From ac86f27b69b03ac213c4ecabef78807255a254d6 Mon Sep 17 00:00:00 2001 From: CI Date: Fri, 6 Sep 2024 22:05:55 +0000 Subject: [PATCH] Build branch main with version main (99dec59) Build pipeline: viash-hub.biobox.main-vzh9h Source commit: https://github.com/viash-hub/biobox/commit/99dec5923bfb3da165601a3f13502d498395b14d Source message: Bedtools genomecov (#150 and #128) * Initial commit * Update config.vsh.yaml * Update script.sh * update on test.sh * bug fixing * adding ibam option tests * depthzero and strand option tests * 5prime and max tests * more tests * Changelog * Update config.vsh.yaml * Update config.vsh.yaml * Update script.sh * Update test.sh * TMPDIR * Unset Variables * par_trackopts multiple: true * Minor update to CHANGELOG --------- Co-authored-by: tgaspe --- CHANGELOG.md | 2 + .../bedtools_genomecov/config.vsh.yaml | 208 + src/bedtools/bedtools_genomecov/help.txt | 101 + src/bedtools/bedtools_genomecov/script.sh | 55 + src/bedtools/bedtools_genomecov/test.sh | 333 ++ 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.../star_genome_generate/.config.vsh.yaml | 2 +- .../star/star_genome_generate/main.nf | 2 +- .../umi_tools_dedup/.config.vsh.yaml | 2 +- .../umi_tools/umi_tools_dedup/main.nf | 2 +- .../umi_tools_extract/.config.vsh.yaml | 2 +- .../umi_tools/umi_tools_extract/main.nf | 2 +- 216 files changed, 7557 insertions(+), 255 deletions(-) create mode 100644 src/bedtools/bedtools_genomecov/config.vsh.yaml create mode 100644 src/bedtools/bedtools_genomecov/help.txt create mode 100644 src/bedtools/bedtools_genomecov/script.sh create mode 100644 src/bedtools/bedtools_genomecov/test.sh create mode 100644 src/bedtools/bedtools_genomecov/test_data/example.bam create mode 100644 target/executable/bedtools/bedtools_genomecov/.config.vsh.yaml create mode 100755 target/executable/bedtools/bedtools_genomecov/bedtools_genomecov create mode 100644 target/nextflow/bedtools/bedtools_genomecov/.config.vsh.yaml create mode 100644 target/nextflow/bedtools/bedtools_genomecov/main.nf create mode 100644 target/nextflow/bedtools/bedtools_genomecov/nextflow.config create mode 100644 target/nextflow/bedtools/bedtools_genomecov/nextflow_schema.json diff --git a/CHANGELOG.md b/CHANGELOG.md index 98e78c17..8f772450 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -29,6 +29,7 @@ * `bedtools`: - `bedtools/bedtools_intersect`: Allows one to screen for overlaps between two sets of genomic features (PR #94). - `bedtools/bedtools_sort`: Sorts a feature file (bed/gff/vcf) by chromosome and other criteria (PR #98). + - `bedtools/bedtools_genomecov`: Compute the coverage of a feature file (bed/gff/vcf/bam) among a genome (PR #128). - `bedtools/bedtools_groupby`: Summarizes a dataset column based upon common column groupings. Akin to the SQL "group by" command (PR #123). - `bedtools/bedtools_merge`: Merges overlapping BED/GFF/VCF entries into a single interval (PR #118). - `bedtools/bedtools_bamtofastq`: Convert BAM alignments to FASTQ files (PR #101). @@ -45,6 +46,7 @@ * `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/bedtools/bedtools_genomecov/config.vsh.yaml b/src/bedtools/bedtools_genomecov/config.vsh.yaml new file mode 100644 index 00000000..775587de --- /dev/null +++ b/src/bedtools/bedtools_genomecov/config.vsh.yaml @@ -0,0 +1,208 @@ +name: bedtools_genomecov +namespace: bedtools +description: | + Compute the coverage of a feature file among a genome. +keywords: [genome coverage, BED, GFF, VCF, BAM] +links: + homepage: https://bedtools.readthedocs.io/en/latest/# + documentation: https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html + repository: https://github.com/arq5x/bedtools2 + issue_tracker: https://github.com/arq5x/bedtools2/issues +references: + doi: 10.1093/bioinformatics/btq033 +license: MIT +requirements: + commands: [bedtools] +authors: + - __merge__: /src/_authors/theodoro_gasperin.yaml + roles: [ author, maintainer ] + +argument_groups: + - name: Inputs + arguments: + - name: --input + alternatives: -i + type: file + direction: input + description: | + The input file (BED/GFF/VCF) to be used. + example: input.bed + + - name: --input_bam + alternatives: -ibam + type: file + description: | + The input file is in BAM format. + Note: BAM _must_ be sorted by positions. + '--genome' option is ignored if you use '--input_bam' option! + + - name: --genome + alternatives: -g + type: file + direction: input + description: | + The genome file to be used. + example: genome.txt + + - name: Outputs + arguments: + - name: --output + type: file + direction: output + description: | + The output BED file. + required: true + example: output.bed + + - name: Options + arguments: + + - name: --depth + alternatives: -d + type: boolean_true + description: | + Report the depth at each genome position (with one-based coordinates). + Default behavior is to report a histogram. + + - name: --depth_zero + alternatives: -dz + type: boolean_true + description: | + Report the depth at each genome position (with zero-based coordinates). + Reports only non-zero positions. + Default behavior is to report a histogram. + + - name: --bed_graph + alternatives: -bg + type: boolean_true + description: | + Report depth in BedGraph format. For details, see: + genome.ucsc.edu/goldenPath/help/bedgraph.html + + - name: --bed_graph_zero_coverage + alternatives: -bga + type: boolean_true + description: | + Report depth in BedGraph format, as above (-bg). + However with this option, regions with zero + coverage are also reported. This allows one to + quickly extract all regions of a genome with 0 + coverage by applying: "grep -w 0$" to the output. + + - name: --split + type: boolean_true + description: | + Treat "split" BAM or BED12 entries as distinct BED intervals. + when computing coverage. + For BAM files, this uses the CIGAR "N" and "D" operations + to infer the blocks for computing coverage. + For BED12 files, this uses the BlockCount, BlockStarts, and BlockEnds + fields (i.e., columns 10,11,12). + + - name: --ignore_deletion + alternatives: -ignoreD + type: boolean_true + description: | + Ignore local deletions (CIGAR "D" operations) in BAM entries + when computing coverage. + + - name: --strand + type: string + choices: ["+", "-"] + description: | + Calculate coverage of intervals from a specific strand. + With BED files, requires at least 6 columns (strand is column 6). + + - name: --pair_end_coverage + alternatives: -pc + type: boolean_true + description: | + Calculate coverage of pair-end fragments. + Works for BAM files only + + - name: --fragment_size + alternatives: -fs + type: boolean_true + description: | + Force to use provided fragment size instead of read length + Works for BAM files only + + - name: --du + type: boolean_true + description: | + Change strand af the mate read (so both reads from the same strand) useful for strand specific + Works for BAM files only + + - name: --five_prime + alternatives: -5 + type: boolean_true + description: | + Calculate coverage of 5" positions (instead of entire interval). + + - name: --three_prime + alternatives: -3 + type: boolean_true + description: | + Calculate coverage of 3" positions (instead of entire interval). + + - name: --max + type: integer + min: 0 + description: | + Combine all positions with a depth >= max into + a single bin in the histogram. Irrelevant + for -d and -bedGraph + - (INTEGER) + + - name: --scale + type: double + min: 0 + description: | + Scale the coverage by a constant factor. + Each coverage value is multiplied by this factor before being reported. + Useful for normalizing coverage by, e.g., reads per million (RPM). + - Default is 1.0; i.e., unscaled. + - (FLOAT) + + - name: --trackline + type: boolean_true + description: | + Adds a UCSC/Genome-Browser track line definition in the first line of the output. + - See here for more details about track line definition: + http://genome.ucsc.edu/goldenPath/help/bedgraph.html + - NOTE: When adding a trackline definition, the output BedGraph can be easily + uploaded to the Genome Browser as a custom track, + BUT CAN NOT be converted into a BigWig file (w/o removing the first line). + + - name: --trackopts + type: string + description: | + Writes additional track line definition parameters in the first line. + - Example: + -trackopts 'name="My Track" visibility=2 color=255,30,30' + Note the use of single-quotes if you have spaces in your parameters. + - (TEXT) + multiple: true + +resources: + - type: bash_script + path: script.sh + +test_resources: + - type: bash_script + path: test.sh + - path: test_data + +engines: + - type: docker + image: debian:stable-slim + setup: + - type: apt + packages: [bedtools, procps] + - type: docker + run: | + echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var/software_versions.txt + +runners: + - type: executable + - type: nextflow \ No newline at end of file diff --git a/src/bedtools/bedtools_genomecov/help.txt b/src/bedtools/bedtools_genomecov/help.txt new file mode 100644 index 00000000..f13a71d3 --- /dev/null +++ b/src/bedtools/bedtools_genomecov/help.txt @@ -0,0 +1,101 @@ +```bash +bedtools genomecov +``` + +Tool: bedtools genomecov (aka genomeCoverageBed) +Version: v2.30.0 +Summary: Compute the coverage of a feature file among a genome. + +Usage: bedtools genomecov [OPTIONS] -i -g + +Options: + -ibam The input file is in BAM format. + Note: BAM _must_ be sorted by position + + -d Report the depth at each genome position (with one-based coordinates). + Default behavior is to report a histogram. + + -dz Report the depth at each genome position (with zero-based coordinates). + Reports only non-zero positions. + Default behavior is to report a histogram. + + -bg Report depth in BedGraph format. For details, see: + genome.ucsc.edu/goldenPath/help/bedgraph.html + + -bga Report depth in BedGraph format, as above (-bg). + However with this option, regions with zero + coverage are also reported. This allows one to + quickly extract all regions of a genome with 0 + coverage by applying: "grep -w 0$" to the output. + + -split Treat "split" BAM or BED12 entries as distinct BED intervals. + when computing coverage. + For BAM files, this uses the CIGAR "N" and "D" operations + to infer the blocks for computing coverage. + For BED12 files, this uses the BlockCount, BlockStarts, and BlockEnds + fields (i.e., columns 10,11,12). + + -ignoreD Ignore local deletions (CIGAR "D" operations) in BAM entries + when computing coverage. + + -strand Calculate coverage of intervals from a specific strand. + With BED files, requires at least 6 columns (strand is column 6). + - (STRING): can be + or - + + -pc Calculate coverage of pair-end fragments. + Works for BAM files only + -fs Force to use provided fragment size instead of read length + Works for BAM files only + -du Change strand af the mate read (so both reads from the same strand) useful for strand specific + Works for BAM files only + -5 Calculate coverage of 5" positions (instead of entire interval). + + -3 Calculate coverage of 3" positions (instead of entire interval). + + -max Combine all positions with a depth >= max into + a single bin in the histogram. Irrelevant + for -d and -bedGraph + - (INTEGER) + + -scale Scale the coverage by a constant factor. + Each coverage value is multiplied by this factor before being reported. + Useful for normalizing coverage by, e.g., reads per million (RPM). + - Default is 1.0; i.e., unscaled. + - (FLOAT) + + -trackline Adds a UCSC/Genome-Browser track line definition in the first line of the output. + - See here for more details about track line definition: + http://genome.ucsc.edu/goldenPath/help/bedgraph.html + - NOTE: When adding a trackline definition, the output BedGraph can be easily + uploaded to the Genome Browser as a custom track, + BUT CAN NOT be converted into a BigWig file (w/o removing the first line). + + -trackopts Writes additional track line definition parameters in the first line. + - Example: + -trackopts 'name="My Track" visibility=2 color=255,30,30' + Note the use of single-quotes if you have spaces in your parameters. + - (TEXT) + +Notes: + (1) The genome file should tab delimited and structured as follows: + + + For example, Human (hg19): + chr1 249250621 + chr2 243199373 + ... + chr18_gl000207_random 4262 + + (2) The input BED (-i) file must be grouped by chromosome. + A simple "sort -k 1,1 > .sorted" will suffice. + + (3) The input BAM (-ibam) file must be sorted by position. + A "samtools sort " should suffice. + +Tips: + One can use the UCSC Genome Browser's MySQL database to extract + chromosome sizes. For example, H. sapiens: + + mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e \ + "select chrom, size from hg19.chromInfo" > hg19.genome + diff --git a/src/bedtools/bedtools_genomecov/script.sh b/src/bedtools/bedtools_genomecov/script.sh new file mode 100644 index 00000000..20fbd968 --- /dev/null +++ b/src/bedtools/bedtools_genomecov/script.sh @@ -0,0 +1,55 @@ +#!/bin/bash + +## VIASH START +## VIASH END + +# Exit on error +set -eo pipefail + +# Unset variables +unset_if_false=( + par_input_bam + par_depth + par_depth_zero + par_bed_graph + par_bed_graph_zero_coverage + par_split + par_ignore_deletion + par_pair_end_coverage + par_fragment_size + par_du + par_five_prime + par_three_prime + par_trackline +) + +for par in ${unset_if_false[@]}; do + test_val="${!par}" + [[ "$test_val" == "false" ]] && unset $par +done + +# Create input array +IFS=";" read -ra trackopts <<< $par_trackopts + +bedtools genomecov \ + ${par_depth:+-d} \ + ${par_depth_zero:+-dz} \ + ${par_bed_graph:+-bg} \ + ${par_bed_graph_zero_coverage:+-bga} \ + ${par_split:+-split} \ + ${par_ignore_deletion:+-ignoreD} \ + ${par_du:+-du} \ + ${par_five_prime:+-5} \ + ${par_three_prime:+-3} \ + ${par_trackline:+-trackline} \ + ${par_strand:+-strand "$par_strand"} \ + ${par_max:+-max "$par_max"} \ + ${par_scale:+-scale "$par_scale"} \ + ${par_trackopts:+-trackopts "${trackopts[*]}"} \ + ${par_input_bam:+-ibam "$par_input_bam"} \ + ${par_input:+-i "$par_input"} \ + ${par_genome:+-g "$par_genome"} \ + ${par_pair_end_coverage:+-pc} \ + ${par_fragment_size:+-fs} \ + > "$par_output" + \ No newline at end of file diff --git a/src/bedtools/bedtools_genomecov/test.sh b/src/bedtools/bedtools_genomecov/test.sh new file mode 100644 index 00000000..7e4487da --- /dev/null +++ b/src/bedtools/bedtools_genomecov/test.sh @@ -0,0 +1,333 @@ +#!