name: "--force" + description: "continue even when parsing errors, such as undefined tags, are encountered.\ + \ \nNote this can be an unsafe operation and can result in corrupted BCF files.\ + \ \nIf this option is used, make sure to sanity check the result thoroughly.\n" + info: null + direction: "input" + - type: "string" + name: "--header_line" + alternatives: + - "--H" + description: "Header line which should be appended to the VCF header, can be given\ + \ multiple times.\n" + info: null + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "file" + name: "--header_lines" + alternatives: + - "--h" + description: "File with header lines to append to the VCF header.\nFor example:\n\ + \ ##INFO=\n ##INFO=\n" + info: null + must_exist: true + create_parent: true + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "string" + name: "--set_id" + alternatives: + - "--I" + description: "Set ID column using a `bcftools query`-like expression, see man\ + \ page for details.\n" + info: null + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "string" + name: "--include" + description: "Select sites for which the expression is true.\nSee https://samtools.github.io/bcftools/bcftools.html#expressions\ + \ for details.\n" + info: null + example: + - "QUAL >= 30 && DP >= 10" + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "boolean_true" + name: "--keep_sites" + alternatives: + - "--k" + description: "Leave --include/--exclude sites unchanged instead of discarding\ + \ them.\n" + info: null + direction: "input" + - type: "string" + name: "--merge_logic" + alternatives: + - "--l" + description: "When multiple regions overlap a single record, this option defines\ + \ how to treat multiple annotation values.\nSee man page for more details.\n" + info: null + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "string" + name: "--mark_sites" + alternatives: + - "--m" + description: "Annotate sites which are present (\"+\") or absent (\"-\") in the\ + \ -a file with a new INFO/TAG flag.\n" + info: null + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "string" + name: "--min_overlap" + description: "Minimum overlap required as a fraction of the variant in the annotation\ + \ -a file (ANN), \nin the target VCF file (:VCF), or both for reciprocal overlap\ + \ (ANN:VCF). \nBy default overlaps of arbitrary length are sufficient. \nThe\ + \ option can be used only with the tab-delimited annotation -a file and with\ + \ BEG and END columns present.\n" + info: null + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "boolean_true" + name: "--no_version" + description: "Do not append version and command line information to the output\ + \ VCF header.\n" + info: null + direction: "input" + - type: "string" + name: "--output_type" + alternatives: + - "--O" + description: "Output type:\n u: uncompressed BCF\n z: compressed VCF\n b: compressed\ + \ BCF\n v: uncompressed VCF\n" + info: null + required: false + choices: + - "u" + - "z" + - "b" + - "v" + direction: "input" + multiple: false + multiple_sep: ";" + - type: "string" + name: "--pair_logic" + description: "Controls how to match records from the annotation file to the target\ + \ VCF. \nEffective only when -a is a VCF or BCF file. \nThe option replaces\ + \ the former uninuitive --collapse. \nSee Common Options for more.\n" + info: null + required: false + choices: + - "snps" + - "indels" + - "both" + - "all" + - "some" + - "exact" + direction: "input" + multiple: false + multiple_sep: ";" + - type: "string" + name: "--regions" + alternatives: + - "--r" + description: "Restrict to comma-separated list of regions. \nFollowing formats\ + \ are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​].\n" + info: null + example: + - "20:1000000-2000000" + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "file" + name: "--regions_file" + alternatives: + - "--R" + description: "Restrict to regions listed in a file. \nRegions can be specified\ + \ either on a VCF, BED, or tab-delimited file (the default). \nFor more information\ + \ check manual.\n" + info: null + must_exist: true + create_parent: true + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "string" + name: "--regions_overlap" + description: "This option controls how overlapping records are determined: \n\ + set to 'pos' or '0' if the VCF record has to have POS inside a region (this\ + \ corresponds to the default behavior of -t/-T); \nset to 'record' or '1' if\ + \ also overlapping records with POS outside a region should be included (this\ + \ is the default behavior of -r/-R, \nand includes indels with POS at the end\ + \ of a region, which are technically outside the region); \nor set to 'variant'\ + \ or '2' to include only true overlapping variation (compare the full VCF representation\ + \ \"TA>T-\" vs the true sequence variation \"A>-\").\n" + info: null + required: false + choices: + - "pos" + - "record" + - "variant" + - "0" + - "1" + - "2" + direction: "input" + multiple: false + multiple_sep: ";" + - type: "file" + name: "--rename_annotations" + description: "Rename annotations: TYPE/old\\tnew, where TYPE is one of FILTER,INFO,FORMAT.\n" + info: null + must_exist: true + create_parent: true + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "file" + name: "--rename_chromosomes" + description: "Rename chromosomes according to the map in file, with \"old_name\ + \ new_name\\n\" pairs \nseparated by whitespaces, each on a separate line.\n" + info: null + must_exist: true + create_parent: true + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "string" + name: "--samples" + description: "Subset of samples to annotate.\nSee also https://samtools.github.io/bcftools/bcftools.html#common_options.\n" + info: null + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "file" + name: "--samples_file" + description: "Subset of samples to annotate in file format.\nSee also https://samtools.github.io/bcftools/bcftools.html#common_options.\n" + info: null + must_exist: true + create_parent: true + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "boolean_true" + name: "--single_overlaps" + description: "Use this option to keep memory requirements low with very large\ + \ annotation files. \nNote, however, that this comes at a cost, only single\ + \ overlapping intervals are considered in this mode. \nThis was the default\ + \ mode until the commit af6f0c9 (Feb 24 2019).\n" + info: null + direction: "input" + - type: "string" + name: "--remove" + alternatives: + - "--x" + description: "List of annotations to remove. \nUse \"FILTER\" to remove all filters\ + \ or \"FILTER/SomeFilter\" to remove a specific filter. \nSimilarly, \"INFO\"\ + \ can be used to remove all INFO tags and \"FORMAT\" to remove all FORMAT tags\ + \ except GT. \nTo remove all INFO tags except \"FOO\" and \"BAR\", use \"^INFO/FOO,INFO/BAR\"\ + \ (and similarly for FORMAT and FILTER). \n\"INFO\" can be abbreviated to \"\ + INF\" and \"FORMAT\" to \"FMT\".\n" + info: null + required: false + direction: "input" + multiple: false + multiple_sep: ";" +resources: +- type: "bash_script" + path: "script.sh" + is_executable: true +description: "Add or remove annotations from a VCF/BCF file.\n" +test_resources: +- type: "bash_script" + path: "test.sh" + is_executable: true +info: null +status: "enabled" +requirements: + commands: + - "ps" +keywords: +- "Annotate" +- "VCF" +- "BCF" +license: "MIT/Expat, GNU" +references: + doi: + - "https://doi.org/10.1093/gigascience/giab008" +links: + repository: "https://github.com/samtools/bcftools" + homepage: "https://samtools.github.io/bcftools/" + documentation: "https://samtools.github.io/bcftools/bcftools.html#annotate" + issue_tracker: "https://github.com/samtools/bcftools/issues" +runners: +- type: "executable" + id: "executable" + docker_setup_strategy: "ifneedbepullelsecachedbuild" +- type: "nextflow" + id: "nextflow" + directives: + tag: "$id" + auto: + simplifyInput: true + simplifyOutput: false + transcript: false + publish: false + config: + labels: + mem1gb: "memory = 1000000000.B" + mem2gb: "memory = 2000000000.B" + mem5gb: "memory = 5000000000.B" + mem10gb: "memory = 10000000000.B" + mem20gb: "memory = 20000000000.B" + mem50gb: "memory = 50000000000.B" + mem100gb: "memory = 100000000000.B" + mem200gb: "memory = 200000000000.B" + mem500gb: "memory = 500000000000.B" + mem1tb: "memory = 1000000000000.B" + mem2tb: "memory = 2000000000000.B" + mem5tb: "memory = 5000000000000.B" + mem10tb: "memory = 10000000000000.B" + mem20tb: "memory = 20000000000000.B" + mem50tb: "memory = 50000000000000.B" + mem100tb: "memory = 100000000000000.B" + mem200tb: "memory = 200000000000000.B" + mem500tb: "memory = 500000000000000.B" + mem1gib: "memory = 1073741824.B" + mem2gib: "memory = 2147483648.B" + mem4gib: "memory = 4294967296.B" + mem8gib: "memory = 8589934592.B" + mem16gib: "memory = 17179869184.B" + mem32gib: "memory = 34359738368.B" + mem64gib: "memory = 68719476736.B" + mem128gib: "memory = 137438953472.B" + mem256gib: "memory = 274877906944.B" + mem512gib: "memory = 549755813888.B" + mem1tib: "memory = 1099511627776.B" + mem2tib: "memory = 2199023255552.B" + mem4tib: "memory = 4398046511104.B" + mem8tib: "memory = 8796093022208.B" + mem16tib: "memory = 17592186044416.B" + mem32tib: "memory = 35184372088832.B" + mem64tib: "memory = 70368744177664.B" + mem128tib: "memory = 140737488355328.B" + mem256tib: "memory = 281474976710656.B" + mem512tib: "memory = 562949953421312.B" + cpu1: "cpus = 1" + cpu2: "cpus = 2" + cpu5: "cpus = 5" + cpu10: "cpus = 10" + cpu20: "cpus = 20" + cpu50: "cpus = 50" + cpu100: "cpus = 100" + cpu200: "cpus = 200" + cpu500: "cpus = 500" + cpu1000: "cpus = 1000" + debug: false + container: "docker" +engines: +- type: "docker" + id: "docker" + image: "debian:stable-slim" + target_registry: "images.viash-hub.com" + target_tag: "main" + namespace_separator: "/" + setup: + - type: "apt" + packages: + - "bcftools" + - "procps" + interactive: false + - type: "docker" + run: + - "echo \"bcftools: \\\"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftools\ + \ //p')\\\"\" > /var/software_versions.txt\n" + test_setup: + - type: "apt" + packages: + - "tabix" + interactive: false + entrypoint: [] + cmd: null +- type: "native" + id: "native" +build_info: + config: "src/bcftools/bcftools_annotate/config.vsh.yaml" + runner: "nextflow" + engine: "docker|native" + output: "target/nextflow/bcftools/bcftools_annotate" + executable: "target/nextflow/bcftools/bcftools_annotate/main.nf" + viash_version: "0.9.0-RC7" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" + git_remote: "https://github.com/viash-hub/biobox" +package_config: + name: "biobox" + version: "main" + description: "A collection of bioinformatics tools for working with sequence data.\n" + info: null + viash_version: "0.9.0-RC7" + source: "src" + target: "target" + config_mods: + - ".requirements.commands := ['ps']\n" + - ".engines += { type: \"native\" }" + - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" + - ".engines[.type == 'docker'].target_tag := 'main'" + keywords: + - "bioinformatics" + - "modules" + - "sequencing" + license: "MIT" + organization: "vsh" + links: + repository: "https://github.com/viash-hub/biobox" + issue_tracker: "https://github.com/viash-hub/biobox/issues" diff --git a/target/nextflow/bcftools/bcftools_annotate/main.nf b/target/nextflow/bcftools/bcftools_annotate/main.nf new file mode 100644 index 00000000..f491e8a6 --- /dev/null +++ b/target/nextflow/bcftools/bcftools_annotate/main.nf @@ -0,0 +1,3948 @@ +// bcftools_annotate main +// +// This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a +// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from +// Data Intuitive. +// +// The component may contain files which fall under a different license. The +// authors of this component should specify the license in the header of such +// files, or include a separate license file detailing the licenses of all included +// files. +// +// Component authors: +// * Theodoro Gasperin Terra Camargo (author) + +//////////////////////////// +// 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('\\$key', key_) + + // TODO: do the pathnames in state_ match up with the outputFilenames_? + + // convert state to yaml blob + def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename)) + + [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_] + } + | publishStatesProc + emit: input_ch + } + return publishStatesWf +} +process publishStatesProc { + // todo: check publishpath? + publishDir path: "${getPublishDir()}/", mode: "copy" + tag "$id" + input: + tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles) + output: + tuple val(id), path{[yamlFile] + outputFiles} + script: + def copyCommands = [ + inputFiles instanceof List ? inputFiles : [inputFiles], + outputFiles instanceof List ? outputFiles : [outputFiles] + ] + .transpose() + .collectMany{infile, outfile -> + if (infile.toString() != outfile.toString()) { + [ + "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"", + "cp -r '${infile.toString()}' '${outfile.toString()}'" + ] + } else { + // no need to copy if infile is the same as outfile + [] + } + } + """ +mkdir -p "\$(dirname '${yamlFile}')" +echo "Storing state as yaml" +echo '${yamlBlob}' > '${yamlFile}' +echo "Copying output files to destination folder" +${copyCommands.join("\n ")} +""" +} + + +// this assumes that the state contains no other values other than those specified in the config +def publishStatesByConfig(Map args) { + def config = args.get("config") + assert config != null : "publishStatesByConfig: config must be specified" + + def key_ = args.get("key", config.name) + assert key_ != null : "publishStatesByConfig: key must be specified" + + workflow publishStatesSimpleWf { + take: input_ch + main: + input_ch + | map { tup -> + def id_ = tup[0] + def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10] + def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad'] + + // TODO: allow overriding the state.yaml template + // TODO TODO: if auto.publish == "state", add output_state as an argument + def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' + def yamlFilename = yamlTemplate + .replaceAll('\\$id', id_) + .replaceAll('\\$key', key_) + def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() + + // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where + // - key is a String + // - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path) + // - inputPath is a List[Path] + // - outputFilename is a List[String] + // - (key, value) are the tuples that will be saved to the state.yaml file + // - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml) + def processedState = + config.allArguments + .findAll { it.direction == "output" } + .collectMany { par -> + def plainName_ = par.plainName + // if the state does not contain the key, it's an + // optional argument for which the component did + // not generate any output + if (!state_.containsKey(plainName_)) { + return [] + } + def value = state_[plainName_] + // if the parameter is not a file, it should be stored + // in the state as-is, but is not something that needs + // to be copied from the source path to the dest path + if (par.type != "file") { + return [[key: plainName_, value: value, inputPath: [], outputFilename: []]] + } + // if the orig state does not contain this filename, + // it's an optional argument for which the user specified + // that it should not be returned as a state + if (!origState_.containsKey(plainName_)) { + return [] + } + def filenameTemplate = origState_[plainName_] + // if the pararameter is multiple: true, fetch the template + if (par.multiple && filenameTemplate instanceof List) { + filenameTemplate = filenameTemplate[0] + } + // instantiate the template + def filename = filenameTemplate + .replaceAll('\\$id', id_) + .replaceAll('\\$key', key_) + if (par.multiple) { + // if the parameter is multiple: true, the filename + // should contain a wildcard '*' that is replaced with + // the index of the file + assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}" + def outputPerFile = value.withIndex().collect{ val, ix -> + def filename_ix = filename.replace("*", ix.toString()) + def value_ = java.nio.file.Paths.get(filename_ix) + // if id contains a slash + if (yamlDir != null) { + value_ = yamlDir.relativize(value_) + } + def inputPath = val instanceof File ? val.toPath() : val + [value: value_, inputPath: inputPath, outputFilename: filename_ix] + } + def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> + [key, outputPerFile.collect{dic -> dic[key]}] + } + return [[key: plainName_] + transposedOutputs] + } else { + def value_ = java.nio.file.Paths.get(filename) + // if id contains a slash + if (yamlDir != null) { + value_ = yamlDir.relativize(value_) + } + def inputPath = value instanceof File ? value.toPath() : value + return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]] + } + } + + def updatedState_ = processedState.collectEntries{[it.key, it.value]} + def inputPaths = processedState.collectMany{it.inputPath} + def outputFilenames = processedState.collectMany{it.outputFilename} + + // convert state to yaml blob + def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_) + + [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames] + } + | publishStatesProc + emit: input_ch + } + return publishStatesSimpleWf +} + +// helper file: 'src/main/resources/io/viash/runners/nextflow/states/setState.nf' +def setState(fun) { + assert fun instanceof Closure || fun instanceof Map || fun instanceof List : + "Error in setState: Expected process argument to be a Closure, a Map, or a List. Found: class ${fun.getClass()}" + + // if fun is a List, convert to map + if (fun instanceof List) { + // check whether fun is a list[string] + assert fun.every{it instanceof CharSequence} : "Error in setState: argument is a List, but not all elements are Strings" + fun = fun.collectEntries{[it, it]} + } + + // if fun is a map, convert to closure + if (fun instanceof Map) { + // check whether fun is a map[string, string] + assert fun.values().every{it instanceof CharSequence} : "Error in setState: argument is a Map, but not all values are Strings" + assert fun.keySet().every{it instanceof CharSequence} : "Error in setState: argument is a Map, but not all keys are Strings" + def funMap = fun.clone() + // turn the map into a closure to be used later on + fun = { id_, state_ -> + assert state_ instanceof Map : "Error in setState: the state is not a Map" + funMap.collectMany{newkey, origkey -> + if (state_.containsKey(origkey)) { + [[newkey, state_[origkey]]] + } else { + [] + } + }.collectEntries() + } + } + + map { tup -> + def id = tup[0] + def state = tup[1] + def unfilteredState = fun(id, state) + def newState = unfilteredState.findAll{key, val -> val != null} + [id, newState] + tup.drop(2) + } +} + +// helper file: 'src/main/resources/io/viash/runners/nextflow/workflowFactory/processAuto.nf' +// TODO: unit test processAuto +def processAuto(Map auto) { + // remove null values + auto = auto.findAll{k, v -> v != null} + + // check for unexpected keys + def expectedKeys = ["simplifyInput", "simplifyOutput", "transcript", "publish"] + def unexpectedKeys = auto.keySet() - expectedKeys + assert unexpectedKeys.isEmpty(), "unexpected keys in auto: '${unexpectedKeys.join("', '")}'" + + // check auto.simplifyInput + assert auto.simplifyInput instanceof Boolean, "auto.simplifyInput must be a boolean" + + // check auto.simplifyOutput + assert auto.simplifyOutput instanceof Boolean, "auto.simplifyOutput must be a boolean" + + // check auto.transcript + assert auto.transcript instanceof Boolean, "auto.transcript must be a boolean" + + // check auto.publish + assert auto.publish instanceof Boolean || auto.publish == "state", "auto.publish must be a boolean or 'state'" + + return auto.subMap(expectedKeys) +} + +// helper file: 'src/main/resources/io/viash/runners/nextflow/workflowFactory/processDirectives.nf' +def assertMapKeys(map, expectedKeys, requiredKeys, mapName) { + assert map instanceof Map : "Expected argument '$mapName' to be a Map. Found: class ${map.getClass()}" + map.forEach { key, val -> + assert key in expectedKeys : "Unexpected key '$key' in ${mapName ? mapName + " " : ""}map" + } + requiredKeys.forEach { requiredKey -> + assert map.containsKey(requiredKey) : "Missing required key '$key' in ${mapName ? mapName + " " : ""}map" + } +} + +// TODO: unit test processDirectives +def processDirectives(Map drctv) { + // remove null values + drctv = drctv.findAll{k, v -> v != null} + + // check for unexpected keys + def expectedKeys = [ + "accelerator", "afterScript", "beforeScript", "cache", "conda", "container", "containerOptions", "cpus", "disk", "echo", "errorStrategy", "executor", "machineType", "maxErrors", "maxForks", "maxRetries", "memory", "module", "penv", "pod", "publishDir", "queue", "label", "scratch", "storeDir", "stageInMode", "stageOutMode", "tag", "time" + ] + def unexpectedKeys = drctv.keySet() - expectedKeys + assert unexpectedKeys.isEmpty() : "Unexpected keys in process directive: '${unexpectedKeys.join("', '")}'" + + /* DIRECTIVE accelerator + accepted examples: + - [ limit: 4, type: "nvidia-tesla-k80" ] + */ + if (drctv.containsKey("accelerator")) { + assertMapKeys(drctv["accelerator"], ["type", "limit", "request", "runtime"], [], "accelerator") + } + + /* DIRECTIVE afterScript + accepted examples: + - "source /cluster/bin/cleanup" + */ + if (drctv.containsKey("afterScript")) { + assert drctv["afterScript"] instanceof CharSequence + } + + /* DIRECTIVE beforeScript + accepted examples: + - "source /cluster/bin/setup" + */ + if (drctv.containsKey("beforeScript")) { + assert drctv["beforeScript"] instanceof CharSequence + } + + /* DIRECTIVE cache + accepted examples: + - true + - false + - "deep" + - "lenient" + */ + if (drctv.containsKey("cache")) { + assert drctv["cache"] instanceof CharSequence || drctv["cache"] instanceof Boolean + if (drctv["cache"] instanceof CharSequence) { + assert drctv["cache"] in ["deep", "lenient"] : "Unexpected value for cache" + } + } + + /* DIRECTIVE conda + accepted examples: + - "bwa=0.7.15" + - "bwa=0.7.15 fastqc=0.11.5" + - ["bwa=0.7.15", "fastqc=0.11.5"] + */ + if (drctv.containsKey("conda")) { + if (drctv["conda"] instanceof List) { + drctv["conda"] = drctv["conda"].join(" ") + } + assert drctv["conda"] instanceof CharSequence + } + + /* DIRECTIVE container + accepted examples: + - "foo/bar:tag" + - [ registry: "reg", image: "im", tag: "ta" ] + is transformed to "reg/im:ta" + - [ image: "im" ] + is transformed to "im:latest" + */ + if (drctv.containsKey("container")) { + assert drctv["container"] instanceof Map || drctv["container"] instanceof CharSequence + if (drctv["container"] instanceof Map) { + def m = drctv["container"] + assertMapKeys(m, [ "registry", "image", "tag" ], ["image"], "container") + def part1 = + System.getenv('OVERRIDE_CONTAINER_REGISTRY') ? System.getenv('OVERRIDE_CONTAINER_REGISTRY') + "/" : + params.containsKey("override_container_registry") ? params["override_container_registry"] + "/" : // todo: remove? + m.registry ? m.registry + "/" : + "" + def part2 = m.image + def part3 = m.tag ? ":" + m.tag : ":latest" + drctv["container"] = part1 + part2 + part3 + } + } + + /* DIRECTIVE containerOptions + accepted examples: + - "--foo bar" + - ["--foo bar", "-f b"] + */ + if (drctv.containsKey("containerOptions")) { + if (drctv["containerOptions"] instanceof List) { + drctv["containerOptions"] = drctv["containerOptions"].join(" ") + } + assert drctv["containerOptions"] instanceof CharSequence + } + + /* DIRECTIVE cpus + accepted examples: + - 1 + - 10 + */ + if (drctv.containsKey("cpus")) { + assert drctv["cpus"] instanceof Integer + } + + /* DIRECTIVE disk + accepted examples: + - "1 GB" + - "2TB" + - "3.2KB" + - "10.B" + */ + if (drctv.containsKey("disk")) { + assert drctv["disk"] instanceof CharSequence + // assert drctv["disk"].matches("[0-9]+(\\.[0-9]*)? *[KMGTPEZY]?B") + // ^ does not allow closures + } + + /* DIRECTIVE echo + accepted examples: + - true + - false + */ + if (drctv.containsKey("echo")) { + assert drctv["echo"] instanceof Boolean + } + + /* DIRECTIVE errorStrategy + accepted examples: + - "terminate" + - "finish" + */ + if (drctv.containsKey("errorStrategy")) { + assert drctv["errorStrategy"] instanceof CharSequence + assert drctv["errorStrategy"] in ["terminate", "finish", "ignore", "retry"] : "Unexpected value for errorStrategy" + } + + /* DIRECTIVE executor + accepted examples: + - "local" + - "sge" + */ + if (drctv.containsKey("executor")) { + assert drctv["executor"] instanceof CharSequence + assert drctv["executor"] in ["local", "sge", "uge", "lsf", "slurm", "pbs", "pbspro", "moab", "condor", "nqsii", "ignite", "k8s", "awsbatch", "google-pipelines"] : "Unexpected value for executor" + } + + /* DIRECTIVE machineType + accepted examples: + - "n1-highmem-8" + */ + if (drctv.containsKey("machineType")) { + assert drctv["machineType"] instanceof CharSequence + } + + /* DIRECTIVE maxErrors + accepted examples: + - 1 + - 3 + */ + if (drctv.containsKey("maxErrors")) { + assert drctv["maxErrors"] instanceof Integer + } + + /* DIRECTIVE maxForks + accepted examples: + - 1 + - 3 + */ + if (drctv.containsKey("maxForks")) { + assert drctv["maxForks"] instanceof Integer + } + + /* DIRECTIVE maxRetries + accepted examples: + - 1 + - 3 + */ + if (drctv.containsKey("maxRetries")) { + assert drctv["maxRetries"] instanceof Integer + } + + /* DIRECTIVE memory + accepted examples: + - "1 GB" + - "2TB" + - "3.2KB" + - "10.B" + */ + if (drctv.containsKey("memory")) { + assert drctv["memory"] instanceof CharSequence + // assert drctv["memory"].matches("[0-9]+(\\.[0-9]*)? *[KMGTPEZY]?B") + // ^ does not allow closures + } + + /* DIRECTIVE module + accepted examples: + - "ncbi-blast/2.2.27" + - "ncbi-blast/2.2.27:t_coffee/10.0" + - ["ncbi-blast/2.2.27", "t_coffee/10.0"] + */ + if (drctv.containsKey("module")) { + if (drctv["module"] instanceof List) { + drctv["module"] = drctv["module"].join(":") + } + assert drctv["module"] instanceof CharSequence + } + + /* DIRECTIVE penv + accepted examples: + - "smp" + */ + if (drctv.containsKey("penv")) { + assert drctv["penv"] instanceof CharSequence + } + + /* DIRECTIVE pod + accepted examples: + - [ label: "key", value: "val" ] + - [ annotation: "key", value: "val" ] + - [ env: "key", value: "val" ] + - [ [label: "l", value: "v"], [env: "e", value: "v"]] + */ + if (drctv.containsKey("pod")) { + if (drctv["pod"] instanceof Map) { + drctv["pod"] = [ drctv["pod"] ] + } + assert drctv["pod"] instanceof List + drctv["pod"].forEach { pod -> + assert pod instanceof Map + // TODO: should more checks be added? + // See https://www.nextflow.io/docs/latest/process.html?highlight=directives#pod + // e.g. does it contain 'label' and 'value', or 'annotation' and 'value', or ...? + } + } + + /* DIRECTIVE publishDir + accepted examples: + - [] + - [ [ path: "foo", enabled: true ], [ path: "bar", enabled: false ] ] + - "/path/to/dir" + is transformed to [[ path: "/path/to/dir" ]] + - [ path: "/path/to/dir", mode: "cache" ] + is transformed to [[ path: "/path/to/dir", mode: "cache" ]] + */ + // TODO: should we also look at params["publishDir"]? + if (drctv.containsKey("publishDir")) { + def pblsh = drctv["publishDir"] + + // check different options + assert pblsh instanceof List || pblsh instanceof Map || pblsh instanceof CharSequence + + // turn into list if not already so + // for some reason, 'if (!pblsh instanceof List) pblsh = [ pblsh ]' doesn't work. + pblsh = pblsh instanceof List ? pblsh : [ pblsh ] + + // check elements of publishDir + pblsh = pblsh.collect{ elem -> + // turn into map if not already so + elem = elem instanceof CharSequence ? [ path: elem ] : elem + + // check types and keys + assert elem instanceof Map : "Expected publish argument '$elem' to be a String or a Map. Found: class ${elem.getClass()}" + assertMapKeys(elem, [ "path", "mode", "overwrite", "pattern", "saveAs", "enabled" ], ["path"], "publishDir") + + // check elements in map + assert elem.containsKey("path") + assert elem["path"] instanceof CharSequence + if (elem.containsKey("mode")) { + assert elem["mode"] instanceof CharSequence + assert elem["mode"] in [ "symlink", "rellink", "link", "copy", "copyNoFollow", "move" ] + } + if (elem.containsKey("overwrite")) { + assert elem["overwrite"] instanceof Boolean + } + if (elem.containsKey("pattern")) { + assert elem["pattern"] instanceof CharSequence + } + if (elem.containsKey("saveAs")) { + assert elem["saveAs"] instanceof CharSequence //: "saveAs as a Closure is currently not supported. Surround your closure with single quotes to get the desired effect. Example: '\{ foo \}'" + } + if (elem.containsKey("enabled")) { + assert elem["enabled"] instanceof Boolean + } + + // return final result + elem + } + // store final directive + drctv["publishDir"] = pblsh + } + + /* DIRECTIVE queue + accepted examples: + - "long" + - "short,long" + - ["short", "long"] + */ + if (drctv.containsKey("queue")) { + if (drctv["queue"] instanceof List) { + drctv["queue"] = drctv["queue"].join(",") + } + assert drctv["queue"] instanceof CharSequence + } + + /* DIRECTIVE label + accepted examples: + - "big_mem" + - "big_cpu" + - ["big_mem", "big_cpu"] + */ + if (drctv.containsKey("label")) { + if (drctv["label"] instanceof CharSequence) { + drctv["label"] = [ drctv["label"] ] + } + assert drctv["label"] instanceof List + drctv["label"].forEach { label -> + assert label instanceof CharSequence + // assert label.matches("[a-zA-Z0-9]([a-zA-Z0-9_]*[a-zA-Z0-9])?") + // ^ does not allow closures + } + } + + /* DIRECTIVE scratch + accepted examples: + - true + - "/path/to/scratch" + - '$MY_PATH_TO_SCRATCH' + - "ram-disk" + */ + if (drctv.containsKey("scratch")) { + assert drctv["scratch"] == true || drctv["scratch"] instanceof CharSequence + } + + /* DIRECTIVE storeDir + accepted examples: + - "/path/to/storeDir" + */ + if (drctv.containsKey("storeDir")) { + assert drctv["storeDir"] instanceof CharSequence + } + + /* DIRECTIVE stageInMode + accepted examples: + - "copy" + - "link" + */ + if (drctv.containsKey("stageInMode")) { + assert drctv["stageInMode"] instanceof CharSequence + assert drctv["stageInMode"] in ["copy", "link", "symlink", "rellink"] + } + + /* DIRECTIVE stageOutMode + accepted examples: + - "copy" + - "link" + */ + if (drctv.containsKey("stageOutMode")) { + assert drctv["stageOutMode"] instanceof CharSequence + assert drctv["stageOutMode"] in ["copy", "move", "rsync"] + } + + /* DIRECTIVE tag + accepted examples: + - "foo" + - '$id' + */ + if (drctv.containsKey("tag")) { + assert drctv["tag"] instanceof CharSequence + } + + /* DIRECTIVE time + accepted examples: + - "1h" + - "2days" + - "1day 6hours 3minutes 30seconds" + */ + if (drctv.containsKey("time")) { + assert drctv["time"] instanceof CharSequence + // todo: validation regex? + } + + return drctv +} + +// helper file: 'src/main/resources/io/viash/runners/nextflow/workflowFactory/processWorkflowArgs.nf' +def processWorkflowArgs(Map args, Map defaultWfArgs, Map meta) { + // override defaults with args + def workflowArgs = defaultWfArgs + args + + // check whether 'key' exists + assert workflowArgs.containsKey("key") : "Error in module '${meta.config.name}': key is a required argument" + + // if 'key' is a closure, apply it to the original key + if (workflowArgs["key"] instanceof Closure) { + workflowArgs["key"] = workflowArgs["key"](meta.config.name) + } + def key = workflowArgs["key"] + assert key instanceof CharSequence : "Expected process argument 'key' to be a String. Found: class ${key.getClass()}" + assert key ==~ /^[a-zA-Z_]\w*$/ : "Error in module '$key': Expected process argument 'key' to consist of only letters, digits or underscores. Found: ${key}" + + // check for any unexpected keys + def expectedKeys = ["key", "directives", "auto", "map", "mapId", "mapData", "mapPassthrough", "filter", "runIf", "fromState", "toState", "args", "renameKeys", "debug"] + def unexpectedKeys = workflowArgs.keySet() - expectedKeys + assert unexpectedKeys.isEmpty() : "Error in module '$key': unexpected arguments to the '.run()' function: '${unexpectedKeys.join("', '")}'" + + // check whether directives exists and apply defaults + assert workflowArgs.containsKey("directives") : "Error in module '$key': directives is a required argument" + assert workflowArgs["directives"] instanceof Map : "Error in module '$key': Expected process argument 'directives' to be a Map. Found: class ${workflowArgs['directives'].getClass()}" + workflowArgs["directives"] = processDirectives(defaultWfArgs.directives + workflowArgs["directives"]) + + // check whether directives exists and apply defaults + assert workflowArgs.containsKey("auto") : "Error in module '$key': auto is a required argument" + assert workflowArgs["auto"] instanceof Map : "Error in module '$key': Expected process argument 'auto' to be a Map. Found: class ${workflowArgs['auto'].getClass()}" + workflowArgs["auto"] = processAuto(defaultWfArgs.auto + workflowArgs["auto"]) + + // auto define publish, if so desired + if (workflowArgs.auto.publish == true && (workflowArgs.directives.publishDir != null ? workflowArgs.directives.publishDir : [:]).isEmpty()) { + // can't assert at this level thanks to the no_publish profile + // assert params.containsKey("publishDir") || params.containsKey("publish_dir") : + // "Error in module '${workflowArgs['key']}': if auto.publish is true, params.publish_dir needs to be defined.