From 240ee4328cffce14e983f6871cc0ea39cf7a5041 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Mon, 28 Mar 2022 16:29:46 +0200 Subject: [PATCH 1/3] Dastool update to allow non-gzipped inputs (#1458) * fix: remove left-over unnecessary code * Make gzipping optional for DAS_Tool scaffolds2bin * Add optional unzipping * Make gunzip optional for DAS_Tool scaffolds2bin * Apply suggestions from code review Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com> * Update modules/dastool/scaffolds2bin/meta.yml Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com> --- modules/dastool/scaffolds2bin/main.nf | 5 ++-- modules/dastool/scaffolds2bin/meta.yml | 9 ++---- tests/modules/dastool/scaffolds2bin/main.nf | 31 +++++++++++++++++--- tests/modules/dastool/scaffolds2bin/test.yml | 20 ++++++++----- 4 files changed, 46 insertions(+), 19 deletions(-) diff --git a/modules/dastool/scaffolds2bin/main.nf b/modules/dastool/scaffolds2bin/main.nf index 6e9fcdc2..365872fd 100644 --- a/modules/dastool/scaffolds2bin/main.nf +++ b/modules/dastool/scaffolds2bin/main.nf @@ -22,9 +22,10 @@ process DASTOOL_SCAFFOLDS2BIN { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def file_extension = extension ? extension : "fasta" - + def clean_fasta = fasta.toString() - ".gz" + def decompress_fasta = fasta.toString() == clean_fasta ? "" : "gunzip -q -f $fasta" """ - gunzip -f *.${file_extension}.gz + $decompress_fasta Fasta_to_Scaffolds2Bin.sh \\ $args \\ diff --git a/modules/dastool/scaffolds2bin/meta.yml b/modules/dastool/scaffolds2bin/meta.yml index 0bf8618d..823084b3 100644 --- a/modules/dastool/scaffolds2bin/meta.yml +++ b/modules/dastool/scaffolds2bin/meta.yml @@ -30,14 +30,11 @@ input: e.g. [ id:'test', single_end:false ] - fasta: type: file - description: Fasta of list of fasta files recommended to be gathered via with .collect() of bins - pattern: "*.{fa,fas,fasta}" - - binner: - type: val - description: Name of the binning software (optional) + description: Fasta or list of fasta files recommended to be gathered via with .collect() of bins + pattern: "*.{fa,fa.gz,fas,fas.gz,fna,fna.gz,fasta,fasta.gz}" - extension: type: val - description: Fasta file extension (fa | fas | fasta | ...) + description: Fasta file extension (fa | fas | fasta | ...), but without .gz suffix, even if gzipped input. output: - meta: diff --git a/tests/modules/dastool/scaffolds2bin/main.nf b/tests/modules/dastool/scaffolds2bin/main.nf index a0cd6726..c45a6f2b 100644 --- a/tests/modules/dastool/scaffolds2bin/main.nf +++ b/tests/modules/dastool/scaffolds2bin/main.nf @@ -2,9 +2,10 @@ nextflow.enable.dsl = 2 -include { METABAT2_METABAT2 } from '../../../../modules/metabat2/metabat2/main.nf' -include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS } from '../../../../modules/metabat2/jgisummarizebamcontigdepths/main.nf' -include { DASTOOL_SCAFFOLDS2BIN } from '../../../../modules/dastool/scaffolds2bin/main.nf' +include { GUNZIP } from '../../../../modules/gunzip/main.nf' +include { METABAT2_METABAT2 } from '../../../../modules/metabat2/metabat2/main.nf' +include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS } from '../../../../modules/metabat2/jgisummarizebamcontigdepths/main.nf' +include { DASTOOL_SCAFFOLDS2BIN } from '../../../../modules/dastool/scaffolds2bin/main.nf' workflow test_dastool_scaffolds2bin { @@ -22,4 +23,26 @@ workflow test_dastool_scaffolds2bin { METABAT2_METABAT2 ( input_metabat2 ) DASTOOL_SCAFFOLDS2BIN ( METABAT2_METABAT2.out.fasta.collect(), "fa") -} \ No newline at end of file +} + +workflow test_dastool_scaffolds2bin_ungzipped { + + input_depth = [ [ id:'test', single_end:false ], // meta map + file(params.test_data['bacteroides_fragilis']['illumina']['test1_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['bacteroides_fragilis']['illumina']['test1_paired_end_sorted_bam_bai'], checkIfExists: true) ] + + + METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS ( input_depth ) + + Channel.fromPath(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true) + .map { it -> [[ id:'test', single_end:false ], it] } + .join(METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS.out.depth) + .set { input_metabat2 } + + METABAT2_METABAT2 ( input_metabat2 ) + + // TODO test unzipped input files + ch_input_2_scaffolds2bin = GUNZIP( METABAT2_METABAT2.out.fasta ).gunzip + + DASTOOL_SCAFFOLDS2BIN ( ch_input_2_scaffolds2bin, "fa") +} diff --git a/tests/modules/dastool/scaffolds2bin/test.yml b/tests/modules/dastool/scaffolds2bin/test.yml index 26f528c9..3d91c8c1 100644 --- a/tests/modules/dastool/scaffolds2bin/test.yml +++ b/tests/modules/dastool/scaffolds2bin/test.yml @@ -1,14 +1,20 @@ - name: dastool scaffolds2bin test_dastool_scaffolds2bin - command: nextflow run ./tests/modules/dastool/scaffolds2bin -entry test_dastool_scaffolds2bin -c ./tests/config/nextflow.config -c ./tests/modules/dastool/scaffolds2bin/nextflow.config + command: nextflow run tests/modules/dastool/scaffolds2bin -entry test_dastool_scaffolds2bin -c tests/config/nextflow.config tags: - dastool - dastool/scaffolds2bin files: - path: output/dastool/test.tsv md5sum: 6e46c0be14dded7cb13af38f54feea47 - - path: output/metabat2/bins/test.1.fa.gz - md5sum: 2b297bf557cc3831b800348859331268 - - path: output/metabat2/test.tsv.gz - md5sum: 619338fa5019e361d5545ce385a6961f - - path: output/metabat2/test.txt.gz - md5sum: 745a0446af6ef68b930975e9ce5a95d6 + - path: output/dastool/versions.yml + md5sum: d0831ed159eb5a1a1565d1d211012ad6 +- name: dastool scaffolds2bin test_dastool_scaffolds2bin_ungzipped + command: nextflow run tests/modules/dastool/scaffolds2bin -entry test_dastool_scaffolds2bin_ungzipped -c tests/config/nextflow.config + tags: + - dastool + - dastool/scaffolds2bin + files: + - path: output/dastool/test.tsv + md5sum: 6e46c0be14dded7cb13af38f54feea47 + - path: output/dastool/versions.yml + md5sum: da58e477b7f4c16a9ea495ec1a4a4d4f From 49b18b1639f4f7104187058866a8fab33332bdfe Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Mon, 28 Mar 2022 17:48:39 +0200 Subject: [PATCH 2/3] add stub to modules used in raredisease pipeline (#1206) * add stub section * add stub for bcftools norm * add stub to more modules * fix expansionhunter tests * revert changes -picard * Update stub to write version no.s to a file * add picard * revert picard again * add stubs to more modules * fix bwamem2 * add bcftools view * add stubs * fix svdb query * review suggestions --- modules/bcftools/norm/main.nf | 11 +++ modules/bcftools/view/main.nf | 11 +++ modules/bwamem2/index/main.nf | 15 ++++ modules/bwamem2/mem/main.nf | 11 +++ modules/cat/cat/main.nf | 10 +++ modules/deepvariant/main.nf | 12 ++++ modules/expansionhunter/main.nf | 11 +++ modules/fastqc/main.nf | 12 ++++ modules/gatk4/bedtointervallist/main.nf | 11 +++ .../gatk4/createsequencedictionary/main.nf | 11 +++ modules/gatk4/intervallisttools/main.nf | 18 +++++ modules/glnexus/main.nf | 11 +++ modules/multiqc/main.nf | 12 ++++ modules/picard/collecthsmetrics/main.nf | 11 +++ modules/picard/collectmultiplemetrics/main.nf | 20 ++++++ modules/picard/markduplicates/main.nf | 13 ++++ modules/picard/sortvcf/main.nf | 13 ++++ modules/qualimap/bamqc/main.nf | 68 +++++++++++++++++++ modules/samtools/faidx/main.nf | 10 +++ modules/samtools/index/main.nf | 12 ++++ modules/samtools/merge/main.nf | 12 ++++ modules/samtools/sort/main.nf | 11 +++ modules/samtools/stats/main.nf | 11 +++ modules/svdb/query/main.nf | 1 - modules/tabix/bgziptabix/main.nf | 12 ++++ modules/tabix/tabix/main.nf | 11 +++ modules/tiddit/cov/main.nf | 12 ++++ modules/tiddit/sv/main.nf | 13 ++++ modules/ucsc/wigtobigwig/main.nf | 11 +++ modules/untar/main.nf | 11 +++ modules/vcfanno/main.nf | 11 +++ tests/modules/expansionhunter/main.nf | 4 +- tests/modules/expansionhunter/test.yml | 2 +- 33 files changed, 421 insertions(+), 4 deletions(-) diff --git a/modules/bcftools/norm/main.nf b/modules/bcftools/norm/main.nf index cd681f21..b81a4310 100644 --- a/modules/bcftools/norm/main.nf +++ b/modules/bcftools/norm/main.nf @@ -34,4 +34,15 @@ process BCFTOOLS_NORM { bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.vcf.gz + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') + END_VERSIONS + """ } diff --git a/modules/bcftools/view/main.nf b/modules/bcftools/view/main.nf index 2a240f4a..ca1121a5 100644 --- a/modules/bcftools/view/main.nf +++ b/modules/bcftools/view/main.nf @@ -41,4 +41,15 @@ process BCFTOOLS_VIEW { bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.vcf.gz + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') + END_VERSIONS + """ } diff --git a/modules/bwamem2/index/main.nf b/modules/bwamem2/index/main.nf index 0e9cc2f8..900f27d4 100644 --- a/modules/bwamem2/index/main.nf +++ b/modules/bwamem2/index/main.nf @@ -31,4 +31,19 @@ process BWAMEM2_INDEX { bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //') END_VERSIONS """ + + stub: + """ + mkdir bwamem2 + touch bwamem2/${fasta}.0123 + touch bwamem2/${fasta}.ann + touch bwamem2/${fasta}.pac + touch bwamem2/${fasta}.amb + touch bwamem2/${fasta}.bwt.2bit.64 + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //') + END_VERSIONS + """ } diff --git a/modules/bwamem2/mem/main.nf b/modules/bwamem2/mem/main.nf index 21dfb1d6..e3a3d164 100644 --- a/modules/bwamem2/mem/main.nf +++ b/modules/bwamem2/mem/main.nf @@ -43,4 +43,15 @@ process BWAMEM2_MEM { samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.bam + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //') + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS + """ } diff --git a/modules/cat/cat/main.nf b/modules/cat/cat/main.nf index 25dcc652..b02ca7ee 100644 --- a/modules/cat/cat/main.nf +++ b/modules/cat/cat/main.nf @@ -47,4 +47,14 @@ process CAT_CAT { pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' ) END_VERSIONS """ + + stub: + """ + touch $prefix + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' ) + END_VERSIONS + """ } diff --git a/modules/deepvariant/main.nf b/modules/deepvariant/main.nf index 8e5f10df..f0c6b47b 100644 --- a/modules/deepvariant/main.nf +++ b/modules/deepvariant/main.nf @@ -44,4 +44,16 @@ process DEEPVARIANT { deepvariant: \$(echo \$(/opt/deepvariant/bin/run_deepvariant --version) | sed 's/^.*version //; s/ .*\$//' ) END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.vcf.gz + touch ${prefix}.g.vcf.gz + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + deepvariant: \$(echo \$(/opt/deepvariant/bin/run_deepvariant --version) | sed 's/^.*version //; s/ .*\$//' ) + END_VERSIONS + """ } diff --git a/modules/expansionhunter/main.nf b/modules/expansionhunter/main.nf index 4e62b2a6..f60b75b4 100644 --- a/modules/expansionhunter/main.nf +++ b/modules/expansionhunter/main.nf @@ -37,4 +37,15 @@ process EXPANSIONHUNTER { expansionhunter: \$( echo \$(ExpansionHunter --version 2>&1) | sed 's/^.*ExpansionHunter v//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.vcf + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + expansionhunter: \$( echo \$(ExpansionHunter --version 2>&1) | sed 's/^.