/bin/bash + +# exit on error +set -eo pipefail + +## VIASH START +meta_executable="target/executable/bedtools/bedtools_intersect/bedtools_intersect" +meta_resources_dir="src/bedtools/bedtools_intersect" +## VIASH END + +# directory of the bam file +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 "$TMPDIR" +} +trap clean_up EXIT + +# Create and populate input files +printf "chr1\t248956422\nchr2\t198295559\nchr3\t242193529\n" > "$TMPDIR/genome.txt" +printf "chr2\t128\t228\tmy_read/1\t37\t+\nchr2\t428\t528\tmy_read/2\t37\t-\n" > "$TMPDIR/example.bed" +printf "chr2\t128\t228\tmy_read/1\t60\t+\t128\t228\t255,0,0\t1\t100\t0\nchr2\t428\t528\tmy_read/2\t60\t-\t428\t528\t255,0,0\t1\t100\t0\n" > "$TMPDIR/example.bed12" +printf "chr2\t100\t103\n" > "$TMPDIR/example_dz.bed" + +# expected outputs +cat > "$TMPDIR/expected_default.bed" < "$TMPDIR/expected_ibam.bed" < "$TMPDIR/expected_ibam_pc.bed" < "$TMPDIR/expected_ibam_fs.bed" < "$TMPDIR/expected_dz.bed" < "$TMPDIR/expected_strand.bed" < "$TMPDIR/expected_5.bed" < "$TMPDIR/expected_bg_scale.bed" < "$TMPDIR/expected_trackopts.bed" < "$TMPDIR/expected_split.bed" < "$TMPDIR/expected_ignoreD_du.bed" < /dev/null + +echo "> Run bedtools_genomecov on BED file" +"$meta_executable" \ + --input "../example.bed" \ + --genome "../genome.txt" \ + --output "output.bed" + +# checks +assert_file_exists "output.bed" +assert_file_not_empty "output.bed" +assert_identical_content "output.bed" "../expected_default.bed" +echo "- test1 succeeded -" + +popd > /dev/null + +# Test 2: ibam option +mkdir "$TMPDIR/test2" && pushd "$TMPDIR/test2" > /dev/null + +echo "> Run bedtools_genomecov on BAM file with -ibam" +"$meta_executable" \ + --input_bam "$test_data/example.bam" \ + --output "output.bed" \ + +# checks +assert_file_exists "output.bed" +assert_file_not_empty "output.bed" +assert_identical_content "output.bed" "../expected_ibam.bed" +echo "- test2 succeeded -" + +popd > /dev/null + +# Test 3: depth option +mkdir "$TMPDIR/test3" && pushd "$TMPDIR/test3" > /dev/null + +echo "> Run bedtools_genomecov on BED file with -dz" +"$meta_executable" \ + --input "../example_dz.bed" \ + --genome "../genome.txt" \ + --output "output.bed" \ + --depth_zero + +# checks +assert_file_exists "output.bed" +assert_file_not_empty "output.bed" +assert_identical_content "output.bed" "../expected_dz.bed" +echo "- test3 succeeded -" + +popd > /dev/null + +# Test 4: strand option +mkdir "$TMPDIR/test4" && pushd "$TMPDIR/test4" > /dev/null + +echo "> Run bedtools_genomecov on BED file with -strand" +"$meta_executable" \ + --input "../example.bed" \ + --genome "../genome.txt" \ + --output "output.bed" \ + --strand "-" \ + +# checks +assert_file_exists "output.bed" +assert_file_not_empty "output.bed" +assert_identical_content "output.bed" "../expected_strand.bed" +echo "- test4 succeeded -" + +popd > /dev/null + +# Test 5: 5' end option +mkdir "$TMPDIR/test5" && pushd "$TMPDIR/test5" > /dev/null + +echo "> Run bedtools_genomecov on BED file with -5" +"$meta_executable" \ + --input "../example.bed" \ + --genome "../genome.txt" \ + --output "output.bed" \ + --five_prime \ + +# checks +assert_file_exists "output.bed" +assert_file_not_empty "output.bed" +assert_identical_content "output.bed" "../expected_5.bed" +echo "- test5 succeeded -" + +popd > /dev/null + +# Test 6: max option +mkdir "$TMPDIR/test6" && pushd "$TMPDIR/test6" > /dev/null + +echo "> Run bedtools_genomecov on BED file with -max" +"$meta_executable" \ + --input "../example.bed" \ + --genome "../genome.txt" \ + --output "output.bed" \ + --max 100 \ + +# checks +assert_file_exists "output.bed" +assert_file_not_empty "output.bed" +assert_identical_content "output.bed" "../expected_default.bed" +echo "- test6 succeeded -" + +popd > /dev/null + +# Test 7: bedgraph and scale option +mkdir "$TMPDIR/test7" && pushd "$TMPDIR/test7" > /dev/null + +echo "> Run bedtools_genomecov on BED file with -bg and -scale" +"$meta_executable" \ + --input "../example.bed" \ + --genome "../genome.txt" \ + --output "output.bed" \ + --bed_graph \ + --scale 100 \ + +# checks +assert_file_exists "output.bed" +assert_file_not_empty "output.bed" +assert_identical_content "output.bed" "../expected_bg_scale.bed" +echo "- test7 succeeded -" + +popd > /dev/null + +# Test 8: trackopts option +mkdir "$TMPDIR/test8" && pushd "$TMPDIR/test8" > /dev/null + +echo "> Run bedtools_genomecov on BED file with -bg and -trackopts" +"$meta_executable" \ + --input "../example.bed" \ + --genome "../genome.txt" \ + --output "output.bed" \ + --bed_graph \ + --trackopts "name=example" \ + --trackopts "llama=Alpaco" \ + +# checks +assert_file_exists "output.bed" +assert_file_not_empty "output.bed" +assert_identical_content "output.bed" "../expected_trackopts.bed" +echo "- test8 succeeded -" + +popd > /dev/null + +# Test 9: ibam pc options +mkdir "$TMPDIR/test9" && pushd "$TMPDIR/test9" > /dev/null + +echo "> Run bedtools_genomecov on BAM file with -ibam, -pc" +"$meta_executable" \ + --input_bam "$test_data/example.bam" \ + --output "output.bed" \ + --fragment_size \ + --pair_end_coverage \ + +# checks +assert_file_exists "output.bed" +assert_file_not_empty "output.bed" +assert_identical_content "output.bed" "../expected_ibam_pc.bed" +echo "- test9 succeeded -" + +popd > /dev/null + +# Test 10: ibam fs options +mkdir "$TMPDIR/test10" && pushd "$TMPDIR/test10" > /dev/null + +echo "> Run bedtools_genomecov on BAM file with -ibam, -fs" +"$meta_executable" \ + --input_bam "$test_data/example.bam" \ + --output "output.bed" \ + --fragment_size \ + +# checks +assert_file_exists "output.bed" +assert_file_not_empty "output.bed" +assert_identical_content "output.bed" "../expected_ibam_fs.bed" +echo "- test10 succeeded -" + +popd > /dev/null + +# Test 11: split +mkdir "$TMPDIR/test11" && pushd "$TMPDIR/test11" > /dev/null + +echo "> Run bedtools_genomecov on BED12 file with -split" +"$meta_executable" \ + --input "../example.bed12" \ + --genome "../genome.txt" \ + --output "output.bed" \ + --split \ + +# checks +assert_file_exists "output.bed" +assert_file_not_empty "output.bed" +assert_identical_content "output.bed" "../expected_split.bed" +echo "- test11 succeeded -" + +popd > /dev/null + +# Test 12: ignore deletion and du +mkdir "$TMPDIR/test12" && pushd "$TMPDIR/test12" > /dev/null + +echo "> Run bedtools_genomecov on BAM file with -ignoreD and -du" +"$meta_executable" \ + --input_bam "$test_data/example.bam" \ + --output "output.bed" \ + --ignore_deletion \ + --du \ + +# checks +assert_file_exists "output.bed" +assert_file_not_empty "output.bed" +assert_identical_content "output.bed" "../expected_ignoreD_du.bed" +echo "- test12 succeeded -" + +popd > /dev/null + +echo "---- All tests succeeded! ----" +exit 0 diff --git a/src/bedtools/bedtools_genomecov/test_data/example.bam b/src/bedtools/bedtools_genomecov/test_data/example.bam new file mode 100644 index 0000000000000000000000000000000000000000..ffc075ab83a83a98ed1edbf88b26cc27ad8946c6 GIT binary patch literal 334 zcmb2|=3rp}f&Xj_PR>jWAq>SuUsA6mBqS7Y@IB%Aw%O~PhS4S?6Z1_bX2zRMuCZ>` z;o;@Ato^fw$CpQUheTtRYNNz-r#8JXHa3Ry>s4lk0?m>~GxQF_-U<7&m>dP#pU;|5 z)~CHK)-&PMX8(zQnRkjz7tzu&Q_9lpm^;_nXXDZb**~)OH9hZA+GbYw!F2!1eU^u& z=6?J8db>^n+vnS58VqGOpQde!^LhT^FPno$sK1R;RVb&i_o5|>-LG;Kg??MHCx&;~ ziZww?R#r16X1LX_ZFYQZ=WBLl9Y-y@V*W$>-;Wo3eOwoN_@m-GsXhDI /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="2024-09-03T08:58:45Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:30Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" 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 76880906..cb03d55c 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 fbc7f2bd..0d4074f0 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="2024-09-03T08:58:45Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:29Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" 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 da11d938..3a661819 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 b8078dba..f2da0fc1 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="2024-09-03T08:58:45Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:30Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" 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 20464708..015691c1 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 ae0ae683..cb4546cd 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="2024-09-03T08:58:45Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:29Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" 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 0664956c..38d4fae0 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 6f2c1d2a..b9026182 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="2024-09-03T08:58:44Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:29Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/arriba/.config.vsh.yaml b/target/executable/arriba/.config.vsh.yaml index c01cedef..56f79e18 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 87427e20..9c67f4f9 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="2024-09-03T08:58:47Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:31Z" LABEL org.opencontainers.image.source="https://github.com/suhrig/arriba" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bcftools/bcftools_sort/.config.vsh.yaml b/target/executable/bcftools/bcftools_sort/.config.vsh.yaml index 4f1d4470..70319065 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 3767bf0f..720dfcbb 100755 --- a/target/executable/bcftools/bcftools_sort/bcftools_sort +++ b/target/executable/bcftools/bcftools_sort/bcftools_sort @@ -483,9 +483,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_sort" -LABEL org.opencontainers.image.created="2024-09-03T08:58:40Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:25Z" LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bcl_convert/.config.vsh.yaml b/target/executable/bcl_convert/.config.vsh.yaml index 14d71b5d..8abd8a79 100644 --- a/target/executable/bcl_convert/.config.vsh.yaml +++ b/target/executable/bcl_convert/.config.vsh.yaml @@ -418,7 +418,7 @@ build_info: output: "target/executable/bcl_convert" executable: "target/executable/bcl_convert/bcl_convert" viash_version: "0.9.0-RC7" - git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/bcl_convert/bcl_convert b/target/executable/bcl_convert/bcl_convert index 32eda5c7..510592e9 100755 --- a/target/executable/bcl_convert/bcl_convert +++ b/target/executable/bcl_convert/bcl_convert @@ -599,9 +599,9 @@ RUN echo "bcl-convert: \"$(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="2024-09-03T08:58:46Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:31Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" 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 c3511a59..a762eb83 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 6f25b1a2..c6e8d512 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="2024-09-03T08:58:49Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:34Z" LABEL org.opencontainers.image.source="https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1/Extra_Utilities/" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" 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 ef8271ce..944d0c2a 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 b214af8a..d2d0e838 100755 --- a/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq +++ b/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq @@ -483,9 +483,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bamtofastq" -LABEL org.opencontainers.image.created="2024-09-03T08:58:33Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:19Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml b/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml index f3a34b21..28a5874b 100644 --- a/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml @@ -176,7 +176,7 @@ build_info: output: "target/executable/bedtools/bedtools_bed12tobed6" executable: "target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6" viash_version: "0.9.0-RC7" - git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6 b/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6 index b68b6295..3a2306f4 100755 --- a/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6 +++ b/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6 @@ -480,9 +480,9 @@ RUN echo "bedtools: \"$(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="2024-09-03T08:58:32Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:17Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" 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 e431ed7c..9745e0ca 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 26ce1222..c9357e6b 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="2024-09-03T08:58:34Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:19Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" 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 new file mode 100644 index 00000000..4b077b50 --- /dev/null +++ b/target/executable/bedtools/bedtools_genomecov/.config.vsh.yaml @@ -0,0 +1,363 @@ +name: "bedtools_genomecov" +namespace: "bedtools" +version: "main" +authors: +- name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + - "maintainer" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatician" +argument_groups: +- name: "Inputs" + arguments: + - type: "file" + name: "--input" + alternatives: + - "-i" + description: "The input file (BED/GFF/VCF) to be used.\n" + info: null + example: + - "input.bed" + must_exist: true + create_parent: true + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "file" + name: "--input_bam" + alternatives: + - "-ibam" + description: "The input file is in BAM format.\nNote: BAM _must_ be sorted by\ + \ positions.\n'--genome' option is ignored if you use '--input_bam' option!\n" + info: null + must_exist: true + create_parent: true + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "file" + name: "--genome" + alternatives: + - "-g" + description: "The genome file to be used.\n" + info: null + example: + - "genome.txt" + must_exist: true + create_parent: true + required: false + direction: "input" + multiple: false + multiple_sep: ";" +- name: "Outputs" + arguments: + - type: "file" + name: "--output" + description: "The output BED file. \n" + info: null + example: + - "output.bed" + must_exist: true + create_parent: true + required: true + direction: "output" + multiple: false + multiple_sep: ";" +- name: "Options" + arguments: + - type: "boolean_true" + name: "--depth" + alternatives: + - "-d" + description: "Report the depth at each genome position (with one-based coordinates).\n\ + Default behavior is to report a histogram.\n" + info: null + direction: "input" + - type: "boolean_true" + name: "--depth_zero" + alternatives: + - "-dz" + description: "Report the depth at each genome position (with zero-based coordinates).\n\ + Reports only non-zero positions.\nDefault behavior is to report a histogram.\n" + info: null + direction: "input" + - type: "boolean_true" + name: "--bed_graph" + alternatives: + - "-bg" + description: "Report depth in BedGraph format. For details, see:\ngenome.ucsc.edu/goldenPath/help/bedgraph.html\n" + info: null + direction: "input" + - type: "boolean_true" + name: "--bed_graph_zero_coverage" + alternatives: + - "-bga" + description: "Report depth in BedGraph format, as above (-bg).\nHowever with this\ + \ option, regions with zero \ncoverage are also reported. This allows one to\n\ + quickly extract all regions of a genome with 0 \ncoverage by applying: \"grep\ + \ -w 0$\" to the output.\n" + info: null + direction: "input" + - type: "boolean_true" + name: "--split" + description: "Treat \"split\" BAM or BED12 entries as distinct BED intervals.\n\ + when computing coverage.\nFor BAM files, this uses the CIGAR \"N\" and \"D\"\ + \ operations \nto infer the blocks for computing coverage.\nFor BED12 files,\ + \ this uses the BlockCount, BlockStarts, and BlockEnds\nfields (i.e., columns\ + \ 10,11,12).\n" + info: null + direction: "input" + - type: "boolean_true" + name: "--ignore_deletion" + alternatives: + - "-ignoreD" + description: "Ignore local deletions (CIGAR \"D\" operations) in BAM entries\n\ + when computing coverage.\n" + info: null + direction: "input" + - type: "string" + name: "--strand" + description: "Calculate coverage of intervals from a specific strand.