\n" + + // " Example: params.publish_dir = \"./output/\"" + def publishDir = getPublishDir() + + if (publishDir != null) { + workflowArgs.directives.publishDir = [[ + path: publishDir, + saveAs: "{ it.startsWith('.') ? null : it }", // don't publish hidden files, by default + mode: "copy" + ]] + } + } + + // auto define transcript, if so desired + if (workflowArgs.auto.transcript == true) { + // can't assert at this level thanks to the no_publish profile + // assert params.containsKey("transcriptsDir") || params.containsKey("transcripts_dir") || params.containsKey("publishDir") || params.containsKey("publish_dir") : + // "Error in module '${workflowArgs['key']}': if auto.transcript is true, either params.transcripts_dir or params.publish_dir needs to be defined.\n" + + // " Example: params.transcripts_dir = \"./transcripts/\"" + def transcriptsDir = + params.containsKey("transcripts_dir") ? params.transcripts_dir : + params.containsKey("transcriptsDir") ? params.transcriptsDir : + params.containsKey("publish_dir") ? params.publish_dir + "/_transcripts" : + params.containsKey("publishDir") ? params.publishDir + "/_transcripts" : + null + if (transcriptsDir != null) { + def timestamp = nextflow.Nextflow.getSession().getWorkflowMetadata().start.format('yyyy-MM-dd_HH-mm-ss') + def transcriptsPublishDir = [ + path: "$transcriptsDir/$timestamp/\${task.process.replaceAll(':', '-')}/\${id}/", + saveAs: "{ it.startsWith('.') ? it.replaceAll('^.', '') : null }", + mode: "copy" + ] + def publishDirs = workflowArgs.directives.publishDir != null ? workflowArgs.directives.publishDir : null ? workflowArgs.directives.publishDir : [] + workflowArgs.directives.publishDir = publishDirs + transcriptsPublishDir + } + } + + // if this is a stubrun, remove certain directives? + if (workflow.stubRun) { + workflowArgs.directives.keySet().removeAll(["publishDir", "cpus", "memory", "label"]) + } + + for (nam in ["map", "mapId", "mapData", "mapPassthrough", "filter", "runIf"]) { + if (workflowArgs.containsKey(nam) && workflowArgs[nam]) { + assert workflowArgs[nam] instanceof Closure : "Error in module '$key': Expected process argument '$nam' to be null or a Closure. Found: class ${workflowArgs[nam].getClass()}" + } + } + + // TODO: should functions like 'map', 'mapId', 'mapData', 'mapPassthrough' be deprecated as well? + for (nam in ["map", "mapData", "mapPassthrough", "renameKeys"]) { + if (workflowArgs.containsKey(nam) && workflowArgs[nam] != null) { + log.warn "module '$key': workflow argument '$nam' is deprecated and will be removed in Viash 0.9.0. Please use 'fromState' and 'toState' instead." + } + } + + // check fromState + workflowArgs["fromState"] = _processFromState(workflowArgs.get("fromState"), key, meta.config) + + // check toState + workflowArgs["toState"] = _processToState(workflowArgs.get("toState"), key, meta.config) + + // return output + return workflowArgs +} + +def _processFromState(fromState, key_, config_) { + assert fromState == null || fromState instanceof Closure || fromState instanceof Map || fromState instanceof List : + "Error in module '$key_': Expected process argument 'fromState' to be null, a Closure, a Map, or a List. Found: class ${fromState.getClass()}" + if (fromState == null) { + return null + } + + // if fromState is a List, convert to map + if (fromState instanceof List) { + // check whether fromstate is a list[string] + assert fromState.every{it instanceof CharSequence} : "Error in module '$key_': fromState is a List, but not all elements are Strings" + fromState = fromState.collectEntries{[it, it]} + } + + // if fromState is a map, convert to closure + if (fromState instanceof Map) { + // check whether fromstate is a map[string, string] + assert fromState.values().every{it instanceof CharSequence} : "Error in module '$key_': fromState is a Map, but not all values are Strings" + assert fromState.keySet().every{it instanceof CharSequence} : "Error in module '$key_': fromState is a Map, but not all keys are Strings" + def fromStateMap = fromState.clone() + def requiredInputNames = meta.config.allArguments.findAll{it.required && it.direction == "Input"}.collect{it.plainName} + // turn the map into a closure to be used later on + fromState = { it -> + def state = it[1] + assert state instanceof Map : "Error in module '$key_': the state is not a Map" + def data = fromStateMap.collectMany{newkey, origkey -> + // check whether newkey corresponds to a required argument + if (state.containsKey(origkey)) { + [[newkey, state[origkey]]] + } else if (!requiredInputNames.contains(origkey)) { + [] + } else { + throw new Exception("Error in module '$key_': fromState key '$origkey' not found in current state") + } + }.collectEntries() + data + } + } + + return fromState +} + +def _processToState(toState, key_, config_) { + if (toState == null) { + toState = { tup -> tup[1] } + } + + // toState should be a closure, map[string, string], or list[string] + assert toState instanceof Closure || toState instanceof Map || toState instanceof List : + "Error in module '$key_': Expected process argument 'toState' to be a Closure, a Map, or a List. Found: class ${toState.getClass()}" + + // if toState is a List, convert to map + if (toState instanceof List) { + // check whether toState is a list[string] + assert toState.every{it instanceof CharSequence} : "Error in module '$key_': toState is a List, but not all elements are Strings" + toState = toState.collectEntries{[it, it]} + } + + // if toState is a map, convert to closure + if (toState instanceof Map) { + // check whether toState is a map[string, string] + assert toState.values().every{it instanceof CharSequence} : "Error in module '$key_': toState is a Map, but not all values are Strings" + assert toState.keySet().every{it instanceof CharSequence} : "Error in module '$key_': toState is a Map, but not all keys are Strings" + def toStateMap = toState.clone() + def requiredOutputNames = config_.allArguments.findAll{it.required && it.direction == "Output"}.collect{it.plainName} + // turn the map into a closure to be used later on + toState = { it -> + def output = it[1] + def state = it[2] + assert output instanceof Map : "Error in module '$key_': the output is not a Map" + assert state instanceof Map : "Error in module '$key_': the state is not a Map" + def extraEntries = toStateMap.collectMany{newkey, origkey -> + // check whether newkey corresponds to a required argument + if (output.containsKey(origkey)) { + [[newkey, output[origkey]]] + } else if (!requiredOutputNames.contains(origkey)) { + [] + } else { + throw new Exception("Error in module '$key_': toState key '$origkey' not found in current output") + } + }.collectEntries() + state + extraEntries + } + } + + return toState +} + +// helper file: 'src/main/resources/io/viash/runners/nextflow/workflowFactory/workflowFactory.nf' +def _debug(workflowArgs, debugKey) { + if (workflowArgs.debug) { + view { "process '${workflowArgs.key}' $debugKey tuple: $it" } + } else { + map { it } + } +} + +// depends on: innerWorkflowFactory +def workflowFactory(Map args, Map defaultWfArgs, Map meta) { + def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta) + def key_ = workflowArgs["key"] + + workflow workflowInstance { + take: input_ + + main: + def chModified = input_ + | checkUniqueIds([:]) + | _debug(workflowArgs, "input") + | map { tuple -> + tuple = deepClone(tuple) + + if (workflowArgs.map) { + tuple = workflowArgs.map(tuple) + } + if (workflowArgs.mapId) { + tuple[0] = workflowArgs.mapId(tuple[0]) + } + if (workflowArgs.mapData) { + tuple[1] = workflowArgs.mapData(tuple[1]) + } + if (workflowArgs.mapPassthrough) { + tuple = tuple.take(2) + workflowArgs.mapPassthrough(tuple.drop(2)) + } + + // check tuple + assert tuple instanceof List : + "Error in module '${key_}': element in channel should be a tuple [id, data, ...otherargs...]\n" + + " Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" + + " Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}" + assert tuple.size() >= 2 : + "Error in module '${key_}': expected length of tuple in input channel to be two or greater.\n" + + " Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" + + " Found: tuple.size() == ${tuple.size()}" + + // check id field + if (tuple[0] instanceof GString) { + tuple[0] = tuple[0].toString() + } + assert tuple[0] instanceof CharSequence : + "Error in module '${key_}': first element of tuple in channel should be a String\n" + + " Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" + + " Found: ${tuple[0]}" + + // match file to input file + if (workflowArgs.auto.simplifyInput && (tuple[1] instanceof Path || tuple[1] instanceof List)) { + def inputFiles = meta.config.allArguments + .findAll { it.type == "file" && it.direction == "input" } + + assert inputFiles.size() == 1 : + "Error in module '${key_}' id '${tuple[0]}'.\n" + + " Anonymous file inputs are only allowed when the process has exactly one file input.\n" + + " Expected: inputFiles.size() == 1. Found: inputFiles.size() is ${inputFiles.size()}" + + tuple[1] = [[ inputFiles[0].plainName, tuple[1] ]].collectEntries() + } + + // check data field + assert tuple[1] instanceof Map : + "Error in module '${key_}' id '${tuple[0]}': second element of tuple in channel should be a Map\n" + + " Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" + + " Expected class: Map. Found: tuple[1].getClass() is ${tuple[1].getClass()}" + + // rename keys of data field in tuple + if (workflowArgs.renameKeys) { + assert workflowArgs.renameKeys instanceof Map : + "Error renaming data keys in module '${key_}' id '${tuple[0]}'.\n" + + " Example: renameKeys: ['new_key': 'old_key'].\n" + + " Expected class: Map. Found: renameKeys.getClass() is ${workflowArgs.renameKeys.getClass()}" + assert tuple[1] instanceof Map : + "Error renaming data keys in module '${key_}' id '${tuple[0]}'.\n" + + " Expected class: Map. Found: tuple[1].getClass() is ${tuple[1].getClass()}" + + // TODO: allow renameKeys to be a function? + workflowArgs.renameKeys.each { newKey, oldKey -> + assert newKey instanceof CharSequence : + "Error renaming data keys in module '${key_}' id '${tuple[0]}'.\n" + + " Example: renameKeys: ['new_key': 'old_key'].\n" + + " Expected class of newKey: String. Found: newKey.getClass() is ${newKey.getClass()}" + assert oldKey instanceof CharSequence : + "Error renaming data keys in module '${key_}' id '${tuple[0]}'.\n" + + " Example: renameKeys: ['new_key': 'old_key'].\n" + + " Expected class of oldKey: String. Found: oldKey.getClass() is ${oldKey.getClass()}" + assert tuple[1].containsKey(oldKey) : + "Error renaming data keys in module '${key}' id '${tuple[0]}'.\n" + + " Key '$oldKey' is missing in the data map. tuple[1].keySet() is '${tuple[1].keySet()}'" + tuple[1].put(newKey, tuple[1][oldKey]) + } + tuple[1].keySet().removeAll(workflowArgs.renameKeys.collect{ newKey, oldKey -> oldKey }) + } + tuple + } + + + def 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" : "bcftools_annotate", + "namespace" : "bcftools", + "version" : "main", + "authors" : [ + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatician" + } + ] + } + } + ], + "argument_groups" : [ + { + "name" : "Inputs", + "arguments" : [ + { + "type" : "file", + "name" : "--input", + "alternatives" : [ + "-i" + ], + "description" : "Input VCF/BCF file.", + "must_exist" : true, + "create_parent" : true, + "required" : true, + "direction" : "input", + "multiple" : true, + "multiple_sep" : ";" + } + ] + }, + { + "name" : "Outputs", + "arguments" : [ + { + "type" : "file", + "name" : "--output", + "alternatives" : [ + "-o" + ], + "description" : "Output annotated file.", + "must_exist" : true, + "create_parent" : true, + "required" : true, + "direction" : "output", + "multiple" : false, + "multiple_sep" : ";" + } + ] + }, + { + "name" : "Options", + "description" : "For examples on how to use use bcftools annotate see http://samtools.github.io/bcftools/howtos/annotate.html.\nFor more details on the options see https://samtools.github.io/bcftools/bcftools.html#annotate.\n", + "arguments" : [ + { + "type" : "file", + "name" : "--annotations", + "alternatives" : [ + "--a" + ], + "description" : "VCF file or tabix-indexed FILE with annotations: CHR\\\\tPOS[\\\\tVALUE]+ . \n", + "must_exist" : true, + "create_parent" : true, + "required" : false, + "direction" : "input", + "multiple" : false, + "multiple_sep" : ";" + }, + { + "type" : "string", + "name" : "--columns", + "alternatives" : [ + "--c" + ], + "description" : "List of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. \nSee man page for details.\n", + "required" : false, + "direction" : "input", + "multiple" : false, + "multiple_sep" : ";" + }, + { + "type" : "file", + "name" : "--columns_file", + "alternatives" : [ + "--C" + ], + "description" : "Read -c columns from FILE, one name per row, with optional --merge_logic TYPE: NAME[ TYPE].\n", + "must_exist" : true, + "create_parent" : true, + "required" : false, + "direction" : "input", + "multiple" : false, + "multiple_sep" : ";" + }, + { + "type" : "string", + "name" : "--exclude", + "alternatives" : [ + "--e" + ], + "description" : "Exclude sites for which the expression is true.\nSee https://samtools.github.io/bcftools/bcftools.html#expressions for details.\n", + "example" : [ + "QUAL >= 30 && DP >= 10" + ], + "required" : false, + "direction" : "input", + "multiple" : false, + "multiple_sep" : ";" + }, + { + "type" : "boolean_true", + "name" : "--force", + "description" : "continue even when parsing errors, such as undefined tags, are encountered. \nNote this can be an unsafe operation and can result in corrupted BCF files. \nIf this option is used, make sure to sanity check the result thoroughly.\n", + "direction" : "input" + }, + { + "type" : "string", + "name" : "--header_line", + "alternatives" : [ + "--H" + ], + "description" : "Header line which should be appended to the VCF header, can be given multiple times.\n", + "required" : false, + "direction" : "input", + "multiple" : false, + "multiple_sep" : ";" + }, + { + "type" : "file", + "name" : "--header_lines", + "alternatives" : [ + "--h" + ], + "description" : "File with header lines to append to the VCF header.