*ExpansionHunter v//') + END_VERSIONS + """ } diff --git a/modules/fastqc/main.nf b/modules/fastqc/main.nf index ed6b8c50..05730368 100644 --- a/modules/fastqc/main.nf +++ b/modules/fastqc/main.nf @@ -44,4 +44,16 @@ process FASTQC { END_VERSIONS """ } + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.html + touch ${prefix}.zip + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) + END_VERSIONS + """ } diff --git a/modules/gatk4/bedtointervallist/main.nf b/modules/gatk4/bedtointervallist/main.nf index 74256dd1..c3b624a8 100644 --- a/modules/gatk4/bedtointervallist/main.nf +++ b/modules/gatk4/bedtointervallist/main.nf @@ -39,4 +39,15 @@ process GATK4_BEDTOINTERVALLIST { gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.interval_list + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ } diff --git a/modules/gatk4/createsequencedictionary/main.nf b/modules/gatk4/createsequencedictionary/main.nf index 87d52a59..fe1a6c65 100644 --- a/modules/gatk4/createsequencedictionary/main.nf +++ b/modules/gatk4/createsequencedictionary/main.nf @@ -37,4 +37,15 @@ process GATK4_CREATESEQUENCEDICTIONARY { gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.dict + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ } diff --git a/modules/gatk4/intervallisttools/main.nf b/modules/gatk4/intervallisttools/main.nf index 352a3240..82c3222c 100644 --- a/modules/gatk4/intervallisttools/main.nf +++ b/modules/gatk4/intervallisttools/main.nf @@ -51,4 +51,22 @@ process GATK4_INTERVALLISTTOOLS { gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + mkdir -p ${prefix}_split/temp_0001_of_6 + mkdir -p ${prefix}_split/temp_0002_of_6 + mkdir -p ${prefix}_split/temp_0003_of_6 + mkdir -p ${prefix}_split/temp_0004_of_6 + touch ${prefix}_split/temp_0001_of_6/1scattered.interval_list + touch ${prefix}_split/temp_0002_of_6/2scattered.interval_list + touch ${prefix}_split/temp_0003_of_6/3scattered.interval_list + touch ${prefix}_split/temp_0004_of_6/4scattered.interval_list + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ } diff --git a/modules/glnexus/main.nf b/modules/glnexus/main.nf index 84da95a0..a26ab4ce 100644 --- a/modules/glnexus/main.nf +++ b/modules/glnexus/main.nf @@ -42,4 +42,15 @@ process GLNEXUS { glnexus: \$( echo \$(glnexus_cli 2>&1) | head -n 1 | sed 's/^.*release v//; s/ .*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.bcf + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + glnexus: \$( echo \$(glnexus_cli 2>&1) | head -n 1 | sed 's/^.*release v//; s/ .*\$//') + END_VERSIONS + """ } diff --git a/modules/multiqc/main.nf b/modules/multiqc/main.nf index 1264aac1..ae019dbf 100644 --- a/modules/multiqc/main.nf +++ b/modules/multiqc/main.nf @@ -28,4 +28,16 @@ process MULTIQC { multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) END_VERSIONS """ + + stub: + """ + touch multiqc_data + touch multiqc_plots + touch multiqc_report.html + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) + END_VERSIONS + """ } diff --git a/modules/picard/collecthsmetrics/main.nf b/modules/picard/collecthsmetrics/main.nf index 07e8504f..3acf8bb8 100644 --- a/modules/picard/collecthsmetrics/main.nf +++ b/modules/picard/collecthsmetrics/main.nf @@ -48,4 +48,15 @@ process PICARD_COLLECTHSMETRICS { picard: \$(echo \$(picard CollectHsMetrics --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:) END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}_collecthsmetrics.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + picard: \$(echo \$(picard CollectHsMetrics --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:) + END_VERSIONS + """ } diff --git a/modules/picard/collectmultiplemetrics/main.nf b/modules/picard/collectmultiplemetrics/main.nf index e023ea3c..340463a8 100644 --- a/modules/picard/collectmultiplemetrics/main.nf +++ b/modules/picard/collectmultiplemetrics/main.nf @@ -42,4 +42,24 @@ process PICARD_COLLECTMULTIPLEMETRICS { picard: \$(picard CollectMultipleMetrics --version 2>&1 | grep -o 'Version.