\nWith BED\ + \ files, requires at least 6 columns (strand is column 6). \n" + info: null + required: false + choices: + - "+" + - "-" + direction: "input" + multiple: false + multiple_sep: ";" + - type: "boolean_true" + name: "--pair_end_coverage" + alternatives: + - "-pc" + description: "Calculate coverage of pair-end fragments.\nWorks for BAM files only\n" + info: null + direction: "input" + - type: "boolean_true" + name: "--fragment_size" + alternatives: + - "-fs" + description: "Force to use provided fragment size instead of read length\nWorks\ + \ for BAM files only\n" + info: null + direction: "input" + - type: "boolean_true" + name: "--du" + description: "Change strand af the mate read (so both reads from the same strand)\ + \ useful for strand specific\nWorks for BAM files only\n" + info: null + direction: "input" + - type: "boolean_true" + name: "--five_prime" + alternatives: + - "-5" + description: "Calculate coverage of 5\" positions (instead of entire interval).\n" + info: null + direction: "input" + - type: "boolean_true" + name: "--three_prime" + alternatives: + - "-3" + description: "Calculate coverage of 3\" positions (instead of entire interval).\n" + info: null + direction: "input" + - type: "integer" + name: "--max" + description: "Combine all positions with a depth >= max into\na single bin in\ + \ the histogram. Irrelevant\nfor -d and -bedGraph\n- (INTEGER)\n" + info: null + required: false + min: 0 + direction: "input" + multiple: false + multiple_sep: ";" + - type: "double" + name: "--scale" + description: "Scale the coverage by a constant factor.\nEach coverage value is\ + \ multiplied by this factor before being reported.\nUseful for normalizing coverage\ + \ by, e.g., reads per million (RPM).\n- Default is 1.0; i.e., unscaled.\n- (FLOAT)\n" + info: null + required: false + min: 0.0 + direction: "input" + multiple: false + multiple_sep: ";" + - type: "boolean_true" + name: "--trackline" + description: "Adds a UCSC/Genome-Browser track line definition in the first line\ + \ of the output.\n- See here for more details about track line definition:\n\ + \ http://genome.ucsc.edu/goldenPath/help/bedgraph.html\n- NOTE: When adding\ + \ a trackline definition, the output BedGraph can be easily\n uploaded\ + \ to the Genome Browser as a custom track,\n BUT CAN NOT be converted into\ + \ a BigWig file (w/o removing the first line).\n" + info: null + direction: "input" + - type: "string" + name: "--trackopts" + description: "Writes additional track line definition parameters in the first\ + \ line.\n- Example:\n -trackopts 'name=\"My Track\" visibility=2 color=255,30,30'\n\ + \ Note the use of single-quotes if you have spaces in your parameters.\n- (TEXT)\n" + info: null + required: false + direction: "input" + multiple: true + multiple_sep: ";" +resources: +- type: "bash_script" + path: "script.sh" + is_executable: true +description: "Compute the coverage of a feature file among a genome.\n" +test_resources: +- type: "bash_script" + path: "test.sh" + is_executable: true +- type: "file" + path: "test_data" +info: null +status: "enabled" +requirements: + commands: + - "ps" +keywords: +- "genome coverage" +- "BED" +- "GFF" +- "VCF" +- "BAM" +license: "MIT" +references: + doi: + - "10.1093/bioinformatics/btq033" +links: + repository: "https://github.com/arq5x/bedtools2" + homepage: "https://bedtools.readthedocs.io/en/latest/#" + documentation: "https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html" + issue_tracker: "https://github.com/arq5x/bedtools2/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: + - "bedtools" + - "procps" + interactive: false + - type: "docker" + run: + - "echo \"bedtools: \\\"$(bedtools --version | sed -n 's/^bedtools //p')\\\"\"\ + \ > /var/software_versions.txt\n" + entrypoint: [] + cmd: null +- type: "native" + id: "native" +build_info: + config: "src/bedtools/bedtools_genomecov/config.vsh.yaml" + runner: "executable" + engine: "docker|native" + output: "target/executable/bedtools/bedtools_genomecov" + executable: "target/executable/bedtools/bedtools_genomecov/bedtools_genomecov" + viash_version: "0.9.0-RC7" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" + 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/bedtools/bedtools_genomecov/bedtools_genomecov b/target/executable/bedtools/bedtools_genomecov/bedtools_genomecov new file mode 100755 index 00000000..b966493a --- /dev/null +++ b/target/executable/bedtools/bedtools_genomecov/bedtools_genomecov @@ -0,0 +1,1634 @@ +#!/usr/bin/env bash + +# bedtools_genomecov 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, maintainer) + +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 $VIASH_META_RESOURCES_DIR` + +# define meta fields +VIASH_META_NAME="bedtools_genomecov" +VIASH_META_FUNCTIONALITY_NAME="bedtools_genomecov" +VIASH_META_EXECUTABLE="$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 "bedtools_genomecov main" + echo "" + echo "Compute the coverage of a feature file among a genome." + echo "" + echo "Inputs:" + echo " -i, --input" + echo " type: file, file must exist" + echo " example: input.bed" + echo " The input file (BED/GFF/VCF) to be used." + echo "" + echo " -ibam, --input_bam" + echo " type: file, file must exist" + echo " The input file is in BAM format." + echo " Note: BAM _must_ be sorted by positions." + echo " '--genome' option is ignored if you use '--input_bam' option!" + echo "" + echo " -g, --genome" + echo " type: file, file must exist" + echo " example: genome.txt" + echo " The genome file to be used." + echo "" + echo "Outputs:" + echo " --output" + echo " type: file, required parameter, output, file must exist" + echo " example: output.bed" + echo " The output BED file." + echo "" + echo "Options:" + echo " -d, --depth" + echo " type: boolean_true" + echo " Report the depth at each genome position (with one-based coordinates)." + echo " Default behavior is to report a histogram." + echo "" + echo " -dz, --depth_zero" + echo " type: boolean_true" + echo " Report the depth at each genome position (with zero-based coordinates)." + echo " Reports only non-zero positions." + echo " Default behavior is to report a histogram." + echo "" + echo " -bg, --bed_graph" + echo " type: boolean_true" + echo " Report depth in BedGraph format. For details, see:" + echo " genome.ucsc.edu/goldenPath/help/bedgraph.html" + echo "" + echo " -bga, --bed_graph_zero_coverage" + echo " type: boolean_true" + echo " Report depth in BedGraph format, as above (-bg)." + echo " However with this option, regions with zero" + echo " coverage are also reported. This allows one to" + echo " quickly extract all regions of a genome with 0" + echo " coverage by applying: \"grep -w 0\$\" to the output." + echo "" + echo " --split" + echo " type: boolean_true" + echo " Treat \"split\" BAM or BED12 entries as distinct BED intervals." + echo " when computing coverage." + echo " For BAM files, this uses the CIGAR \"N\" and \"D\" operations" + echo " to infer the blocks for computing coverage." + echo " For BED12 files, this uses the BlockCount, BlockStarts, and BlockEnds" + echo " fields (i.e., columns 10,11,12)." + echo "" + echo " -ignoreD, --ignore_deletion" + echo " type: boolean_true" + echo " Ignore local deletions (CIGAR \"D\" operations) in BAM entries" + echo " when computing coverage." + echo "" + echo " --strand" + echo " type: string" + echo " choices: [ +, - ]" + echo " Calculate coverage of intervals from a specific strand." + echo " With BED files, requires at least 6 columns (strand is column 6)." + echo "" + echo " -pc, --pair_end_coverage" + echo " type: boolean_true" + echo " Calculate coverage of pair-end fragments." + echo " Works for BAM files only" + echo "" + echo " -fs, --fragment_size" + echo " type: boolean_true" + echo " Force to use provided fragment size instead of read length" + echo " Works for BAM files only" + echo "" + echo " --du" + echo " type: boolean_true" + echo " Change strand af the mate read (so both reads from the same strand)" + echo " useful for strand specific" + echo " Works for BAM files only" + echo "" + echo " -5, --five_prime" + echo " type: boolean_true" + echo " Calculate coverage of 5\" positions (instead of entire interval)." + echo "" + echo " -3, --three_prime" + echo " type: boolean_true" + echo " Calculate coverage of 3\" positions (instead of entire interval)." + echo "" + echo " --max" + echo " type: integer" + echo " min: 0" + echo " Combine all positions with a depth >= max into" + echo " a single bin in the histogram. Irrelevant" + echo " for -d and -bedGraph" + echo " - (INTEGER)" + echo "" + echo " --scale" + echo " type: double" + echo " min: 0.0" + echo " Scale the coverage by a constant factor." + echo " Each coverage value is multiplied by this factor before being reported." + echo " Useful for normalizing coverage by, e.g., reads per million (RPM)." + echo " - Default is 1.0; i.e., unscaled." + echo " - (FLOAT)" + echo "" + echo " --trackline" + echo " type: boolean_true" + echo " Adds a UCSC/Genome-Browser track line definition in the first line of" + echo " the output." + echo " - See here for more details about track line definition:" + echo " http://genome.ucsc.edu/goldenPath/help/bedgraph.html" + echo " - NOTE: When adding a trackline definition, the output BedGraph can be" + echo " easily" + echo " uploaded to the Genome Browser as a custom track," + echo " BUT CAN NOT be converted into a BigWig file (w/o removing the" + echo " first line)." + echo "" + echo " --trackopts" + echo " type: string, multiple values allowed" + echo " Writes additional track line definition parameters in the first line." + echo " - Example:" + echo " -trackopts 'name=\"My Track\" visibility=2 color=255,30,30'" + echo " Note the use of single-quotes if you have spaces in your parameters." + echo " - (TEXT)" +} + +# 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 bedtools procps && \ + rm -rf /var/lib/apt/lists/* + +RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var/software_versions.txt + +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="2024-09-06T21:51:17Z" +LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" +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 "$1")" + shift 1 + ;; + --version) + echo "bedtools_genomecov main" + exit + ;; + --input) + [ -n "$VIASH_PAR_INPUT" ] && ViashError Bad arguments for option \'--input\': \'$VIASH_PAR_INPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_INPUT="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --input. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --input=*) + [ -n "$VIASH_PAR_INPUT" ] && ViashError Bad arguments for option \'--input=*\': \'$VIASH_PAR_INPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_INPUT=$(ViashRemoveFlags "$1") + shift 1 + ;; + -i) + [ -n "$VIASH_PAR_INPUT" ] && ViashError Bad arguments for option \'-i\': \'$VIASH_PAR_INPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_INPUT="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to -i. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --input_bam) + [ -n "$VIASH_PAR_INPUT_BAM" ] && ViashError Bad arguments for option \'--input_bam\': \'$VIASH_PAR_INPUT_BAM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_INPUT_BAM="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --input_bam. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --input_bam=*) + [ -n "$VIASH_PAR_INPUT_BAM" ] && ViashError Bad arguments for option \'--input_bam=*\': \'$VIASH_PAR_INPUT_BAM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_INPUT_BAM=$(ViashRemoveFlags "$1") + shift 1 + ;; + -ibam) + [ -n "$VIASH_PAR_INPUT_BAM" ] && ViashError Bad arguments for option \'-ibam\': \'$VIASH_PAR_INPUT_BAM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_INPUT_BAM="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to -ibam. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --genome) + [ -n "$VIASH_PAR_GENOME" ] && ViashError Bad arguments for option \'--genome\': \'$VIASH_PAR_GENOME\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_GENOME="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --genome. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --genome=*) + [ -n "$VIASH_PAR_GENOME" ] && ViashError Bad arguments for option \'--genome=*\': \'$VIASH_PAR_GENOME\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_GENOME=$(ViashRemoveFlags "$1") + shift 1 + ;; + -g) + [ -n "$VIASH_PAR_GENOME" ] && ViashError Bad arguments for option \'-g\': \'$VIASH_PAR_GENOME\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_GENOME="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to -g. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --output) + [ -n "$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 "$1") + shift 1 + ;; + --depth) + [ -n "$VIASH_PAR_DEPTH" ] && ViashError Bad arguments for option \'--depth\': \'$VIASH_PAR_DEPTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_DEPTH=true + shift 1 + ;; + -d) + [ -n "$VIASH_PAR_DEPTH" ] && ViashError Bad arguments for option \'-d\': \'$VIASH_PAR_DEPTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_DEPTH=true + shift 1 + ;; + --depth_zero) + [ -n "$VIASH_PAR_DEPTH_ZERO" ] && ViashError Bad arguments for option \'--depth_zero\': \'$VIASH_PAR_DEPTH_ZERO\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_DEPTH_ZERO=true + shift 1 + ;; + -dz) + [ -n "$VIASH_PAR_DEPTH_ZERO" ] && ViashError Bad arguments for option \'-dz\': \'$VIASH_PAR_DEPTH_ZERO\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_DEPTH_ZERO=true + shift 1 + ;; + --bed_graph) + [ -n "$VIASH_PAR_BED_GRAPH" ] && ViashError Bad arguments for option \'--bed_graph\': \'$VIASH_PAR_BED_GRAPH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_BED_GRAPH=true + shift 1 + ;; + -bg) + [ -n "$VIASH_PAR_BED_GRAPH" ] && ViashError Bad arguments for option \'-bg\': \'$VIASH_PAR_BED_GRAPH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_BED_GRAPH=true + shift 1 + ;; + --bed_graph_zero_coverage) + [ -n "$VIASH_PAR_BED_GRAPH_ZERO_COVERAGE" ] && ViashError Bad arguments for option \'--bed_graph_zero_coverage\': \'$VIASH_PAR_BED_GRAPH_ZERO_COVERAGE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_BED_GRAPH_ZERO_COVERAGE=true + shift 1 + ;; + -bga) + [ -n "$VIASH_PAR_BED_GRAPH_ZERO_COVERAGE" ] && ViashError Bad arguments for option \'-bga\': \'$VIASH_PAR_BED_GRAPH_ZERO_COVERAGE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_BED_GRAPH_ZERO_COVERAGE=true + shift 1 + ;; + --split) + [ -n "$VIASH_PAR_SPLIT" ] && ViashError Bad arguments for option \'--split\': \'$VIASH_PAR_SPLIT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_SPLIT=true + shift 1 + ;; + --ignore_deletion) + [ -n "$VIASH_PAR_IGNORE_DELETION" ] && ViashError Bad arguments for option \'--ignore_deletion\': \'$VIASH_PAR_IGNORE_DELETION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_IGNORE_DELETION=true + shift 1 + ;; + -ignoreD) + [ -n "$VIASH_PAR_IGNORE_DELETION" ] && ViashError Bad arguments for option \'-ignoreD\': \'$VIASH_PAR_IGNORE_DELETION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_IGNORE_DELETION=true + shift 1 + ;; + --strand) + [ -n "$VIASH_PAR_STRAND" ] && ViashError Bad arguments for option \'--strand\': \'$VIASH_PAR_STRAND\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_STRAND="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --strand. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --strand=*) + [ -n "$VIASH_PAR_STRAND" ] && ViashError Bad arguments for option \'--strand=*\': \'$VIASH_PAR_STRAND\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_STRAND=$(ViashRemoveFlags "$1") + shift 1 + ;; + --pair_end_coverage) + [ -n "$VIASH_PAR_PAIR_END_COVERAGE" ] && ViashError Bad arguments for option \'--pair_end_coverage\': \'$VIASH_PAR_PAIR_END_COVERAGE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_PAIR_END_COVERAGE=true + shift 1 + ;; + -pc) + [ -n "$VIASH_PAR_PAIR_END_COVERAGE" ] && ViashError Bad arguments for option \'-pc\': \'$VIASH_PAR_PAIR_END_COVERAGE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_PAIR_END_COVERAGE=true + shift 1 + ;; + --fragment_size) + [ -n "$VIASH_PAR_FRAGMENT_SIZE" ] && ViashError Bad arguments for option \'--fragment_size\': \'$VIASH_PAR_FRAGMENT_SIZE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_FRAGMENT_SIZE=true + shift 1 + ;; + -fs) + [ -n "$VIASH_PAR_FRAGMENT_SIZE" ] && ViashError Bad arguments for option \'-fs\': \'$VIASH_PAR_FRAGMENT_SIZE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_FRAGMENT_SIZE=true + shift 1 + ;; + --du) + [ -n "$VIASH_PAR_DU" ] && ViashError Bad arguments for option \'--du\': \'$VIASH_PAR_DU\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_DU=true + shift 1 + ;; + --five_prime) + [ -n "$VIASH_PAR_FIVE_PRIME" ] && ViashError Bad arguments for option \'--five_prime\': \'$VIASH_PAR_FIVE_PRIME\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_FIVE_PRIME=true + shift 1 + ;; + -5) + [ -n "$VIASH_PAR_FIVE_PRIME" ] && ViashError Bad arguments for option \'-5\': \'$VIASH_PAR_FIVE_PRIME\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_FIVE_PRIME=true + shift 1 + ;; + --three_prime) + [ -n "$VIASH_PAR_THREE_PRIME" ] && ViashError Bad arguments for option \'--three_prime\': \'$VIASH_PAR_THREE_PRIME\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_THREE_PRIME=true + shift 1 + ;; + -3) + [ -n "$VIASH_PAR_THREE_PRIME" ] && ViashError Bad arguments for option \'-3\': \'$VIASH_PAR_THREE_PRIME\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_THREE_PRIME=true + shift 1 + ;; + --max) + [ -n "$VIASH_PAR_MAX" ] && ViashError Bad arguments for option \'--max\': \'$VIASH_PAR_MAX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_MAX="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --max. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --max=*) + [ -n "$VIASH_PAR_MAX" ] && ViashError Bad arguments for option \'--max=*\': \'$VIASH_PAR_MAX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_MAX=$(ViashRemoveFlags "$1") + shift 1 + ;; + --scale) + [ -n "$VIASH_PAR_SCALE" ] && ViashError Bad arguments for option \'--scale\': \'$VIASH_PAR_SCALE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_SCALE="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --scale. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --scale=*) + [ -n "$VIASH_PAR_SCALE" ] && ViashError Bad arguments for option \'--scale=*\': \'$VIASH_PAR_SCALE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_SCALE=$(ViashRemoveFlags "$1") + shift 1 + ;; + --trackline) + [ -n "$VIASH_PAR_TRACKLINE" ] && ViashError Bad arguments for option \'--trackline\': \'$VIASH_PAR_TRACKLINE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_TRACKLINE=true + shift 1 + ;; + --trackopts) + if [ -z "$VIASH_PAR_TRACKOPTS" ]; then + VIASH_PAR_TRACKOPTS="$2" + else + VIASH_PAR_TRACKOPTS="$VIASH_PAR_TRACKOPTS;""$2" + fi + [ $# -lt 2 ] && ViashError Not enough arguments passed to --trackopts. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --trackopts=*) + if [ -z "$VIASH_PAR_TRACKOPTS" ]; then + VIASH_PAR_TRACKOPTS=$(ViashRemoveFlags "$1") + else + VIASH_PAR_TRACKOPTS="$VIASH_PAR_TRACKOPTS;"$(ViashRemoveFlags "$1") + fi + shift 1 + ;; + ---engine) + VIASH_ENGINE_ID="$2" + shift 2 + ;; + ---engine=*) + VIASH_ENGINE_ID="$(ViashRemoveFlags "$1")" + shift 1 + ;; + ---setup) + VIASH_MODE='setup' + VIASH_SETUP_STRATEGY="$2" + shift 2 + ;; + ---setup=*) + VIASH_MODE='setup' + VIASH_SETUP_STRATEGY="$(ViashRemoveFlags "$1")" + shift 1 + ;; + ---dockerfile) + VIASH_MODE='dockerfile' + shift 1 + ;; + ---docker_run_args) + VIASH_DOCKER_RUN_ARGS+=("$2") + shift 2 + ;; + ---docker_run_args=*) + VIASH_DOCKER_RUN_ARGS+=("$(ViashRemoveFlags "$1")") + shift 1 + ;; + ---docker_image_id) + VIASH_MODE='docker_image_id' + shift 1 + ;; + ---debug) + VIASH_MODE='debug' + shift 1 + ;; + ---cpus) + [ -n "$VIASH_META_CPUS" ] && ViashError Bad arguments for option \'---cpus\': \'$VIASH_META_CPUS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_META_CPUS="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to ---cpus. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + ---cpus=*) + [ -n "$VIASH_META_CPUS" ] && ViashError Bad arguments for option \'---cpus=*\': \'$VIASH_META_CPUS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_META_CPUS=$(ViashRemoveFlags "$1") + shift 1 + ;; + ---memory) + [ -n "$VIASH_META_MEMORY" ] && ViashError Bad arguments for option \'---memory\': \'$VIASH_META_MEMORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_META_MEMORY="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to ---memory. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + ---memory=*) + [ -n "$VIASH_META_MEMORY" ] && ViashError Bad arguments for option \'---memory=*\': \'$VIASH_META_MEMORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_META_MEMORY=$(ViashRemoveFlags "$1") + shift 1 + ;; + *) # positional arg or unknown option + # since the positional args will be eval'd, can we always quote, instead of using ViashQuote + VIASH_POSITIONAL_ARGS="$VIASH_POSITIONAL_ARGS '$1'" + [[ $1 == -* ]] && ViashWarning $1 looks like a parameter but is not a defined parameter and will instead be treated as a positional argument. Use "--help" to get more information on the parameters. + shift # past argument + ;; + esac +done + +# parse positional parameters +eval set -- $VIASH_POSITIONAL_ARGS + + +if [ "$VIASH_ENGINE_ID" == "native" ] ; then + VIASH_ENGINE_TYPE='native' +elif [ "$VIASH_ENGINE_ID" == "docker" ] ; then + VIASH_ENGINE_TYPE='docker' +else + ViashError "Engine '$VIASH_ENGINE_ID' is not recognized. Options are: docker, native." + exit 1 +fi + +if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then + # check if docker is installed properly + ViashDockerInstallationCheck + + # determine docker image id + if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bedtools/bedtools_genomecov: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_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_DEPTH+x} ]; then + VIASH_PAR_DEPTH="false" +fi +if [ -z ${VIASH_PAR_DEPTH_ZERO+x} ]; then + VIASH_PAR_DEPTH_ZERO="false" +fi +if [ -z ${VIASH_PAR_BED_GRAPH+x} ]; then + VIASH_PAR_BED_GRAPH="false" +fi +if [ -z ${VIASH_PAR_BED_GRAPH_ZERO_COVERAGE+x} ]; then + VIASH_PAR_BED_GRAPH_ZERO_COVERAGE="false" +fi +if [ -z ${VIASH_PAR_SPLIT+x} ]; then + VIASH_PAR_SPLIT="false" +fi +if [ -z ${VIASH_PAR_IGNORE_DELETION+x} ]; then + VIASH_PAR_IGNORE_DELETION="false" +fi +if [ -z ${VIASH_PAR_PAIR_END_COVERAGE+x} ]; then + VIASH_PAR_PAIR_END_COVERAGE="false" +fi +if [ -z ${VIASH_PAR_FRAGMENT_SIZE+x} ]; then + VIASH_PAR_FRAGMENT_SIZE="false" +fi +if [ -z ${VIASH_PAR_DU+x} ]; then + VIASH_PAR_DU="false" +fi +if [ -z ${VIASH_PAR_FIVE_PRIME+x} ]; then + VIASH_PAR_FIVE_PRIME="false" +fi +if [ -z ${VIASH_PAR_THREE_PRIME+x} ]; then + VIASH_PAR_THREE_PRIME="false" +fi +if [ -z ${VIASH_PAR_TRACKLINE+x} ]; then + VIASH_PAR_TRACKLINE="false" +fi + +# check whether required files exist +if [ ! -z "$VIASH_PAR_INPUT" ] && [ ! -e "$VIASH_PAR_INPUT" ]; then + ViashError "Input file '$VIASH_PAR_INPUT' does not exist." + exit 1 +fi +if [ ! -z "$VIASH_PAR_INPUT_BAM" ] && [ ! -e "$VIASH_PAR_INPUT_BAM" ]; then + ViashError "Input file '$VIASH_PAR_INPUT_BAM' does not exist." + exit 1 +fi +if [ ! -z "$VIASH_PAR_GENOME" ] && [ ! -e "$VIASH_PAR_GENOME" ]; then + ViashError "Input file '$VIASH_PAR_GENOME' does not exist." + exit 1 +fi + +# check whether parameters values are of the right type +if [[ -n "$VIASH_PAR_DEPTH" ]]; then + if ! [[ "$VIASH_PAR_DEPTH" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then + ViashError '--depth' has to be a boolean_true. Use "--help" to get more information on the parameters. + exit 1 + fi +fi +if [[ -n "$VIASH_PAR_DEPTH_ZERO" ]]; then + if ! [[ "$VIASH_PAR_DEPTH_ZERO" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then + ViashError '--depth_zero' has to be a boolean_true. Use "--help" to get more information on the parameters. + exit 1 + fi +fi +if [[ -n "$VIASH_PAR_BED_GRAPH" ]]; then + if ! [[ "$VIASH_PAR_BED_GRAPH" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then + ViashError '--bed_graph' has to be a boolean_true. Use "--help" to get more information on the parameters. + exit 1 + fi +fi +if [[ -n "$VIASH_PAR_BED_GRAPH_ZERO_COVERAGE" ]]; then + if ! [[ "$VIASH_PAR_BED_GRAPH_ZERO_COVERAGE" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then + ViashError '--bed_graph_zero_coverage' has to be a boolean_true. Use "--help" to get more information on the parameters. + exit 1 + fi +fi +if [[ -n "$VIASH_PAR_SPLIT" ]]; then + if ! [[ "$VIASH_PAR_SPLIT" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then + ViashError '--split' has to be a boolean_true. Use "--help" to get more information on the parameters. + exit 1 + fi +fi +if [[ -n "$VIASH_PAR_IGNORE_DELETION" ]]; then + if ! [[ "$VIASH_PAR_IGNORE_DELETION" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then + ViashError '--ignore_deletion' has to be a boolean_true. Use "--help" to get more information on the parameters. + exit 1 + fi +fi +if [[ -n "$VIASH_PAR_PAIR_END_COVERAGE" ]]; then + if ! [[ "$VIASH_PAR_PAIR_END_COVERAGE" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then + ViashError '--pair_end_coverage' has to be a boolean_true. Use "--help" to get more information on the parameters. + exit 1 + fi +fi +if [[ -n "$VIASH_PAR_FRAGMENT_SIZE" ]]; then + if ! [[ "$VIASH_PAR_FRAGMENT_SIZE" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then + ViashError '--fragment_size' has to be a boolean_true. Use "--help" to get more information on the parameters. + exit 1 + fi +fi +if [[ -n "$VIASH_PAR_DU" ]]; then + if ! [[ "$VIASH_PAR_DU" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then + ViashError '--du' has to be a boolean_true. Use "--help" to get more information on the parameters. + exit 1 + fi +fi +if [[ -n "$VIASH_PAR_FIVE_PRIME" ]]; then + if ! [[ "$VIASH_PAR_FIVE_PRIME" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then + ViashError '--five_prime' has to be a boolean_true. Use "--help" to get more information on the parameters. + exit 1 + fi +fi +if [[ -n "$VIASH_PAR_THREE_PRIME" ]]; then + if ! [[ "$VIASH_PAR_THREE_PRIME" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then + ViashError '--three_prime' has to be a boolean_true. Use "--help" to get more information on the parameters. + exit 1 + fi +fi +if [[ -n "$VIASH_PAR_MAX" ]]; then + if ! [[ "$VIASH_PAR_MAX" =~ ^[-+]?[0-9]+$ ]]; then + ViashError '--max' has to be an integer. Use "--help" to get more information on the parameters. + exit 1 + fi + if [[ $VIASH_PAR_MAX -lt 0 ]]; then + ViashError '--max' has be more than or equal to 0. Use "--help" to get more information on the parameters. + exit 1 + fi +fi +if [[ -n "$VIASH_PAR_SCALE" ]]; then + if ! [[ "$VIASH_PAR_SCALE" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then + ViashError '--scale' has to be a double. Use "--help" to get more information on the parameters. + exit 1 + fi + if command -v bc &> /dev/null; then + if ! [[ `echo $VIASH_PAR_SCALE '>=' 0.0 | bc` -eq 1 ]]; then + ViashError '--scale' has be more than or equal to 0.0. Use "--help" to get more information on the parameters. + exit 1 + fi + elif command -v awk &> /dev/null; then + if ! [[ `awk -v n1=$VIASH_PAR_SCALE -v n2=0.0 'BEGIN { print (n1 >= n2) ? "1" : "0" }'` -eq 1 ]]; then + ViashError '--scale' has be more than or equal to 0.0. Use "--help" to get more information on the parameters. + exit 1 + fi + else + ViashWarning '--scale' specifies a minimum value but the value was not verified as neither \'bc\' or \`awk\` are present on the system. + fi +fi +if [[ -n "$VIASH_PAR_TRACKLINE" ]]; then + if ! [[ "$VIASH_PAR_TRACKLINE" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then + ViashError '--trackline' 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 "$VIASH_PAR_STRAND" ]; then + VIASH_PAR_STRAND_CHOICES=("+;-") + IFS=';' + set -f + if ! [[ ";${VIASH_PAR_STRAND_CHOICES[*]};" =~ ";$VIASH_PAR_STRAND;" ]]; then + ViashError '--strand' specified value of \'$VIASH_PAR_STRAND\' 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 "$VIASH_PAR_INPUT" ]; then + VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_INPUT")" ) + VIASH_PAR_INPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_INPUT") +fi +if [ ! -z "$VIASH_PAR_INPUT_BAM" ]; then + VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_INPUT_BAM")" ) + VIASH_PAR_INPUT_BAM=$(ViashDockerAutodetectMount "$VIASH_PAR_INPUT_BAM") +fi +if [ ! -z "$VIASH_PAR_GENOME" ]; then + VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_GENOME")" ) + VIASH_PAR_GENOME=$(ViashDockerAutodetectMount "$VIASH_PAR_GENOME") +fi +if [ ! -z "$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_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-bedtools_genomecov-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 ${VIASH_PAR_INPUT_BAM+x} ]; then echo "${VIASH_PAR_INPUT_BAM}" | sed "s#'#'\"'\"'#g;s#.*#par_input_bam='&'#" ; else echo "# par_input_bam="; fi ) +$( if [ ! -z ${VIASH_PAR_GENOME+x} ]; then echo "${VIASH_PAR_GENOME}" | sed "s#'#'\"'\"'#g;s#.*#par_genome='&'#" ; else echo "# par_genome="; 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 ${VIASH_PAR_DEPTH+x} ]; then echo "${VIASH_PAR_DEPTH}" | sed "s#'#'\"'\"'#g;s#.*#par_depth='&'#" ; else echo "# par_depth="; fi ) +$( if [ ! -z ${VIASH_PAR_DEPTH_ZERO+x} ]; then echo "${VIASH_PAR_DEPTH_ZERO}" | sed "s#'#'\"'\"'#g;s#.*#par_depth_zero='&'#" ; else echo "# par_depth_zero="; fi ) +$( if [ ! -z ${VIASH_PAR_BED_GRAPH+x} ]; then echo "${VIASH_PAR_BED_GRAPH}" | sed "s#'#'\"'\"'#g;s#.*#par_bed_graph='&'#" ; else echo "# par_bed_graph="; fi ) +$( if [ ! -z ${VIASH_PAR_BED_GRAPH_ZERO_COVERAGE+x} ]; then echo "${VIASH_PAR_BED_GRAPH_ZERO_COVERAGE}" | sed "s#'#'\"'\"'#g;s#.*#par_bed_graph_zero_coverage='&'#" ; else echo "# par_bed_graph_zero_coverage="; fi ) +$( if [ ! -z ${VIASH_PAR_SPLIT+x} ]; then echo "${VIASH_PAR_SPLIT}" | sed "s#'#'\"'\"'#g;s#.*#par_split='&'#" ; else echo "# par_split="; fi ) +$( if [ ! -z ${VIASH_PAR_IGNORE_DELETION+x} ]; then echo "${VIASH_PAR_IGNORE_DELETION}" | sed "s#'#'\"'\"'#g;s#.*#par_ignore_deletion='&'#" ; else echo "# par_ignore_deletion="; fi ) +$( if [ ! -z ${VIASH_PAR_STRAND+x} ]; then echo "${VIASH_PAR_STRAND}" | sed "s#'#'\"'\"'#g;s#.*#par_strand='&'#" ; else echo "# par_strand="; fi ) +$( if [ ! -z ${VIASH_PAR_PAIR_END_COVERAGE+x} ]; then echo "${VIASH_PAR_PAIR_END_COVERAGE}" | sed "s#'#'\"'\"'#g;s#.*#par_pair_end_coverage='&'#" ; else echo "# par_pair_end_coverage="; fi ) +$( if [ ! -z ${VIASH_PAR_FRAGMENT_SIZE+x} ]; then echo "${VIASH_PAR_FRAGMENT_SIZE}" | sed "s#'#'\"'\"'#g;s#.*#par_fragment_size='&'#" ; else echo "# par_fragment_size="; fi ) +$( if [ ! -z ${VIASH_PAR_DU+x} ]; then echo "${VIASH_PAR_DU}" | sed "s#'#'\"'\"'#g;s#.