\nFor example:\n ##INFO=\n ##INFO=\n", + "must_exist" : true, + "create_parent" : true, + "required" : false, + "direction" : "input", + "multiple" : false, + "multiple_sep" : ";" + }, + { + "type" : "string", + "name" : "--set_id", + "alternatives" : [ + "--I" + ], + "description" : "Set ID column using a `bcftools query`-like expression, see man page for details.\n", + "required" : false, + "direction" : "input", + "multiple" : false, + "multiple_sep" : ";" + }, + { + "type" : "string", + "name" : "--include", + "description" : "Select sites for which the expression is true.\nSee https://samtools.github.io/bcftools/bcftools.html#expressions for details.\n", + "example" : [ + "QUAL >= 30 && DP >= 10" + ], + "required" : false, + "direction" : "input", + "multiple" : false, + "multiple_sep" : ";" + }, + { + "type" : "boolean_true", + "name" : "--keep_sites", + "alternatives" : [ + "--k" + ], + "description" : "Leave --include/--exclude sites unchanged instead of discarding them.\n", + "direction" : "input" + }, + { + "type" : "string", + "name" : "--merge_logic", + "alternatives" : [ + "--l" + ], + "description" : "When multiple regions overlap a single record, this option defines how to treat multiple annotation values.\nSee man page for more details.\n", + "required" : false, + "direction" : "input", + "multiple" : false, + "multiple_sep" : ";" + }, + { + "type" : "string", + "name" : "--mark_sites", + "alternatives" : [ + "--m" + ], + "description" : "Annotate sites which are present (\\"+\\") or absent (\\"-\\") in the -a file with a new INFO/TAG flag.\n", + "required" : false, + "direction" : "input", + "multiple" : false, + "multiple_sep" : ";" + }, + { + "type" : "string", + "name" : "--min_overlap", + "description" : "Minimum overlap required as a fraction of the variant in the annotation -a file (ANN), \nin the target VCF file (:VCF), or both for reciprocal overlap (ANN:VCF). \nBy default overlaps of arbitrary length are sufficient. \nThe option can be used only with the tab-delimited annotation -a file and with BEG and END columns present.\n", + "required" : false, + "direction" : "input", + "multiple" : false, + "multiple_sep" : ";" + }, + { + "type" : "boolean_true", + "name" : "--no_version", + "description" : "Do not append version and command line information to the output VCF header.\n", + "direction" : "input" + }, + { + "type" : "string", + "name" : "--output_type", + "alternatives" : [ + "--O" + ], + "description" : "Output type:\n u: uncompressed BCF\n z: compressed VCF\n b: compressed BCF\n v: uncompressed VCF\n", + "required" : false, + "choices" : [ + "u", + "z", + "b", + "v" + ], + "direction" : "input", + "multiple" : false, + "multiple_sep" : ";" + }, + { + "type" : "string", + "name" : "--pair_logic", + "description" : "Controls how to match records from the annotation file to the target VCF. \nEffective only when -a is a VCF or BCF file. \nThe option replaces the former uninuitive --collapse. \nSee Common Options for more.\n", + "required" : false, + "choices" : [ + "snps", + "indels", + "both", + "all", + "some", + "exact" + ], + "direction" : "input", + "multiple" : false, + "multiple_sep" : ";" + }, + { + "type" : "string", + "name" : "--regions", + "alternatives" : [ + "--r" + ], + "description" : "Restrict to comma-separated list of regions. \nFollowing formats are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​].\n", + "example" : [ + "20:1000000-2000000" + ], + "required" : false, + "direction" : "input", + "multiple" : false, + "multiple_sep" : ";" + }, + { + "type" : "file", + "name" : "--regions_file", + "alternatives" : [ + "--R" + ], + "description" : "Restrict to regions listed in a file. \nRegions can be specified either on a VCF, BED, or tab-delimited file (the default). \nFor more information check manual.\n", + "must_exist" : true, + "create_parent" : true, + "required" : false, + "direction" : "input", + "multiple" : false, + "multiple_sep" : ";" + }, + { + "type" : "string", + "name" : "--regions_overlap", + "description" : "This option controls how overlapping records are determined: \nset to 'pos' or '0' if the VCF record has to have POS inside a region (this corresponds to the default behavior of -t/-T); \nset to 'record' or '1' if also overlapping records with POS outside a region should be included (this is the default behavior of -r/-R, \nand includes indels with POS at the end of a region, which are technically outside the region); \nor set to 'variant' or '2' to include only true overlapping variation (compare the full VCF representation \\"TA>T-\\" vs the true sequence variation \\"A>-\\").\n", + "required" : false, + "choices" : [ + "pos", + "record", + "variant", + "0", + "1", + "2" + ], + "direction" : "input", + "multiple" : false, + "multiple_sep" : ";" + }, + { + "type" : "file", + "name" : "--rename_annotations", + "description" : "Rename annotations: TYPE/old\\\\tnew, where TYPE is one of FILTER,INFO,FORMAT.\n", + "must_exist" : true, + "create_parent" : true, + "required" : false, + "direction" : "input", + "multiple" : false, + "multiple_sep" : ";" + }, + { + "type" : "file", + "name" : "--rename_chromosomes", + "description" : "Rename chromosomes according to the map in file, with \\"old_name new_name\\\\n\\" pairs \nseparated by whitespaces, each on a separate line.\n", + "must_exist" : true, + "create_parent" : true, + "required" : false, + "direction" : "input", + "multiple" : false, + "multiple_sep" : ";" + }, + { + "type" : "string", + "name" : "--samples", + "description" : "Subset of samples to annotate.\nSee also https://samtools.github.io/bcftools/bcftools.html#common_options.\n", + "required" : false, + "direction" : "input", + "multiple" : false, + "multiple_sep" : ";" + }, + { + "type" : "file", + "name" : "--samples_file", + "description" : "Subset of samples to annotate in file format.\nSee also https://samtools.github.io/bcftools/bcftools.html#common_options.\n", + "must_exist" : true, + "create_parent" : true, + "required" : false, + "direction" : "input", + "multiple" : false, + "multiple_sep" : ";" + }, + { + "type" : "boolean_true", + "name" : "--single_overlaps", + "description" : "Use this option to keep memory requirements low with very large annotation files. \nNote, however, that this comes at a cost, only single overlapping intervals are considered in this mode. \nThis was the default mode until the commit af6f0c9 (Feb 24 2019).\n", + "direction" : "input" + }, + { + "type" : "string", + "name" : "--remove", + "alternatives" : [ + "--x" + ], + "description" : "List of annotations to remove. \nUse \\"FILTER\\" to remove all filters or \\"FILTER/SomeFilter\\" to remove a specific filter. \nSimilarly, \\"INFO\\" can be used to remove all INFO tags and \\"FORMAT\\" to remove all FORMAT tags except GT. \nTo remove all INFO tags except \\"FOO\\" and \\"BAR\\", use \\"^INFO/FOO,INFO/BAR\\" (and similarly for FORMAT and FILTER). \n\\"INFO\\" can be abbreviated to \\"INF\\" and \\"FORMAT\\" to \\"FMT\\".\n", + "required" : false, + "direction" : "input", + "multiple" : false, + "multiple_sep" : ";" + } + ] + } + ], + "resources" : [ + { + "type" : "bash_script", + "path" : "script.sh", + "is_executable" : true + } + ], + "description" : "Add or remove annotations from a VCF/BCF file.\n", + "test_resources" : [ + { + "type" : "bash_script", + "path" : "test.sh", + "is_executable" : true + } + ], + "status" : "enabled", + "requirements" : { + "commands" : [ + "ps" + ] + }, + "keywords" : [ + "Annotate", + "VCF", + "BCF" + ], + "license" : "MIT/Expat, GNU", + "references" : { + "doi" : [ + "https://doi.org/10.1093/gigascience/giab008" + ] + }, + "links" : { + "repository" : "https://github.com/samtools/bcftools", + "homepage" : "https://samtools.github.io/bcftools/", + "documentation" : "https://samtools.github.io/bcftools/bcftools.html#annotate", + "issue_tracker" : "https://github.com/samtools/bcftools/issues" + }, + "runners" : [ + { + "type" : "executable", + "id" : "executable", + "docker_setup_strategy" : "ifneedbepullelsecachedbuild" + }, + { + "type" : "nextflow", + "id" : "nextflow", + "directives" : { + "tag" : "$id" + }, + "auto" : { + "simplifyInput" : true, + "simplifyOutput" : false, + "transcript" : false, + "publish" : false + }, + "config" : { + "labels" : { + "mem1gb" : "memory = 1000000000.B", + "mem2gb" : "memory = 2000000000.B", + "mem5gb" : "memory = 5000000000.B", + "mem10gb" : "memory = 10000000000.B", + "mem20gb" : "memory = 20000000000.B", + "mem50gb" : "memory = 50000000000.B", + "mem100gb" : "memory = 100000000000.B", + "mem200gb" : "memory = 200000000000.B", + "mem500gb" : "memory = 500000000000.B", + "mem1tb" : "memory = 1000000000000.B", + "mem2tb" : "memory = 2000000000000.B", + "mem5tb" : "memory = 5000000000000.B", + "mem10tb" : "memory = 10000000000000.B", + "mem20tb" : "memory = 20000000000000.B", + "mem50tb" : "memory = 50000000000000.B", + "mem100tb" : "memory = 100000000000000.B", + "mem200tb" : "memory = 200000000000000.B", + "mem500tb" : "memory = 500000000000000.B", + "mem1gib" : "memory = 1073741824.B", + "mem2gib" : "memory = 2147483648.B", + "mem4gib" : "memory = 4294967296.B", + "mem8gib" : "memory = 8589934592.B", + "mem16gib" : "memory = 17179869184.B", + "mem32gib" : "memory = 34359738368.B", + "mem64gib" : "memory = 68719476736.B", + "mem128gib" : "memory = 137438953472.B", + "mem256gib" : "memory = 274877906944.B", + "mem512gib" : "memory = 549755813888.B", + "mem1tib" : "memory = 1099511627776.B", + "mem2tib" : "memory = 2199023255552.B", + "mem4tib" : "memory = 4398046511104.B", + "mem8tib" : "memory = 8796093022208.B", + "mem16tib" : "memory = 17592186044416.B", + "mem32tib" : "memory = 35184372088832.B", + "mem64tib" : "memory = 70368744177664.B", + "mem128tib" : "memory = 140737488355328.B", + "mem256tib" : "memory = 281474976710656.B", + "mem512tib" : "memory = 562949953421312.B", + "cpu1" : "cpus = 1", + "cpu2" : "cpus = 2", + "cpu5" : "cpus = 5", + "cpu10" : "cpus = 10", + "cpu20" : "cpus = 20", + "cpu50" : "cpus = 50", + "cpu100" : "cpus = 100", + "cpu200" : "cpus = 200", + "cpu500" : "cpus = 500", + "cpu1000" : "cpus = 1000" + } + }, + "debug" : false, + "container" : "docker" + } + ], + "engines" : [ + { + "type" : "docker", + "id" : "docker", + "image" : "debian:stable-slim", + "target_registry" : "images.viash-hub.com", + "target_tag" : "main", + "namespace_separator" : "/", + "setup" : [ + { + "type" : "apt", + "packages" : [ + "bcftools", + "procps" + ], + "interactive" : false + }, + { + "type" : "docker", + "run" : [ + "echo \\"bcftools: \\\\\\"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftools //p')\\\\\\"\\" > /var/software_versions.txt\n" + ] + } + ], + "test_setup" : [ + { + "type" : "apt", + "packages" : [ + "tabix" + ], + "interactive" : false + } + ] + }, + { + "type" : "native", + "id" : "native" + } + ], + "build_info" : { + "config" : "/workdir/root/repo/src/bcftools/bcftools_annotate/config.vsh.yaml", + "runner" : "nextflow", + "engine" : "docker|native", + "output" : "target/nextflow/bcftools/bcftools_annotate", + "viash_version" : "0.9.0-RC7", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", + "git_remote" : "https://github.com/viash-hub/biobox" + }, + "package_config" : { + "name" : "biobox", + "version" : "main", + "description" : "A collection of bioinformatics tools for working with sequence data.\n", + "viash_version" : "0.9.0-RC7", + "source" : "src", + "target" : "target", + "config_mods" : [ + ".requirements.commands := ['ps']\n", + ".engines += { type: \\"native\\" }", + ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", + ".engines[.type == 'docker'].target_tag := 'main'" + ], + "keywords" : [ + "bioinformatics", + "modules", + "sequencing" + ], + "license" : "MIT", + "organization" : "vsh", + "links" : { + "repository" : "https://github.com/viash-hub/biobox", + "issue_tracker" : "https://github.com/viash-hub/biobox/issues" + } + } +}''')) +] + +// resolve dependencies dependencies (if any) + + +// inner workflow +// inner workflow hook +def innerWorkflowFactory(args) { + def rawScript = '''set -e +tempscript=".viash_script.sh" +cat > "$tempscript" << VIASHMAIN +#!/bin/bash + +## VIASH START +# The following code has been auto-generated by Viash. +$( if [ ! -z ${VIASH_PAR_INPUT+x} ]; then echo "${VIASH_PAR_INPUT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_input='&'#" ; else echo "# par_input="; fi ) +$( if [ ! -z ${VIASH_PAR_OUTPUT+x} ]; then echo "${VIASH_PAR_OUTPUT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_output='&'#" ; else echo "# par_output="; fi ) +$( if [ ! -z ${VIASH_PAR_ANNOTATIONS+x} ]; then echo "${VIASH_PAR_ANNOTATIONS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_annotations='&'#" ; else echo "# par_annotations="; fi ) +$( if [ ! -z ${VIASH_PAR_COLUMNS+x} ]; then echo "${VIASH_PAR_COLUMNS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_columns='&'#" ; else echo "# par_columns="; fi ) +$( if [ ! -z ${VIASH_PAR_COLUMNS_FILE+x} ]; then echo "${VIASH_PAR_COLUMNS_FILE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_columns_file='&'#" ; else echo "# par_columns_file="; fi ) +$( if [ ! -z ${VIASH_PAR_EXCLUDE+x} ]; then echo "${VIASH_PAR_EXCLUDE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_exclude='&'#" ; else echo "# par_exclude="; fi ) +$( if [ ! -z ${VIASH_PAR_FORCE+x} ]; then echo "${VIASH_PAR_FORCE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_force='&'#" ; else echo "# par_force="; fi ) +$( if [ ! -z ${VIASH_PAR_HEADER_LINE+x} ]; then echo "${VIASH_PAR_HEADER_LINE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_header_line='&'#" ; else echo "# par_header_line="; fi ) +$( if [ ! -z ${VIASH_PAR_HEADER_LINES+x} ]; then echo "${VIASH_PAR_HEADER_LINES}" | sed "s#'#'\\"'\\"'#g;s#.*#par_header_lines='&'#" ; else echo "# par_header_lines="; fi ) +$( if [ ! -z ${VIASH_PAR_SET_ID+x} ]; then echo "${VIASH_PAR_SET_ID}" | sed "s#'#'\\"'\\"'#g;s#.*#par_set_id='&'#" ; else echo "# par_set_id="; fi ) +$( if [ ! -z ${VIASH_PAR_INCLUDE+x} ]; then echo "${VIASH_PAR_INCLUDE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_include='&'#" ; else echo "# par_include="; fi ) +$( if [ ! -z ${VIASH_PAR_KEEP_SITES+x} ]; then echo "${VIASH_PAR_KEEP_SITES}" | sed "s#'#'\\"'\\"'#g;s#.*#par_keep_sites='&'#" ; else echo "# par_keep_sites="; fi ) +$( if [ ! -z ${VIASH_PAR_MERGE_LOGIC+x} ]; then echo "${VIASH_PAR_MERGE_LOGIC}" | sed "s#'#'\\"'\\"'#g;s#.*#par_merge_logic='&'#" ; else echo "# par_merge_logic="; fi ) +$( if [ ! -z ${VIASH_PAR_MARK_SITES+x} ]; then echo "${VIASH_PAR_MARK_SITES}" | sed "s#'#'\\"'\\"'#g;s#.*#par_mark_sites='&'#" ; else echo "# par_mark_sites="; fi ) +$( if [ ! -z ${VIASH_PAR_MIN_OVERLAP+x} ]; then echo "${VIASH_PAR_MIN_OVERLAP}" | sed "s#'#'\\"'\\"'#g;s#.*#par_min_overlap='&'#" ; else echo "# par_min_overlap="; fi ) +$( if [ ! -z ${VIASH_PAR_NO_VERSION+x} ]; then echo "${VIASH_PAR_NO_VERSION}" | sed "s#'#'\\"'\\"'#g;s#.*#par_no_version='&'#" ; else echo "# par_no_version="; fi ) +$( if [ ! -z ${VIASH_PAR_OUTPUT_TYPE+x} ]; then echo "${VIASH_PAR_OUTPUT_TYPE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_output_type='&'#" ; else echo "# par_output_type="; fi ) +$( if [ ! -z ${VIASH_PAR_PAIR_LOGIC+x} ]; then echo "${VIASH_PAR_PAIR_LOGIC}" | sed "s#'#'\\"'\\"'#g;s#.*#par_pair_logic='&'#" ; else echo "# par_pair_logic="; fi ) +$( if [ ! -z ${VIASH_PAR_REGIONS+x} ]; then echo "${VIASH_PAR_REGIONS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_regions='&'#" ; else echo "# par_regions="; fi ) +$( if [ ! -z ${VIASH_PAR_REGIONS_FILE+x} ]; then echo "${VIASH_PAR_REGIONS_FILE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_regions_file='&'#" ; else echo "# par_regions_file="; fi ) +$( if [ ! -z ${VIASH_PAR_REGIONS_OVERLAP+x} ]; then echo "${VIASH_PAR_REGIONS_OVERLAP}" | sed "s#'#'\\"'\\"'#g;s#.