*' | cut -f2- -d:) END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.CollectMultipleMetrics.alignment_summary_metrics + touch ${prefix}.CollectMultipleMetrics.insert_size_metrics + touch ${prefix}.CollectMultipleMetrics.quality_distribution.pdf + touch ${prefix}.CollectMultipleMetrics.base_distribution_by_cycle_metrics + touch ${prefix}.CollectMultipleMetrics.quality_by_cycle_metrics + touch ${prefix}.CollectMultipleMetrics.read_length_histogram.pdf + touch ${prefix}.CollectMultipleMetrics.base_distribution_by_cycle.pdf + touch ${prefix}.CollectMultipleMetrics.quality_by_cycle.pdf + touch ${prefix}.CollectMultipleMetrics.insert_size_histogram.pdf + touch ${prefix}.CollectMultipleMetrics.quality_distribution_metrics + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + picard: \$(echo \$(picard CollectMultipleMetrics --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:) + END_VERSIONS + """ } diff --git a/modules/picard/markduplicates/main.nf b/modules/picard/markduplicates/main.nf index 5196b6ed..e754a587 100644 --- a/modules/picard/markduplicates/main.nf +++ b/modules/picard/markduplicates/main.nf @@ -42,4 +42,17 @@ process PICARD_MARKDUPLICATES { picard: \$(echo \$(picard MarkDuplicates --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:) END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.bam + touch ${prefix}.bam.bai + touch ${prefix}.MarkDuplicates.metrics.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + picard: \$(echo \$(picard MarkDuplicates --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:) + END_VERSIONS + """ } diff --git a/modules/picard/sortvcf/main.nf b/modules/picard/sortvcf/main.nf index 0f10c1ab..4047545e 100644 --- a/modules/picard/sortvcf/main.nf +++ b/modules/picard/sortvcf/main.nf @@ -46,4 +46,17 @@ process PICARD_SORTVCF { picard: \$(picard SortVcf --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:) END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}_sorted.vcf.gz + touch ${prefix}.bam.bai + touch ${prefix}.MarkDuplicates.metrics.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + picard: \$(picard SortVcf --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:) + END_VERSIONS + """ } diff --git a/modules/qualimap/bamqc/main.nf b/modules/qualimap/bamqc/main.nf index 92f38f8c..3bfcb4c1 100644 --- a/modules/qualimap/bamqc/main.nf +++ b/modules/qualimap/bamqc/main.nf @@ -52,4 +52,72 @@ process QUALIMAP_BAMQC { qualimap: \$(echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//') END_VERSIONS """ + + stub: + prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + """ + mkdir -p $prefix/css + mkdir $prefix/images_qualimapReport + mkdir $prefix/raw_data_qualimapReport + cd $prefix/css + touch agogo.css + touch basic.css + touch bgtop.png + touch comment-close.png + touch doctools.js + touch down-pressed.png + touch jquery.js + touch plus.png + touch qualimap_logo_small.png + touch searchtools.js + touch up.png + touch websupport.js + touch ajax-loader.gif + touch bgfooter.png + touch comment-bright.png + touch comment.png + touch down.png + touch file.png + touch minus.png + touch pygments.css + touch report.css + touch underscore.js + touch up-pressed.png + cd ../images_qualimapReport/ + touch genome_coverage_0to50_histogram.png + touch genome_coverage_quotes.png + touch genome_insert_size_across_reference.png + touch genome_mapping_quality_histogram.png + touch genome_uniq_read_starts_histogram.png + touch genome_coverage_across_reference.png + touch genome_gc_content_per_window.png + touch genome_insert_size_histogram.png + touch genome_reads_clipping_profile.png + touch genome_coverage_histogram.png + touch genome_homopolymer_indels.png + touch