*#par_du='&'#" ; else echo "# par_du="; fi ) +$( if [ ! -z ${VIASH_PAR_FIVE_PRIME+x} ]; then echo "${VIASH_PAR_FIVE_PRIME}" | sed "s#'#'\"'\"'#g;s#.*#par_five_prime='&'#" ; else echo "# par_five_prime="; fi ) +$( if [ ! -z ${VIASH_PAR_THREE_PRIME+x} ]; then echo "${VIASH_PAR_THREE_PRIME}" | sed "s#'#'\"'\"'#g;s#.*#par_three_prime='&'#" ; else echo "# par_three_prime="; fi ) +$( if [ ! -z ${VIASH_PAR_MAX+x} ]; then echo "${VIASH_PAR_MAX}" | sed "s#'#'\"'\"'#g;s#.*#par_max='&'#" ; else echo "# par_max="; fi ) +$( if [ ! -z ${VIASH_PAR_SCALE+x} ]; then echo "${VIASH_PAR_SCALE}" | sed "s#'#'\"'\"'#g;s#.*#par_scale='&'#" ; else echo "# par_scale="; fi ) +$( if [ ! -z ${VIASH_PAR_TRACKLINE+x} ]; then echo "${VIASH_PAR_TRACKLINE}" | sed "s#'#'\"'\"'#g;s#.*#par_trackline='&'#" ; else echo "# par_trackline="; fi ) +$( if [ ! -z ${VIASH_PAR_TRACKOPTS+x} ]; then echo "${VIASH_PAR_TRACKOPTS}" | sed "s#'#'\"'\"'#g;s#.*#par_trackopts='&'#" ; else echo "# par_trackopts="; 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 variables +unset_if_false=( + par_input_bam + par_depth + par_depth_zero + par_bed_graph + par_bed_graph_zero_coverage + par_split + par_ignore_deletion + par_pair_end_coverage + par_fragment_size + par_du + par_five_prime + par_three_prime + par_trackline +) + +for par in \${unset_if_false[@]}; do + test_val="\${!par}" + [[ "\$test_val" == "false" ]] && unset \$par +done + +# Create input array +IFS=";" read -ra trackopts <<< \$par_trackopts + +bedtools genomecov \\ + \${par_depth:+-d} \\ + \${par_depth_zero:+-dz} \\ + \${par_bed_graph:+-bg} \\ + \${par_bed_graph_zero_coverage:+-bga} \\ + \${par_split:+-split} \\ + \${par_ignore_deletion:+-ignoreD} \\ + \${par_du:+-du} \\ + \${par_five_prime:+-5} \\ + \${par_three_prime:+-3} \\ + \${par_trackline:+-trackline} \\ + \${par_strand:+-strand "\$par_strand"} \\ + \${par_max:+-max "\$par_max"} \\ + \${par_scale:+-scale "\$par_scale"} \\ + \${par_trackopts:+-trackopts "\${trackopts[*]}"} \\ + \${par_input_bam:+-ibam "\$par_input_bam"} \\ + \${par_input:+-i "\$par_input"} \\ + \${par_genome:+-g "\$par_genome"} \\ + \${par_pair_end_coverage:+-pc} \\ + \${par_fragment_size:+-fs} \\ + > "\$par_output" + +VIASHMAIN +bash "\$tempscript" & +wait "\$!" + +VIASHEOF + + +if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then + # strip viash automount from file paths + + if [ ! -z "$VIASH_PAR_INPUT" ]; then + VIASH_PAR_INPUT=$(ViashDockerStripAutomount "$VIASH_PAR_INPUT") + fi + if [ ! -z "$VIASH_PAR_INPUT_BAM" ]; then + VIASH_PAR_INPUT_BAM=$(ViashDockerStripAutomount "$VIASH_PAR_INPUT_BAM") + fi + if [ ! -z "$VIASH_PAR_GENOME" ]; then + VIASH_PAR_GENOME=$(ViashDockerStripAutomount "$VIASH_PAR_GENOME") + fi + if [ ! -z "$VIASH_PAR_OUTPUT" ]; then + VIASH_PAR_OUTPUT=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT") + fi + if [ ! -z "$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/bedtools/bedtools_getfasta/.config.vsh.yaml b/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml index 41138162..dbfb54fd 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 0c6aa794..ebb224cf 100755 --- a/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta +++ b/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta @@ -526,9 +526,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_getfasta" -LABEL org.opencontainers.image.created="2024-09-03T08:58:32Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:18Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml b/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml index 0754922c..65357e7c 100644 --- a/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml @@ -273,7 +273,7 @@ build_info: output: "target/executable/bedtools/bedtools_groupby" executable: "target/executable/bedtools/bedtools_groupby/bedtools_groupby" viash_version: "0.9.0-RC7" - git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/bedtools/bedtools_groupby/bedtools_groupby b/target/executable/bedtools/bedtools_groupby/bedtools_groupby index c0ca9d01..8b1e11af 100755 --- a/target/executable/bedtools/bedtools_groupby/bedtools_groupby +++ b/target/executable/bedtools/bedtools_groupby/bedtools_groupby @@ -552,9 +552,9 @@ RUN echo "bedtools: \"$(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="2024-09-03T08:58:34Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:19Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" 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 92ae13de..cd067f7b 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 07d339b3..471cd01f 100755 --- a/target/executable/bedtools/bedtools_intersect/bedtools_intersect +++ b/target/executable/bedtools/bedtools_intersect/bedtools_intersect @@ -633,9 +633,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_intersect" -LABEL org.opencontainers.image.created="2024-09-03T08:58:33Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:18Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bedtools/bedtools_links/.config.vsh.yaml b/target/executable/bedtools/bedtools_links/.config.vsh.yaml index 9c325a0d..1d53e209 100644 --- a/target/executable/bedtools/bedtools_links/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_links/.config.vsh.yaml @@ -210,7 +210,7 @@ build_info: output: "target/executable/bedtools/bedtools_links" executable: "target/executable/bedtools/bedtools_links/bedtools_links" viash_version: "0.9.0-RC7" - git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/bedtools/bedtools_links/bedtools_links b/target/executable/bedtools/bedtools_links/bedtools_links index f0e119cf..be2d9b12 100755 --- a/target/executable/bedtools/bedtools_links/bedtools_links +++ b/target/executable/bedtools/bedtools_links/bedtools_links @@ -500,9 +500,9 @@ RUN echo "bedtools: \"$(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="2024-09-03T08:58:33Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:18Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" 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 655bca30..74340a1d 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 6cd6534a..a695941d 100755 --- a/target/executable/bedtools/bedtools_merge/bedtools_merge +++ b/target/executable/bedtools/bedtools_merge/bedtools_merge @@ -558,9 +558,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_merge" -LABEL org.opencontainers.image.created="2024-09-03T08:58:32Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:17Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bedtools/bedtools_sort/.config.vsh.yaml b/target/executable/bedtools/bedtools_sort/.config.vsh.yaml index 959cc62b..3641597e 100644 --- a/target/executable/bedtools/bedtools_sort/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_sort/.config.vsh.yaml @@ -222,7 +222,7 @@ build_info: output: "target/executable/bedtools/bedtools_sort" executable: "target/executable/bedtools/bedtools_sort/bedtools_sort" viash_version: "0.9.0-RC7" - git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/bedtools/bedtools_sort/bedtools_sort b/target/executable/bedtools/bedtools_sort/bedtools_sort index 2b7c8f50..d8f16e53 100755 --- a/target/executable/bedtools/bedtools_sort/bedtools_sort +++ b/target/executable/bedtools/bedtools_sort/bedtools_sort @@ -509,9 +509,9 @@ RUN echo "bedtools: \"$(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="2024-09-03T08:58:34Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:19Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" 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 499e676e..9905aab9 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 f35d5ac5..0695b8f8 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="2024-09-03T08:58:43Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:28Z" LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" 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 af0594f1..54f1c6f8 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 26ead192..bcfdc50e 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="2024-09-03T08:58:43Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:28Z" LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" 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 ab70d937..99b83a1f 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 90d7cf91..4831446d 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="2024-09-03T08:58:43Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:28Z" LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/cutadapt/.config.vsh.yaml b/target/executable/cutadapt/.config.vsh.yaml index 33fb3c2c..d96984e8 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 34847b25..fc1be7a4 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="2024-09-03T08:58:48Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:33Z" LABEL org.opencontainers.image.source="https://github.com/marcelm/cutadapt" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/falco/.config.vsh.yaml b/target/executable/falco/.config.vsh.yaml index 815926e0..bb388d0c 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 ef1a1635..4f3b0c8c 100755 --- a/target/executable/falco/falco +++ b/target/executable/falco/falco @@ -589,9 +589,9 @@ RUN echo "falco: \"$(falco -v | sed -n 's/^falco //p')\"" > /var/software_versio LABEL org.opencontainers.image.authors="Toni Verbeiren" LABEL org.opencontainers.image.description="Companion container for running component falco" -LABEL org.opencontainers.image.created="2024-09-03T08:58:49Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:33Z" LABEL org.opencontainers.image.source="https://github.com/smithlabcode/falco" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/fastp/.config.vsh.yaml b/target/executable/fastp/.config.vsh.yaml index 184ee3d0..7a49b1f0 100644 --- a/target/executable/fastp/.config.vsh.yaml +++ b/target/executable/fastp/.config.vsh.yaml @@ -1083,7 +1083,7 @@ build_info: output: "target/executable/fastp" executable: "target/executable/fastp/fastp" viash_version: "0.9.0-RC7" - git_commit: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" git_remote: "https://github.com/viash-hub/biobox" package_config: name: "biobox" diff --git a/target/executable/fastp/fastp b/target/executable/fastp/fastp index 8bca72a1..5f13f300 100755 --- a/target/executable/fastp/fastp +++ b/target/executable/fastp/fastp @@ -1028,9 +1028,9 @@ RUN fastp --version 2>&1 | sed 's# #: "#;s#$#"#' > /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="2024-09-03T08:58:46Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:30Z" LABEL org.opencontainers.image.source="https://github.com/OpenGene/fastp" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/fastqc/.config.vsh.yaml b/target/executable/fastqc/.config.vsh.yaml index b2e9e9c5..13cdfa1e 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 33aea913..a492bc64 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="2024-09-03T08:58:39Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:24Z" LABEL org.opencontainers.image.source="https://github.com/s-andrews/FastQC" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/featurecounts/.config.vsh.yaml b/target/executable/featurecounts/.config.vsh.yaml index 07cf9ac4..7c3d7d1b 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 c1ee935e..153323e4 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="2024-09-03T08:58:41Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:26Z" LABEL org.opencontainers.image.source="https://github.com/ShiLab-Bioinformatics/subread" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/gffread/.config.vsh.yaml b/target/executable/gffread/.config.vsh.yaml index 367aeaf8..f6bc99d3 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 8597a24e..d14889dc 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="2024-09-03T08:58:31Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:16Z" LABEL org.opencontainers.image.source="https://github.com/gpertea/gffread" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" 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 e835334c..f2fae6cd 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 7fefc400..e1e2f703 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="2024-09-03T08:58:41Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:25Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" 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 24cadadc..c8c1571c 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 28fb903e..30432d78 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="2024-09-03T08:58:40Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:25Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/multiqc/.config.vsh.yaml b/target/executable/multiqc/.config.vsh.yaml index fd1707cf..bcfd49f7 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 bc4d18ce..8a7b3f2b 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="2024-09-03T08:58:49Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:33Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/pear/.config.vsh.yaml b/target/executable/pear/.config.vsh.yaml index 8f3148b0..3745cb38 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 e00f94cc..156a4ff8 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="2024-09-03T08:58:34Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:20Z" LABEL org.opencontainers.image.source="https://github.com/tseemann/PEAR" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" 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 144a09de..f8dfa0af 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 d356b04e..efdd4b45 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="2024-09-03T08:58:38Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:23Z" LABEL org.opencontainers.image.source="https://bitbucket.org/kokonech/qualimap/commits/branch/master" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" 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 7205c691..b8fcb4ba 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 203b900b..1c8551b9 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="2024-09-03T08:58:44Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:28Z" LABEL org.opencontainers.image.source="https://github.com/deweylab/RSEM" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" 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 a207561c..f0631770 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 a122459d..70d1cc2c 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="2024-09-03T08:58:47Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:32Z" LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" 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 c8d15065..3610040c 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 bea4ba2f..abbf0432 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="2024-09-03T08:58:48Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:32Z" LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" 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 b716fdac..0a11d4e3 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 88adac04..f3ea3061 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="2024-09-03T08:58:37Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:22Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" 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 fbf6658c..16ae8869 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 51404554..cd547af2 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="2024-09-03T08:58:37Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:22Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" 