*#par_regions_overlap='&'#" ; else echo "# par_regions_overlap="; fi ) +$( if [ ! -z ${VIASH_PAR_RENAME_ANNOTATIONS+x} ]; then echo "${VIASH_PAR_RENAME_ANNOTATIONS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_rename_annotations='&'#" ; else echo "# par_rename_annotations="; fi ) +$( if [ ! -z ${VIASH_PAR_RENAME_CHROMOSOMES+x} ]; then echo "${VIASH_PAR_RENAME_CHROMOSOMES}" | sed "s#'#'\\"'\\"'#g;s#.*#par_rename_chromosomes='&'#" ; else echo "# par_rename_chromosomes="; fi ) +$( if [ ! -z ${VIASH_PAR_SAMPLES+x} ]; then echo "${VIASH_PAR_SAMPLES}" | sed "s#'#'\\"'\\"'#g;s#.*#par_samples='&'#" ; else echo "# par_samples="; fi ) +$( if [ ! -z ${VIASH_PAR_SAMPLES_FILE+x} ]; then echo "${VIASH_PAR_SAMPLES_FILE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_samples_file='&'#" ; else echo "# par_samples_file="; fi ) +$( if [ ! -z ${VIASH_PAR_SINGLE_OVERLAPS+x} ]; then echo "${VIASH_PAR_SINGLE_OVERLAPS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_single_overlaps='&'#" ; else echo "# par_single_overlaps="; fi ) +$( if [ ! -z ${VIASH_PAR_REMOVE+x} ]; then echo "${VIASH_PAR_REMOVE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_remove='&'#" ; else echo "# par_remove="; 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 + +# Exit on error +set -eo pipefail + +# Unset parameters +unset_if_false=( + par_force + par_keep_sites + par_no_version + par_single_overlaps +) + +for par in \\${unset_if_false[@]}; do + test_val="\\${!par}" + [[ "\\$test_val" == "false" ]] && unset \\$par +done + +# Execute bcftools annotate with the provided arguments +bcftools annotate \\\\ + \\${par_annotations:+-a "\\$par_annotations"} \\\\ + \\${par_columns:+-c "\\$par_columns"} \\\\ + \\${par_columns_file:+-C "\\$par_columns_file"} \\\\ + \\${par_exclude:+-e "\\$par_exclude"} \\\\ + \\${par_force:+--force} \\\\ + \\${par_header_line:+-H "\\$par_header_line"} \\\\ + \\${par_header_lines:+-h "\\$par_header_lines"} \\\\ + \\${par_set_id:+-I "\\$par_set_id"} \\\\ + \\${par_include:+-i "\\$par_include"} \\\\ + \\${par_keep_sites:+-k} \\\\ + \\${par_merge_logic:+-l "\\$par_merge_logic"} \\\\ + \\${par_mark_sites:+-m "\\$par_mark_sites"} \\\\ + \\${par_min_overlap:+--min-overlap "\\$par_min_overlap"} \\\\ + \\${par_no_version:+--no-version} \\\\ + \\${par_samples_file:+-S "\\$par_samples_file"} \\\\ + \\${par_output_type:+-O "\\$par_output_type"} \\\\ + \\${par_pair_logic:+--pair-logic "\\$par_pair_logic"} \\\\ + \\${par_regions:+-r "\\$par_regions"} \\\\ + \\${par_regions_file:+-R "\\$par_regions_file"} \\\\ + \\${par_regions_overlap:+--regions-overlap "\\$par_regions_overlap"} \\\\ + \\${par_rename_annotations:+--rename-annots "\\$par_rename_annotations"} \\\\ + \\${par_rename_chromosomes:+--rename-chrs "\\$par_rename_chromosomes"} \\\\ + \\${par_samples:+-s "\\$par_samples"} \\\\ + \\${par_single_overlaps:+--single-overlaps} \\\\ + \\${par_threads:+--threads "\\$par_threads"} \\\\ + \\${par_remove:+-x "\\$par_remove"} \\\\ + -o \\$par_output \\\\ + \\$par_input + + + +VIASHMAIN +bash "$tempscript" +''' + + return vdsl3WorkflowFactory(args, meta, rawScript) +} + + + +/** + * Generate a workflow for VDSL3 modules. + * + * This function is called by the workflowFactory() function. + * + * Input channel: [id, input_map] + * Output channel: [id, output_map] + * + * Internally, this workflow will convert the input channel + * to a format which the Nextflow module will be able to handle. + */ +def vdsl3WorkflowFactory(Map args, Map meta, String rawScript) { + def key = args["key"] + def processObj = null + + workflow processWf { + take: input_ + main: + + if (processObj == null) { + processObj = _vdsl3ProcessFactory(args, meta, rawScript) + } + + output_ = input_ + | map { tuple -> + def id = tuple[0] + def data_ = tuple[1] + + if (workflow.stubRun) { + // add id if missing + data_ = [id: 'stub'] + data_ + } + + // process input files separately + def inputPaths = meta.config.allArguments + .findAll { it.type == "file" && it.direction == "input" } + .collect { par -> + def val = data_.containsKey(par.plainName) ? data_[par.plainName] : [] + def inputFiles = [] + if (val == null) { + inputFiles = [] + } else if (val instanceof List) { + inputFiles = val + } else if (val instanceof Path) { + inputFiles = [ val ] + } else { + inputFiles = [] + } + if (!workflow.stubRun) { + // throw error when an input file doesn't exist + inputFiles.each{ file -> + assert file.exists() : + "Error in module '${key}' id '${id}' argument '${par.plainName}'.\n" + + " Required input file does not exist.\n" + + " Path: '$file'.\n" + + " Expected input file to exist" + } + } + inputFiles + } + + // remove input files + def argsExclInputFiles = meta.config.allArguments + .findAll { (it.type != "file" || it.direction != "input") && data_.containsKey(it.plainName) } + .collectEntries { par -> + def parName = par.plainName + def val = data_[parName] + if (par.multiple && val instanceof Collection) { + val = val.join(par.multiple_sep) + } + if (par.direction == "output" && par.type == "file") { + val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + } + [parName, val] + } + + [ id ] + inputPaths + [ argsExclInputFiles, meta.resources_dir ] + } + | processObj + | map { output -> + def outputFiles = meta.config.allArguments + .findAll { it.type == "file" && it.direction == "output" } + .indexed() + .collectEntries{ index, par -> + def out = output[index + 1] + // strip dummy '.exitcode' file from output (see nextflow-io/nextflow#2678) + if (!out instanceof List || out.size() <= 1) { + if (par.multiple) { + out = [] + } else { + assert !par.required : + "Error in module '${key}' id '${output[0]}' argument '${par.plainName}'.\n" + + " Required output file is missing" + out = null + } + } else if (out.size() == 2 && !par.multiple) { + out = out[1] + } else { + out = out.drop(1) + } + [ par.plainName, out ] + } + + // drop null outputs + outputFiles.removeAll{it.value == null} + + [ output[0], outputFiles ] + } + emit: output_ + } + + return processWf +} + +// depends on: session? +def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) { + // autodetect process key + def wfKey = workflowArgs["key"] + def procKeyPrefix = "${wfKey}_process" + def scriptMeta = nextflow.script.ScriptMeta.current() + def existing = scriptMeta.getProcessNames().findAll{it.startsWith(procKeyPrefix)} + def numbers = existing.collect{it.replace(procKeyPrefix, "0").toInteger()} + def newNumber = (numbers + [-1]).max() + 1 + + def procKey = newNumber == 0 ? procKeyPrefix : "$procKeyPrefix$newNumber" + + if (newNumber > 0) { + log.warn "Key for module '${wfKey}' is duplicated.\n", + "If you run a component multiple times in the same workflow,\n" + + "it's recommended you set a unique key for every call,\n" + + "for example: ${wfKey}.run(key: \"foo\")." + } + + // subset directives and convert to list of tuples + def drctv = workflowArgs.directives + + // TODO: unit test the two commands below + // convert publish array into tags + def valueToStr = { val -> + // ignore closures + if (val instanceof CharSequence) { + if (!val.matches('^[{].*[}]$')) { + '"' + val + '"' + } else { + val + } + } else if (val instanceof List) { + "[" + val.collect{valueToStr(it)}.join(", ") + "]" + } else if (val instanceof Map) { + "[" + val.collect{k, v -> k + ": " + valueToStr(v)}.join(", ") + "]" + } else { + val.inspect() + } + } + + // multiple entries allowed: label, publishdir + def drctvStrs = drctv.collect { key, value -> + if (key in ["label", "publishDir"]) { + value.collect{ val -> + if (val instanceof Map) { + "\n$key " + val.collect{ k, v -> k + ": " + valueToStr(v) }.join(", ") + } else if (val == null) { + "" + } else { + "\n$key " + valueToStr(val) + } + }.join() + } else if (value instanceof Map) { + "\n$key " + value.collect{ k, v -> k + ": " + valueToStr(v) }.join(", ") + } else { + "\n$key " + valueToStr(value) + } + }.join() + + def inputPaths = meta.config.allArguments + .findAll { it.type == "file" && it.direction == "input" } + .collect { ', path(viash_par_' + it.plainName + ', stageAs: "_viash_par/' + it.plainName + '_?/*")' } + .join() + + def outputPaths = meta.config.allArguments + .findAll { it.type == "file" && it.direction == "output" } + .collect { par -> + // insert dummy into every output (see nextflow-io/nextflow#2678) + if (!par.multiple) { + ', path{[".exitcode", args.' + par.plainName + ']}' + } else { + ', path{[".exitcode"] + args.' + par.plainName + '}' + } + } + .join() + + // TODO: move this functionality somewhere else? + if (workflowArgs.auto.transcript) { + outputPaths = outputPaths + ', path{[".exitcode", ".command*"]}' + } else { + outputPaths = outputPaths + ', path{[".exitcode"]}' + } + + // create dirs for output files (based on BashWrapper.createParentFiles) + def createParentStr = meta.config.allArguments + .findAll { it.type == "file" && it.direction == "output" && it.create_parent } + .collect { par -> + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + } + .join("\n") + + // construct inputFileExports + def inputFileExports = meta.config.allArguments + .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } + .collect { par -> + def viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + } + + // NOTE: if using docker, use /tmp instead of tmpDir! + def tmpDir = java.nio.file.Paths.get( + System.getenv('NXF_TEMP') ?: + System.getenv('VIASH_TEMP') ?: + System.getenv('VIASH_TMPDIR') ?: + System.getenv('VIASH_TEMPDIR') ?: + System.getenv('VIASH_TMP') ?: + System.getenv('TEMP') ?: + System.getenv('TMPDIR') ?: + System.getenv('TEMPDIR') ?: + System.getenv('TMP') ?: + '/tmp' + ).toAbsolutePath() + + // construct stub + def stub = meta.config.allArguments + .findAll { it.type == "file" && it.direction == "output" } + .collect { par -> + "\${ args.containsKey(\"${par.plainName}\") ? \"touch2 \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"].replace(\"_*\", \"_0\") : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + } + .join("\n") + + // escape script + def escapedScript = rawScript.replace('\\', '\\\\').replace('$', '\\$').replace('"""', '\\"\\"\\"') + + // publishdir assert + def assertStr = (workflowArgs.auto.publish == true) || workflowArgs.auto.transcript ? + """\nassert task.publishDir.size() > 0: "if auto.publish is true, params.publish_dir needs to be defined.\\n Example: --publish_dir './output/'" """ : + "" + + // generate process string + def procStr = + """nextflow.enable.dsl=2 + | + |process $procKey {$drctvStrs + |input: + | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") + |output: + | tuple val("\$id")$outputPaths, optional: true + |stub: + |\"\"\" + |touch2() { mkdir -p "\\\$(dirname "\\\$1")" && touch "\\\$1" ; } + |$stub + |\"\"\" + |script:$assertStr + |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } + |def parInject = args + | .findAll{key, value -> value != null} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .join("\\n") + |\"\"\" + |# meta exports + |export VIASH_META_RESOURCES_DIR="\${resourcesDir}" + |export VIASH_META_TEMP_DIR="${['docker', 'podman', 'charliecloud'].any{ it == workflow.containerEngine } ? '/tmp' : tmpDir}" + |export VIASH_META_NAME="${meta.config.name}" + |# export VIASH_META_EXECUTABLE="\\\$VIASH_META_RESOURCES_DIR/\\\$VIASH_META_NAME" + |export VIASH_META_CONFIG="\\\$VIASH_META_RESOURCES_DIR/.config.vsh.yaml" + |\${task.cpus ? "export VIASH_META_CPUS=\$task.cpus" : "" } + |\${task.memory?.bytes != null ? "export VIASH_META_MEMORY_B=\$task.memory.bytes" : "" } + |if [ ! -z \\\${VIASH_META_MEMORY_B+x} ]; then + | export VIASH_META_MEMORY_KB=\\\$(( (\\\$VIASH_META_MEMORY_B+999) / 1000 )) + | export VIASH_META_MEMORY_MB=\\\$(( (\\\$VIASH_META_MEMORY_KB+999) / 1000 )) + | export VIASH_META_MEMORY_GB=\\\$(( (\\\$VIASH_META_MEMORY_MB+999) / 1000 )) + | export VIASH_META_MEMORY_TB=\\\$(( (\\\$VIASH_META_MEMORY_GB+999) / 1000 )) + | export VIASH_META_MEMORY_PB=\\\$(( (\\\$VIASH_META_MEMORY_TB+999) / 1000 )) + | export VIASH_META_MEMORY_KIB=\\\$(( (\\\$VIASH_META_MEMORY_B+1023) / 1024 )) + | export VIASH_META_MEMORY_MIB=\\\$(( (\\\$VIASH_META_MEMORY_KIB+1023) / 1024 )) + | export VIASH_META_MEMORY_GIB=\\\$(( (\\\$VIASH_META_MEMORY_MIB+1023) / 1024 )) + | export VIASH_META_MEMORY_TIB=\\\$(( (\\\$VIASH_META_MEMORY_GIB+1023) / 1024 )) + | export VIASH_META_MEMORY_PIB=\\\$(( (\\\$VIASH_META_MEMORY_TIB+1023) / 1024 )) + |fi + | + |# meta synonyms + |export VIASH_TEMP="\\\$VIASH_META_TEMP_DIR" + |export TEMP_DIR="\\\$VIASH_META_TEMP_DIR" + | + |# create output dirs if need be + |function mkdir_parent { + | for file in "\\\$@"; do + | mkdir -p "\\\$(dirname "\\\$file")" + | done + |} + |$createParentStr + | + |# argument exports${inputFileExports.join()} + |\$parInject + | + |# process script + |${escapedScript} + |\"\"\" + |} + |""".stripMargin() + + // TODO: print on debug + // if (workflowArgs.debug == true) { + // println("######################\n$procStr\n######################") + // } + + // write process to temp file + def tempFile = java.nio.file.Files.createTempFile("viash-process-${procKey}-", ".nf") + addShutdownHook { java.nio.file.Files.deleteIfExists(tempFile) } + tempFile.text = procStr + + // create process from temp file + def binding = new nextflow.script.ScriptBinding([:]) + def session = nextflow.Nextflow.getSession() + def parser = new nextflow.script.ScriptParser(session) + .setModule(true) + .setBinding(binding) + def moduleScript = parser.runScript(tempFile) + .getScript() + + // register module in meta + def module = new nextflow.script.IncludeDef.Module(name: procKey) + scriptMeta.addModule(moduleScript, module.name, module.alias) + + // retrieve and return process from meta + return scriptMeta.getProcess(procKey) +} + +// defaults +meta["defaults"] = [ + // key to be used to trace the process and determine output names + key: null, + + // fixed arguments to be passed to script + args: [:], + + // default directives + directives: readJsonBlob('''{ + "container" : { + "registry" : "images.viash-hub.com", + "image" : "vsh/biobox/bcftools/bcftools_annotate", + "tag" : "main" + }, + "tag" : "$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/bcftools/bcftools_annotate/nextflow.config b/target/nextflow/bcftools/bcftools_annotate/nextflow.config new file mode 100644 index 00000000..47fc3866 --- /dev/null +++ b/target/nextflow/bcftools/bcftools_annotate/nextflow.config @@ -0,0 +1,126 @@ +manifest { + name = 'bcftools/bcftools_annotate' + mainScript = 'main.nf' + nextflowVersion = '!>=20.12.1-edge' + version = 'main' + description = 'Add or remove annotations from a VCF/BCF file.\n' + author = 'Theodoro Gasperin Terra Camargo' +} + +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/bcftools/bcftools_annotate/nextflow_schema.json b/target/nextflow/bcftools/bcftools_annotate/nextflow_schema.json new file mode 100644 index 00000000..4bda14e8 --- /dev/null +++ b/target/nextflow/bcftools/bcftools_annotate/nextflow_schema.json @@ -0,0 +1,369 @@ +{ +"$schema": "http://json-schema.org/draft-07/schema", +"title": "bcftools_annotate", +"description": "Add or remove annotations from a VCF/BCF file.\n", +"type": "object", +"definitions": { + + + + "inputs" : { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + + + "input": { + "type": + "string", + "description": "Type: List of `file`, required, multiple_sep: `\";\"`. Input VCF/BCF file", + "help_text": "Type: List of `file`, required, multiple_sep: `\";\"`. Input VCF/BCF file." + + } + + +} +}, + + + "outputs" : { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + + + "output": { + "type": + "string", + "description": "Type: `file`, required, default: `$id.$key.output.output`. Output annotated file", + "help_text": "Type: `file`, required, default: `$id.$key.output.output`. Output annotated file." + , + "default": "$id.