genome_mapping_quality_across_reference.png + touch genome_reads_content_per_read_position.png + cd ../raw_data_qualimapReport + touch coverage_across_reference.txt + touch genome_fraction_coverage.txt + touch insert_size_histogram.txt + touch mapped_reads_nucleotide_content.txt + touch coverage_histogram.txt + touch homopolymer_indels.txt + touch mapped_reads_clipping_profile.txt + touch mapping_quality_across_reference.txt + touch duplication_rate_histogram.txt + touch insert_size_across_reference.txt + touch mapped_reads_gc-content_distribution.txt + touch mapping_quality_histogram.txt + cd ../ + touch genome_results.txt + touch qualimapReport.html + cd ../ + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + qualimap: \$(echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//') + END_VERSIONS + """ } diff --git a/modules/samtools/faidx/main.nf b/modules/samtools/faidx/main.nf index 7732a4ec..053279ff 100644 --- a/modules/samtools/faidx/main.nf +++ b/modules/samtools/faidx/main.nf @@ -29,4 +29,14 @@ process SAMTOOLS_FAIDX { samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ + + stub: + """ + touch ${fasta}.fai + cat <<-END_VERSIONS > versions.yml + + "${task.process}": + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS + """ } diff --git a/modules/samtools/index/main.nf b/modules/samtools/index/main.nf index e41cdcc8..fff6e1b8 100644 --- a/modules/samtools/index/main.nf +++ b/modules/samtools/index/main.nf @@ -33,4 +33,16 @@ process SAMTOOLS_INDEX { samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ + + stub: + """ + touch ${input}.bai + touch ${input}.crai + touch ${input}.csi + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS + """ } diff --git a/modules/samtools/merge/main.nf b/modules/samtools/merge/main.nf index 7b771677..9f962a4b 100644 --- a/modules/samtools/merge/main.nf +++ b/modules/samtools/merge/main.nf @@ -38,4 +38,16 @@ process SAMTOOLS_MERGE { samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ + + stub: + prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" + def file_type = input_files[0].getExtension() + """ + touch ${prefix}.${file_type} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS + """ } diff --git a/modules/samtools/sort/main.nf b/modules/samtools/sort/main.nf index 0e2de8ba..ba46f0c9 100644 --- a/modules/samtools/sort/main.nf +++ b/modules/samtools/sort/main.nf @@ -28,4 +28,15 @@ process SAMTOOLS_SORT { samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.bam + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS + """ } diff --git a/modules/samtools/stats/main.nf b/modules/samtools/stats/main.nf index 6efc9d9a..85cb64f3 100644 --- a/modules/samtools/stats/main.nf +++ b/modules/samtools/stats/main.nf @@ -34,4 +34,15 @@ process SAMTOOLS_STATS { samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${input}.stats + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS + """ } diff --git a/modules/svdb/query/main.nf b/modules/svdb/query/main.nf index 37ce432c..15609bad 100644 --- a/modules/svdb/query/main.nf +++ b/modules/svdb/query/main.nf @@ -70,5 +70,4 @@ process SVDB_QUERY { svdb: \$( echo \$(svdb) | head -1 | sed 's/usage: SVDB-\\([0-9]\\.[0-9]\\.[0-9]\\).*/\\1/' ) END_VERSIONS """ - } diff --git a/modules/tabix/bgziptabix/main.nf b/modules/tabix/bgziptabix/main.nf index 12657599..77fd91a5 100644 --- a/modules/tabix/bgziptabix/main.nf +++ b/modules/tabix/bgziptabix/main.nf @@ -30,4 +30,16 @@ process TABIX_BGZIPTABIX { tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.gz + touch ${prefix}.gz.tbi + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//') + END_VERSIONS + """ } diff --git a/modules/tabix/tabix/main.nf b/modules/tabix/tabix/main.nf index 5f516261..c9dab068 100644 --- a/modules/tabix/tabix/main.nf +++ b/modules/tabix/tabix/main.nf @@ -27,4 +27,15 @@ process TABIX_TABIX { tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${tab}.tbi + cat <<-END_VERSIONS > versions.yml + + "${task.process}": + tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//') + END_VERSIONS + """ } diff --git a/modules/tiddit/cov/main.nf b/modules/tiddit/cov/main.nf index a5f8c649..f805cfa7 100644 --- a/modules/tiddit/cov/main.nf +++ b/modules/tiddit/cov/main.nf @@ -36,4 +36,16 @@ process TIDDIT_COV { tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*TIDDIT-//; s/ .*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch $prefix.wig + touch $prefix.tab + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*TIDDIT-//; s/ .*\$//') + END_VERSIONS + """ } diff --git a/modules/tiddit/sv/main.nf b/modules/tiddit/sv/main.nf index 454dfc54..872eeed1 100644 --- a/modules/tiddit/sv/main.nf +++ b/modules/tiddit/sv/main.nf @@ -38,4 +38,17 @@ process TIDDIT_SV { tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*TIDDIT-//; s/ .*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch $prefix.vcf + touch $prefix.ploidy.tab + touch $prefix.signals.tab + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*TIDDIT-//; s/ .*\$//') + END_VERSIONS + """ } diff --git a/modules/ucsc/wigtobigwig/main.nf b/modules/ucsc/wigtobigwig/main.nf index d07e7ec1..2af7190b 100644 --- a/modules/ucsc/wigtobigwig/main.nf +++ b/modules/ucsc/wigtobigwig/main.nf @@ -35,4 +35,15 @@ process UCSC_WIGTOBIGWIG { ucsc: $VERSION END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.bw + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + ucsc: $VERSION + END_VERSIONS + """ } diff --git a/modules/untar/main.nf b/modules/untar/main.nf index dc43fb78..5aa6aa7f 100644 --- a/modules/untar/main.nf +++ b/modules/untar/main.nf @@ -33,4 +33,15 @@ process UNTAR { untar: \$(echo \$(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//') END_VERSIONS """ + + stub: + untar = archive.toString() - '.tar.gz' + """ + touch $untar + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + untar: \$(echo \$(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//') + END_VERSIONS + """ } diff --git a/modules/vcfanno/main.nf b/modules/vcfanno/main.nf index 51b1ec5b..bc0514c9 100644 --- a/modules/vcfanno/main.nf +++ b/modules/vcfanno/main.nf @@ -39,4 +39,15 @@ process VCFANNO { vcfanno: \$(echo \$(vcfanno 2>&1 | grep version | cut -f3 -d' ' )) END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}_annotated.vcf + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + vcfanno: \$(echo \$(vcfanno 2>&1 | grep version | cut -f3 -d' ' )) + END_VERSIONS + """ } diff --git a/tests/modules/expansionhunter/main.nf b/tests/modules/expansionhunter/main.nf index 91faeeb8..d0221234 100644 --- a/tests/modules/expansionhunter/main.nf +++ b/tests/modules/expansionhunter/main.nf @@ -7,8 +7,8 @@ include { EXPANSIONHUNTER } from '../../../modules/expansionhunter/main.nf' workflow test_expansionhunter { input = [ [ id:'test', gender:'male' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), ] fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) variant_catalog = file(params.test_data['homo_sapiens']['genome']['repeat_expansions'], checkIfExists: true) diff --git a/tests/modules/expansionhunter/test.yml b/tests/modules/expansionhunter/test.yml index 19403588..f9282f8c 100644 --- a/tests/modules/expansionhunter/test.yml +++ b/tests/modules/expansionhunter/test.yml @@ -4,4 +4,4 @@ - expansionhunter files: - path: output/expansionhunter/test.vcf - md5sum: ef6c2101d7bd67211bb5a5a132690e02 + md5sum: cfd4a1d35c0e469b99eb6aaa6d22de76 From dbb46c9b635080b132bab4b8d5b9a14f0d1c22e7 Mon Sep 17 00:00:00 2001 From: Jose Espinosa-Carrasco Date: Tue, 29 Mar 2022 16:44:19 +0200 Subject: [PATCH 3/3] Bump chromap version 0.2.1 (#1462) --- modules/chromap/chromap/main.nf | 6 +++--- modules/chromap/index/main.nf | 8 ++++---- tests/modules/chromap/chromap/test.yml | 8 ++++---- tests/modules/chromap/index/test.yml | 2 +- 4 files changed, 12 insertions(+), 12 deletions(-) diff --git a/modules/chromap/chromap/main.nf b/modules/chromap/chromap/main.nf index 4ee86b92..bf3d1234 100644 --- a/modules/chromap/chromap/main.nf +++ b/modules/chromap/chromap/main.nf @@ -2,10 +2,10 @@ process CHROMAP_CHROMAP { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::chromap=0.2.0 bioconda::samtools=1.14" : null) + conda (params.enable_conda ? "bioconda::chromap=0.2.1 bioconda::samtools=1.15" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:ed3529ef5253d7ccbc688b6a4c5c447152685757-0' : - 'quay.io/biocontainers/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:ed3529ef5253d7ccbc688b6a4c5c447152685757-0' }" + 'https://depot.galaxyproject.org/singularity/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:bd74d08a359024829a7aec1638a28607bbcd8a58-0' : + 'quay.io/biocontainers/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:bd74d08a359024829a7aec1638a28607bbcd8a58-0' }" input: tuple val(meta), path(reads) diff --git a/modules/chromap/index/main.nf b/modules/chromap/index/main.nf index 2696d6a5..ee370695 100644 --- a/modules/chromap/index/main.nf +++ b/modules/chromap/index/main.nf @@ -1,11 +1,11 @@ process CHROMAP_INDEX { - tag '$fasta' + tag "$fasta" label 'process_medium' - conda (params.enable_conda ? "bioconda::chromap=0.2.0" : null) + conda (params.enable_conda ? "bioconda::chromap=0.2.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/chromap:0.2.0--hd03093a_1' : - 'quay.io/biocontainers/chromap:0.2.0--hd03093a_1' }" + 'https://depot.galaxyproject.org/singularity/chromap:0.2.1--hd03093a_0' : + 'quay.io/biocontainers/chromap:0.2.1--hd03093a_0' }" input: path fasta diff --git a/tests/modules/chromap/chromap/test.yml b/tests/modules/chromap/chromap/test.yml index 40e45959..d76370b2 100644 --- a/tests/modules/chromap/chromap/test.yml +++ b/tests/modules/chromap/chromap/test.yml @@ -8,7 +8,7 @@ - path: output/chromap/test.bed.gz md5sum: 25e40bde24c7b447292cd68573728694 - path: output/chromap/versions.yml - md5sum: 2d3d2959ac20d98036807964896829e7 + md5sum: d24cfc35ad958206a5bc5694221b4fae - name: chromap chromap test_chromap_chromap_paired_end command: nextflow run ./tests/modules/chromap/chromap -entry test_chromap_chromap_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/chromap/chromap/nextflow.config @@ -20,7 +20,7 @@ - path: output/chromap/test.bed.gz md5sum: 7cdc8448882b75811e0c784f5f20aef2 - path: output/chromap/versions.yml - md5sum: 51cff66779161d8a602cce5989017395 + md5sum: 68ffe268a9d460956de4aad2a55ffd68 - name: chromap chromap test_chromap_chromap_paired_bam command: nextflow run ./tests/modules/chromap/chromap -entry test_chromap_chromap_paired_bam -c ./tests/config/nextflow.config -c ./tests/modules/chromap/chromap/nextflow.config @@ -30,6 +30,6 @@ files: - path: output/chromap/genome.index - path: output/chromap/test.bam - md5sum: f255c7441d5a1f307fc642d2aa19647e + md5sum: df467417407408e42992dc3dd15b22f5 - path: output/chromap/versions.yml - md5sum: f91910c44169549c3923931de5c3afcb + md5sum: ea732b4c6f1312d09745b66c3963dd3f diff --git a/tests/modules/chromap/index/test.yml b/tests/modules/chromap/index/test.yml index b2aa37d8..3e1d6fa6 100644 --- a/tests/modules/chromap/index/test.yml +++ b/tests/modules/chromap/index/test.yml @@ -6,4 +6,4 @@ files: - path: output/chromap/genome.index - path: output/chromap/versions.yml - md5sum: b75dec647f9dc5f4887f36d1db7a9ccd + md5sum: fc5c80190d0622ea3e979e6862f8e32b