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 38f2c4ed..467c7f01 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 21904829..fd9b36b6 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="2024-09-03T08:58:37Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:22Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" 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 024172ac..332d3275 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 e5514278..6db64534 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="2024-09-03T08:58:36Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:21Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" 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 2bce6241..67e91768 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 c3296b8d..501ca79b 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="2024-09-03T08:58:36Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:21Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" 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 b72ab0aa..d8ce1796 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 9f7f9fc0..dcba5661 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="2024-09-03T08:58:35Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:20Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" 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 729ee31f..a5cdb9b9 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 b428a5a6..1c708868 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="2024-09-03T08:58:35Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:20Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" 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 35f5ced0..93b974f6 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 2eec9622..c6f2d74c 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="2024-09-03T08:58:38Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:23Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" 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 1d830f09..85291cb8 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 31b58c40..322b8714 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="2024-09-03T08:58:38Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:23Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" 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 0d4fd826..3eb1663b 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 56c026d3..9b62a9b6 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="2024-09-03T08:58:35Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:21Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" 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 7ac417e9..7c43c6e9 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 033b480a..a20c8b85 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="2024-09-03T08:58:50Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:34Z" LABEL org.opencontainers.image.source="https://github.com/lh3/seqtk/tree/v1.4" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" 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 5162f772..1102e535 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 d21e460f..ff68cb54 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="2024-09-03T08:58:50Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:34Z" LABEL org.opencontainers.image.source="https://github.com/lh3/seqtk/tree/v1.4" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" 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 6c27abfb..517f84f4 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 3c348338..514789b9 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="2024-09-03T08:58:42Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:27Z" LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" 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 33b4d43b..f1b6595e 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 7b9e60ef..72f7097f 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="2024-09-03T08:58:42Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:26Z" LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" 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 6f499a7e..79b6aef6 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 3c77757c..419cfc6c 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="2024-09-03T08:58:40Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:24Z" LABEL org.opencontainers.image.source="https://github.com/CGATOxford/UMI-tools" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" 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 2901d9cc..64eb6bc8 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 2c217767..3ed2eae0 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="2024-09-03T08:58:39Z" +LABEL org.opencontainers.image.created="2024-09-06T21:51:24Z" LABEL org.opencontainers.image.source="https://github.com/CGATOxford/UMI-tools" -LABEL org.opencontainers.image.revision="e6627ec728761fe63fe75b0a10ba51da2bccec21" +LABEL org.opencontainers.image.revision="99dec5923bfb3da165601a3f13502d498395b14d" 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 a78be355..1d073270 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 e2c325ab..89553722 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "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 62425db7..e6035474 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 008ec018..ef1acd64 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "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 18bb2370..00723726 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 06dee78f..bba40c6c 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "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 1b10f2bd..3aea4d27 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 8ad5495e..61ef7354 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "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 09a6e470..ef0515ee 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 4347135a..262ba605 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "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 93a3e486..68fe14ac 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 12b329c8..3477e6a4 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : { diff --git a/target/nextflow/bcftools/bcftools_sort/.config.vsh.yaml b/target/nextflow/bcftools/bcftools_sort/.config.vsh.yaml index cea2c7d9..49dccfda 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 5014b3b7..12cd199d 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "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 e86cec3b..39b9d1e6 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 1b8704fe..2031ea3c 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "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 05afa9c2..48ec6698 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 1ada50be..772e8bae 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "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 a913eae4..f304e5c1 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 5b68c777..3dbdc25c 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "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 de933192..2089c73d 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 27edc191..6202d863 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "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 0a26569b..00f5096d 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 165f4521..8bb54bd8 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "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 new file mode 100644 index 00000000..396dac80 --- /dev/null +++ b/target/nextflow/bedtools/bedtools_genomecov/.config.vsh.yaml @@ -0,0 +1,363 @@ +name: "bedtools_genomecov" +namespace: "bedtools" +version: "main" +authors: +- name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + - "maintainer" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatician" +argument_groups: +- name: "Inputs" + arguments: + - type: "file" + name: "--input" + alternatives: + - "-i" + description: "The input file (BED/GFF/VCF) to be used.\n" + info: null + example: + - "input.bed" + must_exist: true + create_parent: true + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "file" + name: "--input_bam" + alternatives: + - "-ibam" + description: "The input file is in BAM format.\nNote: BAM _must_ be sorted by\ + \ positions.\n'--genome' option is ignored if you use '--input_bam' option!\n" + info: null + must_exist: true + create_parent: true + required: false + direction: "input" + multiple: false + multiple_sep: ";" + - type: "file" + name: "--genome" + alternatives: + - "-g" + description: "The genome file to be used.\n" + info: null + example: + - "genome.txt" + must_exist: true + create_parent: true + required: false + direction: "input" + multiple: false + multiple_sep: ";" +- name: "Outputs" + arguments: + - type: "file" + name: "--output" + description: "The output BED file. \n" + info: null + example: + - "output.bed" + must_exist: true + create_parent: true + required: true + direction: "output" + multiple: false + multiple_sep: ";" +- name: "Options" + arguments: + - type: "boolean_true" + name: "--depth" + alternatives: + - "-d" + description: "Report the depth at each genome position (with one-based coordinates).\n\ + Default behavior is to report a histogram.\n" + info: null + direction: "input" + - type: "boolean_true" + name: "--depth_zero" + alternatives: + - "-dz" + description: "Report the depth at each genome position (with zero-based coordinates).\n\ + Reports only non-zero positions.\nDefault behavior is to report a histogram.\n" + info: null + direction: "input" + - type: "boolean_true" + name: "--bed_graph" + alternatives: + - "-bg" + description: "Report depth in BedGraph format. For details, see:\ngenome.ucsc.edu/goldenPath/help/bedgraph.html\n" + info: null + direction: "input" + - type: "boolean_true" + name: "--bed_graph_zero_coverage" + alternatives: + - "-bga" + description: "Report depth in BedGraph format, as above (-bg).\nHowever with this\ + \ option, regions with zero \ncoverage are also reported. This allows one to\n\ + quickly extract all regions of a genome with 0 \ncoverage by applying: \"grep\ + \ -w 0$\" to the output.\n" + info: null + direction: "input" + - type: "boolean_true" + name: "--split" + description: "Treat \"split\" BAM or BED12 entries as distinct BED intervals.\n\ + when computing coverage.\nFor BAM files, this uses the CIGAR \"N\" and \"D\"\ + \ operations \nto infer the blocks for computing coverage.\nFor BED12 files,\ + \ this uses the BlockCount, BlockStarts, and BlockEnds\nfields (i.e., columns\ + \ 10,11,12).\n" + info: null + direction: "input" + - type: "boolean_true" + name: "--ignore_deletion" + alternatives: + - "-ignoreD" + description: "Ignore local deletions (CIGAR \"D\" operations) in BAM entries\n\ + when computing coverage.\n" + info: null + direction: "input" + - type: "string" + name: "--strand" + description: "Calculate coverage of intervals from a specific strand.\nWith BED\ + \ files, requires at least 6 columns (strand is column 6). \n" + info: null + required: false + choices: + - "+" + - "-" + direction: "input" + multiple: false + multiple_sep: ";" + - type: "boolean_true" + name: "--pair_end_coverage" + alternatives: + - "-pc" + description: "Calculate coverage of pair-end fragments.\nWorks for BAM files only\n" + info: null + direction: "input" + - type: "boolean_true" + name: "--fragment_size" + alternatives: + - "-fs" + description: "Force to use provided fragment size instead of read length\nWorks\ + \ for BAM files only\n" + info: null + direction: "input" + - type: "boolean_true" + name: "--du" + description: "Change strand af the mate read (so both reads from the same strand)\ + \ useful for strand specific\nWorks for BAM files only\n" + info: null + direction: "input" + - type: "boolean_true" + name: "--five_prime" + alternatives: + - "-5" + description: "Calculate coverage of 5\" positions (instead of entire interval).\n" + info: null + direction: "input" + - type: "boolean_true" + name: "--three_prime" + alternatives: + - "-3" + description: "Calculate coverage of 3\" positions (instead of entire interval).\n" + info: null + direction: "input" + - type: "integer" + name: "--max" + description: "Combine all positions with a depth >= max into\na single bin in\ + \ the histogram. Irrelevant\nfor -d and -bedGraph\n- (INTEGER)\n" + info: null + required: false + min: 0 + direction: "input" + multiple: false + multiple_sep: ";" + - type: "double" + name: "--scale" + description: "Scale the coverage by a constant factor.\nEach coverage value is\ + \ multiplied by this factor before being reported.\nUseful for normalizing coverage\ + \ by, e.g., reads per million (RPM).\n- Default is 1.0; i.e., unscaled.\n- (FLOAT)\n" + info: null + required: false + min: 0.0 + direction: "input" + multiple: false + multiple_sep: ";" + - type: "boolean_true" + name: "--trackline" + description: "Adds a UCSC/Genome-Browser track line definition in the first line\ + \ of the output.\n- See here for more details about track line definition:\n\ + \ http://genome.ucsc.edu/goldenPath/help/bedgraph.html\n- NOTE: When adding\ + \ a trackline definition, the output BedGraph can be easily\n uploaded\ + \ to the Genome Browser as a custom track,\n BUT CAN NOT be converted into\ + \ a BigWig file (w/o removing the first line).\n" + info: null + direction: "input" + - type: "string" + name: "--trackopts" + description: "Writes additional track line definition parameters in the first\ + \ line.\n- Example:\n -trackopts 'name=\"My Track\" visibility=2 color=255,30,30'\n\ + \ Note the use of single-quotes if you have spaces in your parameters.\n- (TEXT)\n" + info: null + required: false + direction: "input" + multiple: true + multiple_sep: ";" +resources: +- type: "bash_script" + path: "script.sh" + is_executable: true +description: "Compute the coverage of a feature file among a genome.\n" +test_resources: +- type: "bash_script" + path: "test.sh" + is_executable: true +- type: "file" + path: "test_data" +info: null +status: "enabled" +requirements: + commands: + - "ps" +keywords: +- "genome coverage" +- "BED" +- "GFF" +- "VCF" +- "BAM" +license: "MIT" +references: + doi: + - "10.1093/bioinformatics/btq033" +links: + repository: "https://github.com/arq5x/bedtools2" + homepage: "https://bedtools.readthedocs.io/en/latest/#" + documentation: "https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html" + issue_tracker: "https://github.com/arq5x/bedtools2/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: + - "bedtools" + - "procps" + interactive: false + - type: "docker" + run: + - "echo \"bedtools: \\\"$(bedtools --version | sed -n 's/^bedtools //p')\\\"\"\ + \ > /var/software_versions.txt\n" + entrypoint: [] + cmd: null +- type: "native" + id: "native" +build_info: + config: "src/bedtools/bedtools_genomecov/config.vsh.yaml" + runner: "nextflow" + engine: "docker|native" + output: "target/nextflow/bedtools/bedtools_genomecov" + executable: "target/nextflow/bedtools/bedtools_genomecov/main.nf" + viash_version: "0.9.0-RC7" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" + 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/bedtools/bedtools_genomecov/main.nf b/target/nextflow/bedtools/bedtools_genomecov/main.nf new file mode 100644 index 00000000..f74d971a --- /dev/null +++ b/target/nextflow/bedtools/bedtools_genomecov/main.nf @@ -0,0 +1,3814 @@ +// bedtools_genomecov 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, maintainer) + +//////////////////////////// +// 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" : "bedtools_genomecov", + "namespace" : "bedtools", + "version" : "main", + "authors" : [ + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatician" + } + ] + } + } + ], + "argument_groups" : [ + { + "name" : "Inputs", + "arguments" : [ + { + "type" : "file", + "name" : "--input", + "alternatives" : [ + "-i" + ], + "description" : "The input file (BED/GFF/VCF) to be used.\n", + "example" : [ + "input.bed" + ], + "must_exist" : true, + "create_parent" : true, + "required" : false, + "direction" : "input", + "multiple" : false, + "multiple_sep" : ";" + }, + { + "type" : "file", + "name" : "--input_bam", + "alternatives" : [ + "-ibam" + ], + "description" : "The input file is in BAM format.\nNote: BAM _must_ be sorted by positions.\n'--genome' option is ignored if you use '--input_bam' option!\n", + "must_exist" : true, + "create_parent" : true, + "required" : false, + "direction" : "input", + "multiple" : false, + "multiple_sep" : ";" + }, + { + "type" : "file", + "name" : "--genome", + "alternatives" : [ + "-g" + ], + "description" : "The genome file to be used.\n", + "example" : [ + "genome.txt" + ], + "must_exist" : true, + "create_parent" : true, + "required" : false, + "direction" : "input", + "multiple" : false, + "multiple_sep" : ";" + } + ] + }, + { + "name" : "Outputs", + "arguments" : [ + { + "type" : "file", + "name" : "--output", + "description" : "The output BED file. \n", + "example" : [ + "output.bed" + ], + "must_exist" : true, + "create_parent" : true, + "required" : true, + "direction" : "output", + "multiple" : false, + "multiple_sep" : ";" + } + ] + }, + { + "name" : "Options", + "arguments" : [ + { + "type" : "boolean_true", + "name" : "--depth", + "alternatives" : [ + "-d" + ], + "description" : "Report the depth at each genome position (with one-based coordinates).\nDefault behavior is to report a histogram.\n", + "direction" : "input" + }, + { + "type" : "boolean_true", + "name" : "--depth_zero", + "alternatives" : [ + "-dz" + ], + "description" : "Report the depth at each genome position (with zero-based coordinates).\nReports only non-zero positions.\nDefault behavior is to report a histogram.\n", + "direction" : "input" + }, + { + "type" : "boolean_true", + "name" : "--bed_graph", + "alternatives" : [ + "-bg" + ], + "description" : "Report depth in BedGraph format. For details, see:\ngenome.ucsc.edu/goldenPath/help/bedgraph.html\n", + "direction" : "input" + }, + { + "type" : "boolean_true", + "name" : "--bed_graph_zero_coverage", + "alternatives" : [ + "-bga" + ], + "description" : "Report depth in BedGraph format, as above (-bg).\nHowever with this option, regions with zero \ncoverage are also reported. This allows one to\nquickly extract all regions of a genome with 0 \ncoverage by applying: \\"grep -w 0$\\" to the output.\n", + "direction" : "input" + }, + { + "type" : "boolean_true", + "name" : "--split", + "description" : "Treat \\"split\\" BAM or BED12 entries as distinct BED intervals.\nwhen computing coverage.\nFor BAM files, this uses the CIGAR \\"N\\" and \\"D\\" operations \nto infer the blocks for computing coverage.\nFor BED12 files, this uses the BlockCount, BlockStarts, and BlockEnds\nfields (i.e., columns 10,11,12).\n", + "direction" : "input" + }, + { + "type" : "boolean_true", + "name" : "--ignore_deletion", + "alternatives" : [ + "-ignoreD" + ], + "description" : "Ignore local deletions (CIGAR \\"D\\" operations) in BAM entries\nwhen computing coverage.\n", + "direction" : "input" + }, + { + "type" : "string", + "name" : "--strand", + "description" : "Calculate coverage of intervals from a specific strand.\nWith BED files, requires at least 6 columns (strand is column 6). \n", + "required" : false, + "choices" : [ + "+", + "-" + ], + "direction" : "input", + "multiple" : false, + "multiple_sep" : ";" + }, + { + "type" : "boolean_true", + "name" : "--pair_end_coverage", + "alternatives" : [ + "-pc" + ], + "description" : "Calculate coverage of pair-end fragments.\nWorks for BAM files only\n", + "direction" : "input" + }, + { + "type" : "boolean_true", + "name" : "--fragment_size", + "alternatives" : [ + "-fs" + ], + "description" : "Force to use provided fragment size instead of read length\nWorks for BAM files only\n", + "direction" : "input" + }, + { + "type" : "boolean_true", + "name" : "--du", + "description" : "Change strand af the mate read (so both reads from the same strand) useful for strand specific\nWorks for BAM files only\n", + "direction" : "input" + }, + { + "type" : "boolean_true", + "name" : "--five_prime", + "alternatives" : [ + "-5" + ], + "description" : "Calculate coverage of 5\\" positions (instead of entire interval).\n", + "direction" : "input" + }, + { + "type" : "boolean_true", + "name" : "--three_prime", + "alternatives" : [ + "-3" + ], + "description" : "Calculate coverage of 3\\" positions (instead of entire interval).\n", + "direction" : "input" + }, + { + "type" : "integer", + "name" : "--max", + "description" : "Combine all positions with a depth >= max into\na single bin in the histogram. Irrelevant\nfor -d and -bedGraph\n- (INTEGER)\n", + "required" : false, + "min" : 0, + "direction" : "input", + "multiple" : false, + "multiple_sep" : ";" + }, + { + "type" : "double", + "name" : "--scale", + "description" : "Scale the coverage by a constant factor.\nEach coverage value is multiplied by this factor before being reported.\nUseful for normalizing coverage by, e.g., reads per million (RPM).\n- Default is 1.0; i.e., unscaled.\n- (FLOAT)\n", + "required" : false, + "min" : 0.0, + "direction" : "input", + "multiple" : false, + "multiple_sep" : ";" + }, + { + "type" : "boolean_true", + "name" : "--trackline", + "description" : "Adds a UCSC/Genome-Browser track line definition in the first line of the output.\n- See here for more details about track line definition:\n http://genome.ucsc.edu/goldenPath/help/bedgraph.html\n- NOTE: When adding a trackline definition, the output BedGraph can be easily\n uploaded to the Genome Browser as a custom track,\n BUT CAN NOT be converted into a BigWig file (w/o removing the first line).\n", + "direction" : "input" + }, + { + "type" : "string", + "name" : "--trackopts", + "description" : "Writes additional track line definition parameters in the first line.\n- Example:\n -trackopts 'name=\\"My Track\\" visibility=2 color=255,30,30'\n Note the use of single-quotes if you have spaces in your parameters.\n- (TEXT)\n", + "required" : false, + "direction" : "input", + "multiple" : true, + "multiple_sep" : ";" + } + ] + } + ], + "resources" : [ + { + "type" : "bash_script", + "path" : "script.sh", + "is_executable" : true + } + ], + "description" : "Compute the coverage of a feature file among a genome.\n", + "test_resources" : [ + { + "type" : "bash_script", + "path" : "test.sh", + "is_executable" : true + }, + { + "type" : "file", + "path" : "test_data" + } + ], + "status" : "enabled", + "requirements" : { + "commands" : [ + "ps" + ] + }, + "keywords" : [ + "genome coverage", + "BED", + "GFF", + "VCF", + "BAM" + ], + "license" : "MIT", + "references" : { + "doi" : [ + "10.1093/bioinformatics/btq033" + ] + }, + "links" : { + "repository" : "https://github.com/arq5x/bedtools2", + "homepage" : "https://bedtools.readthedocs.io/en/latest/#", + "documentation" : "https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html", + "issue_tracker" : "https://github.com/arq5x/bedtools2/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" : [ + "bedtools", + "procps" + ], + "interactive" : false + }, + { + "type" : "docker", + "run" : [ + "echo \\"bedtools: \\\\\\"$(bedtools --version | sed -n 's/^bedtools //p')\\\\\\"\\" > /var/software_versions.txt\n" + ] + } + ] + }, + { + "type" : "native", + "id" : "native" + } + ], + "build_info" : { + "config" : "/workdir/root/repo/src/bedtools/bedtools_genomecov/config.vsh.yaml", + "runner" : "nextflow", + "engine" : "docker|native", + "output" : "target/nextflow/bedtools/bedtools_genomecov", + "viash_version" : "0.9.0-RC7", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", + "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 ${VIASH_PAR_INPUT_BAM+x} ]; then echo "${VIASH_PAR_INPUT_BAM}" | sed "s#'#'\\"'\\"'#g;s#.*#par_input_bam='&'#" ; else echo "# par_input_bam="; fi ) +$( if [ ! -z ${VIASH_PAR_GENOME+x} ]; then echo "${VIASH_PAR_GENOME}" | sed "s#'#'\\"'\\"'#g;s#.*#par_genome='&'#" ; else echo "# par_genome="; 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 ${VIASH_PAR_DEPTH+x} ]; then echo "${VIASH_PAR_DEPTH}" | sed "s#'#'\\"'\\"'#g;s#.*#par_depth='&'#" ; else echo "# par_depth="; fi ) +$( if [ ! -z ${VIASH_PAR_DEPTH_ZERO+x} ]; then echo "${VIASH_PAR_DEPTH_ZERO}" | sed "s#'#'\\"'\\"'#g;s#.*#par_depth_zero='&'#" ; else echo "# par_depth_zero="; fi ) +$( if [ ! -z ${VIASH_PAR_BED_GRAPH+x} ]; then echo "${VIASH_PAR_BED_GRAPH}" | sed "s#'#'\\"'\\"'#g;s#.*#par_bed_graph='&'#" ; else echo "# par_bed_graph="; fi ) +$( if [ ! -z ${VIASH_PAR_BED_GRAPH_ZERO_COVERAGE+x} ]; then echo "${VIASH_PAR_BED_GRAPH_ZERO_COVERAGE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_bed_graph_zero_coverage='&'#" ; else echo "# par_bed_graph_zero_coverage="; fi ) +$( if [ ! -z ${VIASH_PAR_SPLIT+x} ]; then echo "${VIASH_PAR_SPLIT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_split='&'#" ; else echo "# par_split="; fi ) +$( if [ ! -z ${VIASH_PAR_IGNORE_DELETION+x} ]; then echo "${VIASH_PAR_IGNORE_DELETION}" | sed "s#'#'\\"'\\"'#g;s#.*#par_ignore_deletion='&'#" ; else echo "# par_ignore_deletion="; fi ) +$( if [ ! -z ${VIASH_PAR_STRAND+x} ]; then echo "${VIASH_PAR_STRAND}" | sed "s#'#'\\"'\\"'#g;s#.*#par_strand='&'#" ; else echo "# par_strand="; fi ) +$( if [ ! -z ${VIASH_PAR_PAIR_END_COVERAGE+x} ]; then echo "${VIASH_PAR_PAIR_END_COVERAGE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_pair_end_coverage='&'#" ; else echo "# par_pair_end_coverage="; fi ) +$( if [ ! -z ${VIASH_PAR_FRAGMENT_SIZE+x} ]; then echo "${VIASH_PAR_FRAGMENT_SIZE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_fragment_size='&'#" ; else echo "# par_fragment_size="; fi ) +$( if [ ! -z ${VIASH_PAR_DU+x} ]; then echo "${VIASH_PAR_DU}" | sed "s#'#'\\"'\\"'#g;s#.*#par_du='&'#" ; else echo "# par_du="; fi ) +$( if [ ! -z ${VIASH_PAR_FIVE_PRIME+x} ]; then echo "${VIASH_PAR_FIVE_PRIME}" | sed "s#'#'\\"'\\"'#g;s#.*#par_five_prime='&'#" ; else echo "# par_five_prime="; fi ) +$( if [ ! -z ${VIASH_PAR_THREE_PRIME+x} ]; then echo "${VIASH_PAR_THREE_PRIME}" | sed "s#'#'\\"'\\"'#g;s#.*#par_three_prime='&'#" ; else echo "# par_three_prime="; fi ) +$( if [ ! -z ${VIASH_PAR_MAX+x} ]; then echo "${VIASH_PAR_MAX}" | sed "s#'#'\\"'\\"'#g;s#.*#par_max='&'#" ; else echo "# par_max="; fi ) +$( if [ ! -z ${VIASH_PAR_SCALE+x} ]; then echo "${VIASH_PAR_SCALE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_scale='&'#" ; else echo "# par_scale="; fi ) +$( if [ ! -z ${VIASH_PAR_TRACKLINE+x} ]; then echo "${VIASH_PAR_TRACKLINE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_trackline='&'#" ; else echo "# par_trackline="; fi ) +$( if [ ! -z ${VIASH_PAR_TRACKOPTS+x} ]; then echo "${VIASH_PAR_TRACKOPTS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_trackopts='&'#" ; else echo "# par_trackopts="; 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 variables +unset_if_false=( + par_input_bam + par_depth + par_depth_zero + par_bed_graph + par_bed_graph_zero_coverage + par_split + par_ignore_deletion + par_pair_end_coverage + par_fragment_size + par_du + par_five_prime + par_three_prime + par_trackline +) + +for par in \\${unset_if_false[@]}; do + test_val="\\${!par}" + [[ "\\$test_val" == "false" ]] && unset \\$par +done + +# Create input array +IFS=";" read -ra trackopts <<< \\$par_trackopts + +bedtools genomecov \\\\ + \\${par_depth:+-d} \\\\ + \\${par_depth_zero:+-dz} \\\\ + \\${par_bed_graph:+-bg} \\\\ + \\${par_bed_graph_zero_coverage:+-bga} \\\\ + \\${par_split:+-split} \\\\ + \\${par_ignore_deletion:+-ignoreD} \\\\ + \\${par_du:+-du} \\\\ + \\${par_five_prime:+-5} \\\\ + \\${par_three_prime:+-3} \\\\ + \\${par_trackline:+-trackline} \\\\ + \\${par_strand:+-strand "\\$par_strand"} \\\\ + \\${par_max:+-max "\\$par_max"} \\\\ + \\${par_scale:+-scale "\\$par_scale"} \\\\ + \\${par_trackopts:+-trackopts "\\${trackopts[*]}"} \\\\ + \\${par_input_bam:+-ibam "\\$par_input_bam"} \\\\ + \\${par_input:+-i "\\$par_input"} \\\\ + \\${par_genome:+-g "\\$par_genome"} \\\\ + \\${par_pair_end_coverage:+-pc} \\\\ + \\${par_fragment_size:+-fs} \\\\ + > "\\$par_output" + +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-${procKey}-", ".nf") + addShutdownHook { java.nio.file.Files.deleteIfExists(tempFile) } + tempFile.text = procStr + + // create process from temp file + def binding = new nextflow.script.ScriptBinding([:]) + def session = nextflow.Nextflow.getSession() + def parser = new nextflow.script.ScriptParser(session) + .setModule(true) + .setBinding(binding) + def moduleScript = parser.runScript(tempFile) + .getScript() + + // register module in meta + def module = new nextflow.script.IncludeDef.Module(name: procKey) + scriptMeta.addModule(moduleScript, module.name, module.alias) + + // retrieve and return process from meta + return scriptMeta.getProcess(procKey) +} + +// defaults +meta["defaults"] = [ + // key to be used to trace the process and determine output names + key: null, + + // fixed arguments to be passed to script + args: [:], + + // default directives + directives: readJsonBlob('''{ + "container" : { + "registry" : "images.viash-hub.com", + "image" : "vsh/biobox/bedtools/bedtools_genomecov", + "tag" : "main" + }, + "tag" : "$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/bedtools/bedtools_genomecov/nextflow.config b/target/nextflow/bedtools/bedtools_genomecov/nextflow.config new file mode 100644 index 00000000..784641e7 --- /dev/null +++ b/target/nextflow/bedtools/bedtools_genomecov/nextflow.config @@ -0,0 +1,126 @@ +manifest { + name = 'bedtools/bedtools_genomecov' + mainScript = 'main.nf' + nextflowVersion = '!>=20.12.1-edge' + version = 'main' + description = 'Compute the coverage of a feature file among a genome.\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/bedtools/bedtools_genomecov/nextflow_schema.json b/target/nextflow/bedtools/bedtools_genomecov/nextflow_schema.json new file mode 100644 index 00000000..3e0bb4b2 --- /dev/null +++ b/target/nextflow/bedtools/bedtools_genomecov/nextflow_schema.json @@ -0,0 +1,303 @@ +{ +"$schema": "http://json-schema.org/draft-07/schema", +"title": "bedtools_genomecov", +"description": "Compute the coverage of a feature file among a genome.\n", +"type": "object", +"definitions": { + + + + "inputs" : { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + + + "input": { + "type": + "string", + "description": "Type: `file`, example: `input.bed`. The input file (BED/GFF/VCF) to be used", + "help_text": "Type: `file`, example: `input.bed`. The input file (BED/GFF/VCF) to be used.\n" + + } + + + , + "input_bam": { + "type": + "string", + "description": "Type: `file`. The input file is in BAM format", + "help_text": "Type: `file`. The input file is in BAM format.\nNote: BAM _must_ be sorted by positions.\n\u0027--genome\u0027 option is ignored if you use \u0027--input_bam\u0027 option!\n" + + } + + + , + "genome": { + "type": + "string", + "description": "Type: `file`, example: `genome.txt`. The genome file to be used", + "help_text": "Type: `file`, example: `genome.txt`. The genome file to be used.\n" + + } + + +} +}, + + + "outputs" : { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + + + "output": { + "type": + "string", + "description": "Type: `file`, required, default: `$id.$key.output.bed`, example: `output.bed`. The output BED file", + "help_text": "Type: `file`, required, default: `$id.$key.output.bed`, example: `output.bed`. The output BED file. \n" + , + "default": "$id.$key.output.bed" + } + + +} +}, + + + "options" : { + "title": "Options", + "type": "object", + "description": "No description", + "properties": { + + + "depth": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Report the depth at each genome position (with one-based coordinates)", + "help_text": "Type: `boolean_true`, default: `false`. Report the depth at each genome position (with one-based coordinates).\nDefault behavior is to report a histogram.\n" + , + "default": "False" + } + + + , + "depth_zero": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Report the depth at each genome position (with zero-based coordinates)", + "help_text": "Type: `boolean_true`, default: `false`. Report the depth at each genome position (with zero-based coordinates).\nReports only non-zero positions.\nDefault behavior is to report a histogram.\n" + , + "default": "False" + } + + + , + "bed_graph": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Report depth in BedGraph format", + "help_text": "Type: `boolean_true`, default: `false`. Report depth in BedGraph format. For details, see:\ngenome.ucsc.edu/goldenPath/help/bedgraph.html\n" + , + "default": "False" + } + + + , + "bed_graph_zero_coverage": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Report depth in BedGraph format, as above (-bg)", + "help_text": "Type: `boolean_true`, default: `false`. Report depth in BedGraph format, as above (-bg).\nHowever with this option, regions with zero \ncoverage are also reported. This allows one to\nquickly extract all regions of a genome with 0 \ncoverage by applying: \"grep -w 0$\" to the output.\n" + , + "default": "False" + } + + + , + "split": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Treat \"split\" BAM or BED12 entries as distinct BED intervals", + "help_text": "Type: `boolean_true`, default: `false`. Treat \"split\" BAM or BED12 entries as distinct BED intervals.\nwhen computing coverage.\nFor BAM files, this uses the CIGAR \"N\" and \"D\" operations \nto infer the blocks for computing coverage.\nFor BED12 files, this uses the BlockCount, BlockStarts, and BlockEnds\nfields (i.e., columns 10,11,12).\n" + , + "default": "False" + } + + + , + "ignore_deletion": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Ignore local deletions (CIGAR \"D\" operations) in BAM entries\nwhen computing coverage", + "help_text": "Type: `boolean_true`, default: `false`. Ignore local deletions (CIGAR \"D\" operations) in BAM entries\nwhen computing coverage.\n" + , + "default": "False" + } + + + , + "strand": { + "type": + "string", + "description": "Type: `string`, choices: ``+`, `-``. Calculate coverage of intervals from a specific strand", + "help_text": "Type: `string`, choices: ``+`, `-``. Calculate coverage of intervals from a specific strand.\nWith BED files, requires at least 6 columns (strand is column 6). \n", + "enum": ["+", "-"] + + + } + + + , + "pair_end_coverage": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Calculate coverage of pair-end fragments", + "help_text": "Type: `boolean_true`, default: `false`. Calculate coverage of pair-end fragments.\nWorks for BAM files only\n" + , + "default": "False" + } + + + , + "fragment_size": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Force to use provided fragment size instead of read length\nWorks for BAM files only\n", + "help_text": "Type: `boolean_true`, default: `false`. Force to use provided fragment size instead of read length\nWorks for BAM files only\n" + , + "default": "False" + } + + + , + "du": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Change strand af the mate read (so both reads from the same strand) useful for strand specific\nWorks for BAM files only\n", + "help_text": "Type: `boolean_true`, default: `false`. Change strand af the mate read (so both reads from the same strand) useful for strand specific\nWorks for BAM files only\n" + , + "default": "False" + } + + + , + "five_prime": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Calculate coverage of 5\" positions (instead of entire interval)", + "help_text": "Type: `boolean_true`, default: `false`. Calculate coverage of 5\" positions (instead of entire interval).\n" + , + "default": "False" + } + + + , + "three_prime": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Calculate coverage of 3\" positions (instead of entire interval)", + "help_text": "Type: `boolean_true`, default: `false`. Calculate coverage of 3\" positions (instead of entire interval).\n" + , + "default": "False" + } + + + , + "max": { + "type": + "integer", + "description": "Type: `integer`. Combine all positions with a depth \u003e= max into\na single bin in the histogram", + "help_text": "Type: `integer`. Combine all positions with a depth \u003e= max into\na single bin in the histogram. Irrelevant\nfor -d and -bedGraph\n- (INTEGER)\n" + + } + + + , + "scale": { + "type": + "number", + "description": "Type: `double`. Scale the coverage by a constant factor", + "help_text": "Type: `double`. Scale the coverage by a constant factor.\nEach coverage value is multiplied by this factor before being reported.\nUseful for normalizing coverage by, e.g., reads per million (RPM).\n- Default is 1.0; i.e., unscaled.\n- (FLOAT)\n" + + } + + + , + "trackline": { + "type": + "boolean", + "description": "Type: `boolean_true`, default: `false`. Adds a UCSC/Genome-Browser track line definition in the first line of the output", + "help_text": "Type: `boolean_true`, default: `false`. Adds a UCSC/Genome-Browser track line definition in the first line of the output.\n- See here for more details about track line definition:\n http://genome.ucsc.edu/goldenPath/help/bedgraph.html\n- NOTE: When adding a trackline definition, the output BedGraph can be easily\n uploaded to the Genome Browser as a custom track,\n BUT CAN NOT be converted into a BigWig file (w/o removing the first line).\n" + , + "default": "False" + } + + + , + "trackopts": { + "type": + "string", + "description": "Type: List of `string`, multiple_sep: `\";\"`. Writes additional track line definition parameters in the first line", + "help_text": "Type: List of `string`, multiple_sep: `\";\"`. Writes additional track line definition parameters in the first line.\n- Example:\n -trackopts \u0027name=\"My Track\" visibility=2 color=255,30,30\u0027\n Note the use of single-quotes if you have spaces in your parameters.\n- (TEXT)\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/bedtools/bedtools_getfasta/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml index ec674e3f..02b9e89e 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 18c9c159..906edbe0 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "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 af662feb..794aec1b 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 9c8b1e42..59784220 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "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 706083ac..fe6f8e39 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 0df9137c..711b9cc0 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "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 0b594a83..7add2e73 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 480f023f..ddf6d6ee 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "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 a6840e90..6bbdab81 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 50c83872..000adb91 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "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 ce3ae9cb..c746447d 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 babe12ae..f4c84801 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "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 8a443214..12416131 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 37f3a35b..58a43ef8 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "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 f45603c4..99993701 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 2ce7eafb..bafb4428 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "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 0eba1a54..c471fd9d 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 d649a734..326bfd9d 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "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 d5215ee0..e6bbfa4d 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 e3d1ebc1..06834639 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "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 20620283..997c6924 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 0e9840ce..cb3a8afa 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "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 931a4faa..a0cdbfa1 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 697e4ea4..531931ce 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "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 f467f82f..bd95933d 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 c85bc740..5a7a41b9 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "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 ad0ca300..7071617f 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 1b8c7c96..9b352b19 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "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 e19db38c..06695ce1 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 47a71752..9d83cd6b 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "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 b6ce1236..6e17272c 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 51f380de..0a9f5015 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "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 a4ebaa9f..28fede58 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 fa5fb64f..a1d1bf53 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "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 1f9e7c32..29ecc063 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 ce727751..725f1cb7 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "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 668255ae..726f6cb9 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 ad1e4666..50037b25 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "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 f5f9658e..26f24d38 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 0306f9dd..4cfc2ce7 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "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 05cf8086..14812aa1 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 67642664..2938d8b0 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "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 8ca8d06c..5f2344e1 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 1ca72d81..9cdb2ffc 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "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 93662d59..8cc56705 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 3a192405..4cf544ac 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "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 1d8a4f56..26629e67 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 351f2243..95fe2106 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "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 3b306bb6..42ff525a 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 22273509..fab23d69 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "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 52c34b53..1b7fa895 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 28658b6e..4afa73b5 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "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 fa92d11f..ab6bd9b1 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 8fbbdba8..3b836d7c 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "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 f4104229..cb4daff7 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 8dc6cac0..fbfaa3fa 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "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 1ac3f452..4ac8322d 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 c16d68e7..e57a980c 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "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 5a748f65..88884de5 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 c6c52fc5..f2dacb03 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "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 21dff091..dde9bebf 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 11518f56..c588521d 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "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 27976871..b0476de9 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 7766cb30..f375fd4f 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "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 0b8eb983..272d2bd8 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 a5a9319a..02e9d26f 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "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 39e5c8e3..ab89f543 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 5c7804ea..9b0ec407 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "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 a9665ab4..5e83ef5f 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 8b8c080d..55585fb2 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "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 13271069..98fe861d 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 52c4f967..19f989f7 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "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 86a780e1..d54763dc 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 7a8fbcb2..05618ad7 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "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 8b5250f0..3f5b2ccc 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 d89ee99d..329e9a4b 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "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 c2f31e6c..fc9a1f51 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: "e6627ec728761fe63fe75b0a10ba51da2bccec21" + git_commit: "99dec5923bfb3da165601a3f13502d498395b14d" 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 3d555393..39e00f73 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" : "e6627ec728761fe63fe75b0a10ba51da2bccec21", + "git_commit" : "99dec5923bfb3da165601a3f13502d498395b14d", "git_remote" : "https://github.com/viash-hub/biobox" }, "package_config" : {