$key.output.output" + } + + +} +}, + + + "options" : { + "title": "Options", + "type": "object", + "description": "For examples on how to use use bcftools annotate see http://samtools.github.io/bcftools/howtos/annotate.html.\nFor more details on the options see https://samtools.github.io/bcftools/bcftools.html#annotate.\n", + "properties": { + + + "annotations": { + "type": + "string", + "description": "Type: `file`. VCF file or tabix-indexed FILE with annotations: CHR\\tPOS[\\tVALUE]+ ", + "help_text": "Type: `file`. VCF file or tabix-indexed FILE with annotations: CHR\\tPOS[\\tVALUE]+ . \n" + + } + + + , + "columns": { + "type": + "string", + "description": "Type: `string`. List of columns in the annotation file, e", + "help_text": "Type: `string`. List of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. \nSee man page for details.\n" + + } + + + , + "columns_file": { + "type": + "string", + "description": "Type: `file`. Read -c columns from FILE, one name per row, with optional --merge_logic TYPE: NAME[ TYPE]", + "help_text": "Type: `file`. Read -c columns from FILE, one name per row, with optional --merge_logic TYPE: NAME[ TYPE].\n" + + } + + + , + "exclude": { + "type": + "string", + "description": "Type: `string`, example: `QUAL \u003e= 30 \u0026\u0026 DP \u003e= 10`. Exclude sites for which the expression is true", + "help_text": "Type: `string`, example: `QUAL \u003e= 30 \u0026\u0026 DP \u003e= 10`. Exclude sites for which the expression is true.\nSee https://samtools.github.io/bcftools/bcftools.html#expressions for details.\n" + + } + + + , + "force": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. continue even when parsing errors, such as undefined tags, are encountered", + "help_text": "Type: `boolean_true`, default: `false`. continue even when parsing errors, such as undefined tags, are encountered. \nNote this can be an unsafe operation and can result in corrupted BCF files. \nIf this option is used, make sure to sanity check the result thoroughly.\n" + , + "default": "False" + } + + + , + "header_line": { + "type": + "string", + "description": "Type: `string`. Header line which should be appended to the VCF header, can be given multiple times", + "help_text": "Type: `string`. Header line which should be appended to the VCF header, can be given multiple times.\n" + + } + + + , + "header_lines": { + "type": + "string", + "description": "Type: `file`. File with header lines to append to the VCF header", + "help_text": "Type: `file`. File with header lines to append to the VCF header.\nFor example:\n ##INFO=\u003cID=NUMERIC_TAG,Number=1,Type=Integer,Description=\"Example header line\"\u003e\n ##INFO=\u003cID=STRING_TAG,Number=1,Type=String,Description=\"Yet another header line\"\u003e\n" + + } + + + , + "set_id": { + "type": + "string", + "description": "Type: `string`. Set ID column using a `bcftools query`-like expression, see man page for details", + "help_text": "Type: `string`. Set ID column using a `bcftools query`-like expression, see man page for details.\n" + + } + + + , + "include": { + "type": + "string", + "description": "Type: `string`, example: `QUAL \u003e= 30 \u0026\u0026 DP \u003e= 10`. Select sites for which the expression is true", + "help_text": "Type: `string`, example: `QUAL \u003e= 30 \u0026\u0026 DP \u003e= 10`. Select sites for which the expression is true.\nSee https://samtools.github.io/bcftools/bcftools.html#expressions for details.\n" + + } + + + , + "keep_sites": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Leave --include/--exclude sites unchanged instead of discarding them", + "help_text": "Type: `boolean_true`, default: `false`. Leave --include/--exclude sites unchanged instead of discarding them.\n" + , + "default": "False" + } + + + , + "merge_logic": { + "type": + "string", + "description": "Type: `string`. When multiple regions overlap a single record, this option defines how to treat multiple annotation values", + "help_text": "Type: `string`. When multiple regions overlap a single record, this option defines how to treat multiple annotation values.\nSee man page for more details.\n" + + } + + + , + "mark_sites": { + "type": + "string", + "description": "Type: `string`. Annotate sites which are present (\"+\") or absent (\"-\") in the -a file with a new INFO/TAG flag", + "help_text": "Type: `string`. Annotate sites which are present (\"+\") or absent (\"-\") in the -a file with a new INFO/TAG flag.\n" + + } + + + , + "min_overlap": { + "type": + "string", + "description": "Type: `string`. Minimum overlap required as a fraction of the variant in the annotation -a file (ANN), \nin the target VCF file (:VCF), or both for reciprocal overlap (ANN:VCF)", + "help_text": "Type: `string`. Minimum overlap required as a fraction of the variant in the annotation -a file (ANN), \nin the target VCF file (:VCF), or both for reciprocal overlap (ANN:VCF). \nBy default overlaps of arbitrary length are sufficient. \nThe option can be used only with the tab-delimited annotation -a file and with BEG and END columns present.\n" + + } + + + , + "no_version": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Do not append version and command line information to the output VCF header", + "help_text": "Type: `boolean_true`, default: `false`. Do not append version and command line information to the output VCF header.\n" + , + "default": "False" + } + + + , + "output_type": { + "type": + "string", + "description": "Type: `string`, choices: ``u`, `z`, `b`, `v``. Output type:\n u: uncompressed BCF\n z: compressed VCF\n b: compressed BCF\n v: uncompressed VCF\n", + "help_text": "Type: `string`, choices: ``u`, `z`, `b`, `v``. Output type:\n u: uncompressed BCF\n z: compressed VCF\n b: compressed BCF\n v: uncompressed VCF\n", + "enum": ["u", "z", "b", "v"] + + + } + + + , + "pair_logic": { + "type": + "string", + "description": "Type: `string`, choices: ``snps`, `indels`, `both`, `all`, `some`, `exact``. Controls how to match records from the annotation file to the target VCF", + "help_text": "Type: `string`, choices: ``snps`, `indels`, `both`, `all`, `some`, `exact``. Controls how to match records from the annotation file to the target VCF. \nEffective only when -a is a VCF or BCF file. \nThe option replaces the former uninuitive --collapse. \nSee Common Options for more.\n", + "enum": ["snps", "indels", "both", "all", "some", "exact"] + + + } + + + , + "regions": { + "type": + "string", + "description": "Type: `string`, example: `20:1000000-2000000`. Restrict to comma-separated list of regions", + "help_text": "Type: `string`, example: `20:1000000-2000000`. Restrict to comma-separated list of regions. \nFollowing formats are supported: chr|chr:pos|chr:beg-end|chr:beg-[,\u2026\u200b].\n" + + } + + + , + "regions_file": { + "type": + "string", + "description": "Type: `file`. Restrict to regions listed in a file", + "help_text": "Type: `file`. Restrict to regions listed in a file. \nRegions can be specified either on a VCF, BED, or tab-delimited file (the default). \nFor more information check manual.\n" + + } + + + , + "regions_overlap": { + "type": + "string", + "description": "Type: `string`, choices: ``pos`, `record`, `variant`, `0`, `1`, `2``. This option controls how overlapping records are determined: \nset to \u0027pos\u0027 or \u00270\u0027 if the VCF record has to have POS inside a region (this corresponds to the default behavior of -t/-T); \nset to \u0027record\u0027 or \u00271\u0027 if also overlapping records with POS outside a region should be included (this is the default behavior of -r/-R, \nand includes indels with POS at the end of a region, which are technically outside the region); \nor set to \u0027variant\u0027 or \u00272\u0027 to include only true overlapping variation (compare the full VCF representation \"TA\u003eT-\" vs the true sequence variation \"A\u003e-\")", + "help_text": "Type: `string`, choices: ``pos`, `record`, `variant`, `0`, `1`, `2``. This option controls how overlapping records are determined: \nset to \u0027pos\u0027 or \u00270\u0027 if the VCF record has to have POS inside a region (this corresponds to the default behavior of -t/-T); \nset to \u0027record\u0027 or \u00271\u0027 if also overlapping records with POS outside a region should be included (this is the default behavior of -r/-R, \nand includes indels with POS at the end of a region, which are technically outside the region); \nor set to \u0027variant\u0027 or \u00272\u0027 to include only true overlapping variation (compare the full VCF representation \"TA\u003eT-\" vs the true sequence variation \"A\u003e-\").\n", + "enum": ["pos", "record", "variant", "0", "1", "2"] + + + } + + + , + "rename_annotations": { + "type": + "string", + "description": "Type: `file`. Rename annotations: TYPE/old\\tnew, where TYPE is one of FILTER,INFO,FORMAT", + "help_text": "Type: `file`. Rename annotations: TYPE/old\\tnew, where TYPE is one of FILTER,INFO,FORMAT.\n" + + } + + + , + "rename_chromosomes": { + "type": + "string", + "description": "Type: `file`. Rename chromosomes according to the map in file, with \"old_name new_name\\n\" pairs \nseparated by whitespaces, each on a separate line", + "help_text": "Type: `file`. Rename chromosomes according to the map in file, with \"old_name new_name\\n\" pairs \nseparated by whitespaces, each on a separate line.\n" + + } + + + , + "samples": { + "type": + "string", + "description": "Type: `string`. Subset of samples to annotate", + "help_text": "Type: `string`. Subset of samples to annotate.\nSee also https://samtools.github.io/bcftools/bcftools.html#common_options.\n" + + } + + + , + "samples_file": { + "type": + "string", + "description": "Type: `file`. Subset of samples to annotate in file format", + "help_text": "Type: `file`. Subset of samples to annotate in file format.\nSee also https://samtools.github.io/bcftools/bcftools.html#common_options.\n" + + } + + + , + "single_overlaps": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Use this option to keep memory requirements low with very large annotation files", + "help_text": "Type: `boolean_true`, default: `false`. Use this option to keep memory requirements low with very large annotation files. \nNote, however, that this comes at a cost, only single overlapping intervals are considered in this mode. \nThis was the default mode until the commit af6f0c9 (Feb 24 2019).\n" + , + "default": "False" + } + + + , + "remove": { + "type": + "string", + "description": "Type: `string`. List of annotations to remove", + "help_text": "Type: `string`. List of annotations to remove. \nUse \"FILTER\" to remove all filters or \"FILTER/SomeFilter\" to remove a specific filter. \nSimilarly, \"INFO\" can be used to remove all INFO tags and \"FORMAT\" to remove all FORMAT tags except GT. \nTo remove all INFO tags except \"FOO\" and \"BAR\", use \"^INFO/FOO,INFO/BAR\" (and similarly for FORMAT and FILTER). \n\"INFO\" can be abbreviated to \"INF\" and \"FORMAT\" to \"FMT\".\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/inputs" + }, + + { + "$ref": "#/definitions/outputs" + }, + + { + "$ref": "#/definitions/options" + }, + + { + "$ref": "#/definitions/nextflow input-output arguments" + } +] +} diff --git a/target/nextflow/bcftools/bcftools_sort/.config.vsh.yaml b/target/nextflow/bcftools/bcftools_sort/.config.vsh.yaml index dfbaef89..a37b373d 100644 --- a/target/nextflow/bcftools/bcftools_sort/.config.vsh.yaml +++ b/target/nextflow/bcftools/bcftools_sort/.config.vsh.yaml @@ -185,7 +185,7 @@ build_info: output: "target/nextflow/bcftools/bcftools_sort" executable: "target/nextflow/bcftools/bcftools_sort/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/bcftools/bcftools_sort/main.nf b/target/nextflow/bcftools/bcftools_sort/main.nf index df6dce2f..09e0d0c4 100644 --- a/target/nextflow/bcftools/bcftools_sort/main.nf +++ b/target/nextflow/bcftools/bcftools_sort/main.nf @@ -3042,7 +3042,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bcftools/bcftools_sort", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/bcftools/bcftools_stats/.config.vsh.yaml b/target/nextflow/bcftools/bcftools_stats/.config.vsh.yaml index 2b54fc05..c276ab6e 100644 --- a/target/nextflow/bcftools/bcftools_stats/.config.vsh.yaml +++ b/target/nextflow/bcftools/bcftools_stats/.config.vsh.yaml @@ -458,7 +458,7 @@ build_info: output: "target/nextflow/bcftools/bcftools_stats" executable: "target/nextflow/bcftools/bcftools_stats/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/bcftools/bcftools_stats/main.nf b/target/nextflow/bcftools/bcftools_stats/main.nf index e6db18b6..01f259e3 100644 --- a/target/nextflow/bcftools/bcftools_stats/main.nf +++ b/target/nextflow/bcftools/bcftools_stats/main.nf @@ -3331,7 +3331,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bcftools/bcftools_stats", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/bcl_convert/.config.vsh.yaml b/target/nextflow/bcl_convert/.config.vsh.yaml index 0164c660..3f132215 100644 --- a/target/nextflow/bcl_convert/.config.vsh.yaml +++ b/target/nextflow/bcl_convert/.config.vsh.yaml @@ -418,7 +418,7 @@ build_info: output: "target/nextflow/bcl_convert" executable: "target/nextflow/bcl_convert/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/bcl_convert/main.nf b/target/nextflow/bcl_convert/main.nf index f91c65cb..eac51efc 100644 --- a/target/nextflow/bcl_convert/main.nf +++ b/target/nextflow/bcl_convert/main.nf @@ -3323,7 +3323,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bcl_convert", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml index 32e7efd3..56c47681 100644 --- a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml +++ b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml @@ -270,7 +270,7 @@ build_info: output: "target/nextflow/bd_rhapsody/bd_rhapsody_make_reference" executable: "target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf index 5e70af6c..ea685784 100644 --- a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf +++ b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf @@ -3136,7 +3136,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bd_rhapsody/bd_rhapsody_make_reference", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml index 7acf431b..5d64cb36 100644 --- a/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml @@ -187,7 +187,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_bamtofastq" executable: "target/nextflow/bedtools/bedtools_bamtofastq/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/bedtools/bedtools_bamtofastq/main.nf b/target/nextflow/bedtools/bedtools_bamtofastq/main.nf index bf3c0bd3..3692671c 100644 --- a/target/nextflow/bedtools/bedtools_bamtofastq/main.nf +++ b/target/nextflow/bedtools/bedtools_bamtofastq/main.nf @@ -3044,7 +3044,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_bamtofastq", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/bedtools/bedtools_bed12tobed6/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_bed12tobed6/.config.vsh.yaml index 2df1b176..0f165e7d 100644 --- a/target/nextflow/bedtools/bedtools_bed12tobed6/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_bed12tobed6/.config.vsh.yaml @@ -176,7 +176,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_bed12tobed6" executable: "target/nextflow/bedtools/bedtools_bed12tobed6/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/bedtools/bedtools_bed12tobed6/main.nf b/target/nextflow/bedtools/bedtools_bed12tobed6/main.nf index 40b1416b..be5e606a 100644 --- a/target/nextflow/bedtools/bedtools_bed12tobed6/main.nf +++ b/target/nextflow/bedtools/bedtools_bed12tobed6/main.nf @@ -3029,7 +3029,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_bed12tobed6", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml index 9e270281..68bfb1f7 100644 --- a/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml @@ -214,7 +214,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_bedtobam" executable: "target/nextflow/bedtools/bedtools_bedtobam/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/bedtools/bedtools_bedtobam/main.nf b/target/nextflow/bedtools/bedtools_bedtobam/main.nf index 1c489aad..305caea7 100644 --- a/target/nextflow/bedtools/bedtools_bedtobam/main.nf +++ b/target/nextflow/bedtools/bedtools_bedtobam/main.nf @@ -3077,7 +3077,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_bedtobam", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/bedtools/bedtools_genomecov/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_genomecov/.config.vsh.yaml index 3181842e..6151588b 100644 --- a/target/nextflow/bedtools/bedtools_genomecov/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_genomecov/.config.vsh.yaml @@ -337,7 +337,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_genomecov" executable: "target/nextflow/bedtools/bedtools_genomecov/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/bedtools/bedtools_genomecov/main.nf b/target/nextflow/bedtools/bedtools_genomecov/main.nf index c132ebcc..ba0bf87e 100644 --- a/target/nextflow/bedtools/bedtools_genomecov/main.nf +++ b/target/nextflow/bedtools/bedtools_genomecov/main.nf @@ -3201,7 +3201,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_genomecov", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml index 8a623016..413b1eff 100644 --- a/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml @@ -232,7 +232,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_getfasta" executable: "target/nextflow/bedtools/bedtools_getfasta/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/bedtools/bedtools_getfasta/main.nf b/target/nextflow/bedtools/bedtools_getfasta/main.nf index ec5fa332..3a34f09e 100644 --- a/target/nextflow/bedtools/bedtools_getfasta/main.nf +++ b/target/nextflow/bedtools/bedtools_getfasta/main.nf @@ -3080,7 +3080,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_getfasta", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/bedtools/bedtools_groupby/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_groupby/.config.vsh.yaml index 47677a8b..f66afc31 100644 --- a/target/nextflow/bedtools/bedtools_groupby/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_groupby/.config.vsh.yaml @@ -273,7 +273,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_groupby" executable: "target/nextflow/bedtools/bedtools_groupby/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/bedtools/bedtools_groupby/main.nf b/target/nextflow/bedtools/bedtools_groupby/main.nf index d9453560..7a919697 100644 --- a/target/nextflow/bedtools/bedtools_groupby/main.nf +++ b/target/nextflow/bedtools/bedtools_groupby/main.nf @@ -3124,7 +3124,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_groupby", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml index dd85f1d8..d401762a 100644 --- a/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml @@ -410,7 +410,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_intersect" executable: "target/nextflow/bedtools/bedtools_intersect/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/bedtools/bedtools_intersect/main.nf b/target/nextflow/bedtools/bedtools_intersect/main.nf index 9a624410..fc6debae 100644 --- a/target/nextflow/bedtools/bedtools_intersect/main.nf +++ b/target/nextflow/bedtools/bedtools_intersect/main.nf @@ -3276,7 +3276,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_intersect", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/bedtools/bedtools_links/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_links/.config.vsh.yaml index ad749c4d..884bba3f 100644 --- a/target/nextflow/bedtools/bedtools_links/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_links/.config.vsh.yaml @@ -210,7 +210,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_links" executable: "target/nextflow/bedtools/bedtools_links/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/bedtools/bedtools_links/main.nf b/target/nextflow/bedtools/bedtools_links/main.nf index 52618738..dc436eb7 100644 --- a/target/nextflow/bedtools/bedtools_links/main.nf +++ b/target/nextflow/bedtools/bedtools_links/main.nf @@ -3067,7 +3067,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_links", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/bedtools/bedtools_merge/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_merge/.config.vsh.yaml index 7227be8e..13d3099a 100644 --- a/target/nextflow/bedtools/bedtools_merge/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_merge/.config.vsh.yaml @@ -279,7 +279,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_merge" executable: "target/nextflow/bedtools/bedtools_merge/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/bedtools/bedtools_merge/main.nf b/target/nextflow/bedtools/bedtools_merge/main.nf index 4fb4f7be..acd73d13 100644 --- a/target/nextflow/bedtools/bedtools_merge/main.nf +++ b/target/nextflow/bedtools/bedtools_merge/main.nf @@ -3128,7 +3128,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_merge", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml index 31ffa006..c16014e9 100644 --- a/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml @@ -222,7 +222,7 @@ build_info: output: "target/nextflow/bedtools/bedtools_sort" executable: "target/nextflow/bedtools/bedtools_sort/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/bedtools/bedtools_sort/main.nf b/target/nextflow/bedtools/bedtools_sort/main.nf index 51ecc722..be844816 100644 --- a/target/nextflow/bedtools/bedtools_sort/main.nf +++ b/target/nextflow/bedtools/bedtools_sort/main.nf @@ -3086,7 +3086,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_sort", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml b/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml index e313635e..bc3851a4 100644 --- a/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml +++ b/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml @@ -158,7 +158,7 @@ build_info: output: "target/nextflow/busco/busco_download_datasets" executable: "target/nextflow/busco/busco_download_datasets/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/busco/busco_download_datasets/main.nf b/target/nextflow/busco/busco_download_datasets/main.nf index 4499203a..c47b6c41 100644 --- a/target/nextflow/busco/busco_download_datasets/main.nf +++ b/target/nextflow/busco/busco_download_datasets/main.nf @@ -3005,7 +3005,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/busco/busco_download_datasets", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml b/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml index dcc54a80..3c93f32c 100644 --- a/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml +++ b/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml @@ -145,7 +145,7 @@ build_info: output: "target/nextflow/busco/busco_list_datasets" executable: "target/nextflow/busco/busco_list_datasets/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/busco/busco_list_datasets/main.nf b/target/nextflow/busco/busco_list_datasets/main.nf index 5da1a5fa..063c0750 100644 --- a/target/nextflow/busco/busco_list_datasets/main.nf +++ b/target/nextflow/busco/busco_list_datasets/main.nf @@ -2991,7 +2991,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/busco/busco_list_datasets", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/busco/busco_run/.config.vsh.yaml b/target/nextflow/busco/busco_run/.config.vsh.yaml index 5b9da003..b3988379 100644 --- a/target/nextflow/busco/busco_run/.config.vsh.yaml +++ b/target/nextflow/busco/busco_run/.config.vsh.yaml @@ -423,7 +423,7 @@ build_info: output: "target/nextflow/busco/busco_run" executable: "target/nextflow/busco/busco_run/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/busco/busco_run/main.nf b/target/nextflow/busco/busco_run/main.nf index afced09f..48a04398 100644 --- a/target/nextflow/busco/busco_run/main.nf +++ b/target/nextflow/busco/busco_run/main.nf @@ -3303,7 +3303,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/busco/busco_run", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/cutadapt/.config.vsh.yaml b/target/nextflow/cutadapt/.config.vsh.yaml index d2f1f4f1..8357516f 100644 --- a/target/nextflow/cutadapt/.config.vsh.yaml +++ b/target/nextflow/cutadapt/.config.vsh.yaml @@ -740,7 +740,7 @@ build_info: output: "target/nextflow/cutadapt" executable: "target/nextflow/cutadapt/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/cutadapt/main.nf b/target/nextflow/cutadapt/main.nf index 64a0a8e8..35b87939 100644 --- a/target/nextflow/cutadapt/main.nf +++ b/target/nextflow/cutadapt/main.nf @@ -3613,7 +3613,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/cutadapt", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/falco/.config.vsh.yaml b/target/nextflow/falco/.config.vsh.yaml index 4922b173..798aa6b7 100644 --- a/target/nextflow/falco/.config.vsh.yaml +++ b/target/nextflow/falco/.config.vsh.yaml @@ -317,7 +317,7 @@ build_info: output: "target/nextflow/falco" executable: "target/nextflow/falco/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/falco/main.nf b/target/nextflow/falco/main.nf index a308495f..a1049b3f 100644 --- a/target/nextflow/falco/main.nf +++ b/target/nextflow/falco/main.nf @@ -3164,7 +3164,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/falco", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/fastp/.config.vsh.yaml b/target/nextflow/fastp/.config.vsh.yaml index 481e96be..f6a4da41 100644 --- a/target/nextflow/fastp/.config.vsh.yaml +++ b/target/nextflow/fastp/.config.vsh.yaml @@ -1083,7 +1083,7 @@ build_info: output: "target/nextflow/fastp" executable: "target/nextflow/fastp/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/fastp/main.nf b/target/nextflow/fastp/main.nf index 60dcb873..618ec189 100644 --- a/target/nextflow/fastp/main.nf +++ b/target/nextflow/fastp/main.nf @@ -4017,7 +4017,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/fastp", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/fastqc/.config.vsh.yaml b/target/nextflow/fastqc/.config.vsh.yaml index 6fa42f8f..51b0eebd 100644 --- a/target/nextflow/fastqc/.config.vsh.yaml +++ b/target/nextflow/fastqc/.config.vsh.yaml @@ -340,7 +340,7 @@ build_info: output: "target/nextflow/fastqc" executable: "target/nextflow/fastqc/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/fastqc/main.nf b/target/nextflow/fastqc/main.nf index 4428595a..fe2fb5fe 100644 --- a/target/nextflow/fastqc/main.nf +++ b/target/nextflow/fastqc/main.nf @@ -3176,7 +3176,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/fastqc", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/featurecounts/.config.vsh.yaml b/target/nextflow/featurecounts/.config.vsh.yaml index 47599c92..94284272 100644 --- a/target/nextflow/featurecounts/.config.vsh.yaml +++ b/target/nextflow/featurecounts/.config.vsh.yaml @@ -645,7 +645,7 @@ build_info: output: "target/nextflow/featurecounts" executable: "target/nextflow/featurecounts/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/featurecounts/main.nf b/target/nextflow/featurecounts/main.nf index 1152f42e..06890576 100644 --- a/target/nextflow/featurecounts/main.nf +++ b/target/nextflow/featurecounts/main.nf @@ -3543,7 +3543,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/featurecounts", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/fq_subsample/.config.vsh.yaml b/target/nextflow/fq_subsample/.config.vsh.yaml index a9cf1635..e08571c3 100644 --- a/target/nextflow/fq_subsample/.config.vsh.yaml +++ b/target/nextflow/fq_subsample/.config.vsh.yaml @@ -190,7 +190,7 @@ build_info: output: "target/nextflow/fq_subsample" executable: "target/nextflow/fq_subsample/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/fq_subsample/main.nf b/target/nextflow/fq_subsample/main.nf index 60c566c9..1cb222a1 100644 --- a/target/nextflow/fq_subsample/main.nf +++ b/target/nextflow/fq_subsample/main.nf @@ -3026,7 +3026,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/fq_subsample", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/gffread/.config.vsh.yaml b/target/nextflow/gffread/.config.vsh.yaml index a9a9f68a..ff194aec 100644 --- a/target/nextflow/gffread/.config.vsh.yaml +++ b/target/nextflow/gffread/.config.vsh.yaml @@ -685,7 +685,7 @@ build_info: output: "target/nextflow/gffread" executable: "target/nextflow/gffread/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/gffread/main.nf b/target/nextflow/gffread/main.nf index 8a982864..7cc8eb3b 100644 --- a/target/nextflow/gffread/main.nf +++ b/target/nextflow/gffread/main.nf @@ -3600,7 +3600,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/gffread", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml b/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml index 48b7a421..98eed168 100644 --- a/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml +++ b/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml @@ -507,7 +507,7 @@ build_info: output: "target/nextflow/lofreq/lofreq_call" executable: "target/nextflow/lofreq/lofreq_call/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/lofreq/lofreq_call/main.nf b/target/nextflow/lofreq/lofreq_call/main.nf index aa6fd904..aa07edf7 100644 --- a/target/nextflow/lofreq/lofreq_call/main.nf +++ b/target/nextflow/lofreq/lofreq_call/main.nf @@ -3408,7 +3408,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/lofreq/lofreq_call", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml b/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml index 2fbfe687..8f0b921e 100644 --- a/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml +++ b/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml @@ -215,7 +215,7 @@ build_info: output: "target/nextflow/lofreq/lofreq_indelqual" executable: "target/nextflow/lofreq/lofreq_indelqual/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/lofreq/lofreq_indelqual/main.nf b/target/nextflow/lofreq/lofreq_indelqual/main.nf index b4a2c674..d5cc3ca3 100644 --- a/target/nextflow/lofreq/lofreq_indelqual/main.nf +++ b/target/nextflow/lofreq/lofreq_indelqual/main.nf @@ -3071,7 +3071,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/lofreq/lofreq_indelqual", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/multiqc/.config.vsh.yaml b/target/nextflow/multiqc/.config.vsh.yaml index 7242be4f..2b0b5048 100644 --- a/target/nextflow/multiqc/.config.vsh.yaml +++ b/target/nextflow/multiqc/.config.vsh.yaml @@ -456,7 +456,7 @@ build_info: output: "target/nextflow/multiqc" executable: "target/nextflow/multiqc/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/multiqc/main.nf b/target/nextflow/multiqc/main.nf index 1a8d1bdb..5f0e9d33 100644 --- a/target/nextflow/multiqc/main.nf +++ b/target/nextflow/multiqc/main.nf @@ -3360,7 +3360,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/multiqc", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/pear/.config.vsh.yaml b/target/nextflow/pear/.config.vsh.yaml index 12c9fc3c..b26a8324 100644 --- a/target/nextflow/pear/.config.vsh.yaml +++ b/target/nextflow/pear/.config.vsh.yaml @@ -398,7 +398,7 @@ build_info: output: "target/nextflow/pear" executable: "target/nextflow/pear/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/pear/main.nf b/target/nextflow/pear/main.nf index 1cfc24a2..9d11fe3d 100644 --- a/target/nextflow/pear/main.nf +++ b/target/nextflow/pear/main.nf @@ -3253,7 +3253,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/pear", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml b/target/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml index a54a67d1..1e1e7f39 100644 --- a/target/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml +++ b/target/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml @@ -264,7 +264,7 @@ build_info: output: "target/nextflow/qualimap/qualimap_rnaseq" executable: "target/nextflow/qualimap/qualimap_rnaseq/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/qualimap/qualimap_rnaseq/main.nf b/target/nextflow/qualimap/qualimap_rnaseq/main.nf index fa25b232..0efb0cf1 100644 --- a/target/nextflow/qualimap/qualimap_rnaseq/main.nf +++ b/target/nextflow/qualimap/qualimap_rnaseq/main.nf @@ -3123,7 +3123,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/qualimap/qualimap_rnaseq", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml b/target/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml index 335cf8e9..1ff32131 100644 --- a/target/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml +++ b/target/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml @@ -416,7 +416,7 @@ build_info: output: "target/nextflow/rsem/rsem_prepare_reference" executable: "target/nextflow/rsem/rsem_prepare_reference/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/rsem/rsem_prepare_reference/main.nf b/target/nextflow/rsem/rsem_prepare_reference/main.nf index 2008c118..9a9b17f2 100644 --- a/target/nextflow/rsem/rsem_prepare_reference/main.nf +++ b/target/nextflow/rsem/rsem_prepare_reference/main.nf @@ -3239,7 +3239,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/rsem/rsem_prepare_reference", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/salmon/salmon_index/.config.vsh.yaml b/target/nextflow/salmon/salmon_index/.config.vsh.yaml index da65e60e..b94b445e 100644 --- a/target/nextflow/salmon/salmon_index/.config.vsh.yaml +++ b/target/nextflow/salmon/salmon_index/.config.vsh.yaml @@ -277,7 +277,7 @@ build_info: output: "target/nextflow/salmon/salmon_index" executable: "target/nextflow/salmon/salmon_index/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/salmon/salmon_index/main.nf b/target/nextflow/salmon/salmon_index/main.nf index ff2f7111..1d58bd5e 100644 --- a/target/nextflow/salmon/salmon_index/main.nf +++ b/target/nextflow/salmon/salmon_index/main.nf @@ -3123,7 +3123,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/salmon/salmon_index", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/salmon/salmon_quant/.config.vsh.yaml b/target/nextflow/salmon/salmon_quant/.config.vsh.yaml index 47357c86..940ad776 100644 --- a/target/nextflow/salmon/salmon_quant/.config.vsh.yaml +++ b/target/nextflow/salmon/salmon_quant/.config.vsh.yaml @@ -1173,7 +1173,7 @@ build_info: output: "target/nextflow/salmon/salmon_quant" executable: "target/nextflow/salmon/salmon_quant/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/salmon/salmon_quant/main.nf b/target/nextflow/salmon/salmon_quant/main.nf index 03f44f3d..98243ee4 100644 --- a/target/nextflow/salmon/salmon_quant/main.nf +++ b/target/nextflow/salmon/salmon_quant/main.nf @@ -3958,7 +3958,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/salmon/salmon_quant", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/samtools/samtools_collate/.config.vsh.yaml b/target/nextflow/samtools/samtools_collate/.config.vsh.yaml index 76480a6e..eeeb9956 100644 --- a/target/nextflow/samtools/samtools_collate/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_collate/.config.vsh.yaml @@ -264,7 +264,7 @@ build_info: output: "target/nextflow/samtools/samtools_collate" executable: "target/nextflow/samtools/samtools_collate/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/samtools/samtools_collate/main.nf b/target/nextflow/samtools/samtools_collate/main.nf index 147eaf25..8f5af979 100644 --- a/target/nextflow/samtools/samtools_collate/main.nf +++ b/target/nextflow/samtools/samtools_collate/main.nf @@ -3134,7 +3134,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_collate", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml b/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml index 3eb440d7..baddb88c 100644 --- a/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml @@ -243,7 +243,7 @@ build_info: output: "target/nextflow/samtools/samtools_faidx" executable: "target/nextflow/samtools/samtools_faidx/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/samtools/samtools_faidx/main.nf b/target/nextflow/samtools/samtools_faidx/main.nf index 8752c09e..95d0345f 100644 --- a/target/nextflow/samtools/samtools_faidx/main.nf +++ b/target/nextflow/samtools/samtools_faidx/main.nf @@ -3106,7 +3106,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_faidx", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml b/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml index ac1edadc..4ec2c4cf 100644 --- a/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml @@ -433,7 +433,7 @@ build_info: output: "target/nextflow/samtools/samtools_fasta" executable: "target/nextflow/samtools/samtools_fasta/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/samtools/samtools_fasta/main.nf b/target/nextflow/samtools/samtools_fasta/main.nf index 3bd20a98..4320487b 100644 --- a/target/nextflow/samtools/samtools_fasta/main.nf +++ b/target/nextflow/samtools/samtools_fasta/main.nf @@ -3298,7 +3298,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_fasta", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml b/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml index 625e320e..cb55faec 100644 --- a/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml @@ -433,7 +433,7 @@ build_info: output: "target/nextflow/samtools/samtools_fastq" executable: "target/nextflow/samtools/samtools_fastq/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/samtools/samtools_fastq/main.nf b/target/nextflow/samtools/samtools_fastq/main.nf index 15acc215..f480939e 100644 --- a/target/nextflow/samtools/samtools_fastq/main.nf +++ b/target/nextflow/samtools/samtools_fastq/main.nf @@ -3298,7 +3298,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_fastq", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml b/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml index 86b2500b..6867fa12 100644 --- a/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml @@ -173,7 +173,7 @@ build_info: output: "target/nextflow/samtools/samtools_flagstat" executable: "target/nextflow/samtools/samtools_flagstat/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/samtools/samtools_flagstat/main.nf b/target/nextflow/samtools/samtools_flagstat/main.nf index a3b373d0..6a9a6901 100644 --- a/target/nextflow/samtools/samtools_flagstat/main.nf +++ b/target/nextflow/samtools/samtools_flagstat/main.nf @@ -3022,7 +3022,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_flagstat", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml b/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml index de013dd0..8c1c96a8 100644 --- a/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml @@ -183,7 +183,7 @@ build_info: output: "target/nextflow/samtools/samtools_idxstats" executable: "target/nextflow/samtools/samtools_idxstats/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/samtools/samtools_idxstats/main.nf b/target/nextflow/samtools/samtools_idxstats/main.nf index 69d74494..5c555741 100644 --- a/target/nextflow/samtools/samtools_idxstats/main.nf +++ b/target/nextflow/samtools/samtools_idxstats/main.nf @@ -3034,7 +3034,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_idxstats", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/samtools/samtools_index/.config.vsh.yaml b/target/nextflow/samtools/samtools_index/.config.vsh.yaml index 98d81329..c7024886 100644 --- a/target/nextflow/samtools/samtools_index/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_index/.config.vsh.yaml @@ -189,7 +189,7 @@ build_info: output: "target/nextflow/samtools/samtools_index" executable: "target/nextflow/samtools/samtools_index/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/samtools/samtools_index/main.nf b/target/nextflow/samtools/samtools_index/main.nf index da694592..4333ebda 100644 --- a/target/nextflow/samtools/samtools_index/main.nf +++ b/target/nextflow/samtools/samtools_index/main.nf @@ -3047,7 +3047,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_index", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/samtools/samtools_sort/.config.vsh.yaml b/target/nextflow/samtools/samtools_sort/.config.vsh.yaml index e6d372ae..e6f7ef62 100644 --- a/target/nextflow/samtools/samtools_sort/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_sort/.config.vsh.yaml @@ -332,7 +332,7 @@ build_info: output: "target/nextflow/samtools/samtools_sort" executable: "target/nextflow/samtools/samtools_sort/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/samtools/samtools_sort/main.nf b/target/nextflow/samtools/samtools_sort/main.nf index 75baf876..2b2a903e 100644 --- a/target/nextflow/samtools/samtools_sort/main.nf +++ b/target/nextflow/samtools/samtools_sort/main.nf @@ -3219,7 +3219,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_sort", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/samtools/samtools_stats/.config.vsh.yaml b/target/nextflow/samtools/samtools_stats/.config.vsh.yaml index a1478e31..feb6ea37 100644 --- a/target/nextflow/samtools/samtools_stats/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_stats/.config.vsh.yaml @@ -401,7 +401,7 @@ build_info: output: "target/nextflow/samtools/samtools_stats" executable: "target/nextflow/samtools/samtools_stats/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/samtools/samtools_stats/main.nf b/target/nextflow/samtools/samtools_stats/main.nf index b34ac650..d90be5dc 100644 --- a/target/nextflow/samtools/samtools_stats/main.nf +++ b/target/nextflow/samtools/samtools_stats/main.nf @@ -3289,7 +3289,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_stats", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/samtools/samtools_view/.config.vsh.yaml b/target/nextflow/samtools/samtools_view/.config.vsh.yaml index f5af3d32..1cac3fb1 100644 --- a/target/nextflow/samtools/samtools_view/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_view/.config.vsh.yaml @@ -665,7 +665,7 @@ build_info: output: "target/nextflow/samtools/samtools_view" executable: "target/nextflow/samtools/samtools_view/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/samtools/samtools_view/main.nf b/target/nextflow/samtools/samtools_view/main.nf index 3deff786..4039e128 100644 --- a/target/nextflow/samtools/samtools_view/main.nf +++ b/target/nextflow/samtools/samtools_view/main.nf @@ -3470,7 +3470,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_view", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml b/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml index e99a4c92..fb605e14 100644 --- a/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml +++ b/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml @@ -173,7 +173,7 @@ build_info: output: "target/nextflow/seqtk/seqtk_sample" executable: "target/nextflow/seqtk/seqtk_sample/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/seqtk/seqtk_sample/main.nf b/target/nextflow/seqtk/seqtk_sample/main.nf index 74d3e496..2a6fdf97 100644 --- a/target/nextflow/seqtk/seqtk_sample/main.nf +++ b/target/nextflow/seqtk/seqtk_sample/main.nf @@ -3024,7 +3024,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/seqtk/seqtk_sample", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml b/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml index cf372a60..51d24f01 100644 --- a/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml +++ b/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml @@ -196,7 +196,7 @@ build_info: output: "target/nextflow/seqtk/seqtk_subseq" executable: "target/nextflow/seqtk/seqtk_subseq/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/seqtk/seqtk_subseq/main.nf b/target/nextflow/seqtk/seqtk_subseq/main.nf index 9080101c..4436e489 100644 --- a/target/nextflow/seqtk/seqtk_subseq/main.nf +++ b/target/nextflow/seqtk/seqtk_subseq/main.nf @@ -3054,7 +3054,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/seqtk/seqtk_subseq", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/sortmerna/.config.vsh.yaml b/target/nextflow/sortmerna/.config.vsh.yaml index 25711b6d..75bdddb0 100644 --- a/target/nextflow/sortmerna/.config.vsh.yaml +++ b/target/nextflow/sortmerna/.config.vsh.yaml @@ -591,7 +591,7 @@ build_info: output: "target/nextflow/sortmerna" executable: "target/nextflow/sortmerna/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/sortmerna/main.nf b/target/nextflow/sortmerna/main.nf index 9bc273e0..f7019e99 100644 --- a/target/nextflow/sortmerna/main.nf +++ b/target/nextflow/sortmerna/main.nf @@ -3450,7 +3450,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/sortmerna", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/star/star_align_reads/.config.vsh.yaml b/target/nextflow/star/star_align_reads/.config.vsh.yaml index 75a07e4d..6eac2f15 100644 --- a/target/nextflow/star/star_align_reads/.config.vsh.yaml +++ b/target/nextflow/star/star_align_reads/.config.vsh.yaml @@ -2663,7 +2663,7 @@ build_info: output: "target/nextflow/star/star_align_reads" executable: "target/nextflow/star/star_align_reads/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/star/star_align_reads/main.nf b/target/nextflow/star/star_align_reads/main.nf index 2a1543e3..680c6a85 100644 --- a/target/nextflow/star/star_align_reads/main.nf +++ b/target/nextflow/star/star_align_reads/main.nf @@ -5937,7 +5937,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/star/star_align_reads", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/star/star_genome_generate/.config.vsh.yaml b/target/nextflow/star/star_genome_generate/.config.vsh.yaml index f54f0fb2..5a7b556c 100644 --- a/target/nextflow/star/star_genome_generate/.config.vsh.yaml +++ b/target/nextflow/star/star_genome_generate/.config.vsh.yaml @@ -333,7 +333,7 @@ build_info: output: "target/nextflow/star/star_genome_generate" executable: "target/nextflow/star/star_genome_generate/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/star/star_genome_generate/main.nf b/target/nextflow/star/star_genome_generate/main.nf index c7d9f32c..a91ac94c 100644 --- a/target/nextflow/star/star_genome_generate/main.nf +++ b/target/nextflow/star/star_genome_generate/main.nf @@ -3189,7 +3189,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/star/star_genome_generate", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/umi_tools/umi_tools_dedup/.config.vsh.yaml b/target/nextflow/umi_tools/umi_tools_dedup/.config.vsh.yaml index e7262a97..21beff51 100644 --- a/target/nextflow/umi_tools/umi_tools_dedup/.config.vsh.yaml +++ b/target/nextflow/umi_tools/umi_tools_dedup/.config.vsh.yaml @@ -611,7 +611,7 @@ build_info: output: "target/nextflow/umi_tools/umi_tools_dedup" executable: "target/nextflow/umi_tools/umi_tools_dedup/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/umi_tools/umi_tools_dedup/main.nf b/target/nextflow/umi_tools/umi_tools_dedup/main.nf index 2f0fe634..d3f85e4a 100644 --- a/target/nextflow/umi_tools/umi_tools_dedup/main.nf +++ b/target/nextflow/umi_tools/umi_tools_dedup/main.nf @@ -3481,7 +3481,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/umi_tools/umi_tools_dedup", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml b/target/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml index bf83d61b..c39e3575 100644 --- a/target/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml +++ b/target/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml @@ -449,7 +449,7 @@ build_info: output: "target/nextflow/umi_tools/umi_tools_extract" executable: "target/nextflow/umi_tools/umi_tools_extract/main.nf" viash_version: "0.9.0-RC7" - git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b" + git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/nextflow/umi_tools/umi_tools_extract/main.nf b/target/nextflow/umi_tools/umi_tools_extract/main.nf index daa3051c..9069912a 100644 --- a/target/nextflow/umi_tools/umi_tools_extract/main.nf +++ b/target/nextflow/umi_tools/umi_tools_extract/main.nf @@ -3310,7 +3310,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/umi_tools/umi_tools_extract", "viash_version" : "0.9.0-RC7", - "git_commit" : "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b", + "git_commit" : "c3ba4a78497f7518725bb7d3e213b2a9bcee511e", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : {