mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 07:42:05 +00:00
Fix version commands: round 3 (#754)
* Fix version commands: round 3 * Fix seqkit/split2 modules
This commit is contained in:
Harshil Patel
GitHub
parent
e971f538a9
commit
9c31cf1566
34 changed files with 184 additions and 129 deletions
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@ -57,6 +57,8 @@ process BBMAP_ALIGN {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(bbversion.sh)
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
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END_VERSIONS
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"""
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}
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@ -58,6 +58,7 @@ process BOWTIE_ALIGN {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo \$(bowtie --version 2>&1) | sed 's/^.*bowtie-align-s version //; s/ .*\$//')
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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END_VERSIONS
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"""
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}
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@ -48,6 +48,8 @@ process BOWTIE2_ALIGN {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
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END_VERSIONS
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"""
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} else {
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@ -70,9 +72,12 @@ process BOWTIE2_ALIGN {
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if [ -f ${prefix}.unmapped.fastq.2.gz ]; then
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mv ${prefix}.unmapped.fastq.2.gz ${prefix}.unmapped_2.fastq.gz
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fi
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
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END_VERSIONS
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"""
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}
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@ -45,6 +45,7 @@ process BWA_MEM {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//')
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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END_VERSIONS
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"""
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}
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@ -44,6 +44,7 @@ process BWA_SAMPE {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//')
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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END_VERSIONS
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"""
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}
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@ -44,6 +44,7 @@ process BWA_SAMSE {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//')
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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END_VERSIONS
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"""
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}
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@ -46,6 +46,7 @@ process BWAMEM2_MEM {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //')
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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END_VERSIONS
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"""
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}
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@ -25,13 +25,15 @@ process CHROMAP_INDEX {
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output:
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path "*.index" , emit: index
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path "versions.yml" , emit: version
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path "versions.yml", emit: version
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script:
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def software = getSoftwareName(task.process)
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def prefix = fasta.baseName
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"""
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chromap -i $options.args \\
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chromap \\
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-i \\
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$options.args \\
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-t $task.cpus \\
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-r $fasta \\
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-o ${prefix}.index
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@ -39,6 +41,7 @@ process CHROMAP_INDEX {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo "$VERSION")
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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END_VERSIONS
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"""
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}
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@ -62,6 +62,7 @@ process HISAT2_ALIGN {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo $VERSION)
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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END_VERSIONS
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"""
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} else {
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@ -93,6 +94,7 @@ process HISAT2_ALIGN {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo $VERSION)
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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END_VERSIONS
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"""
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}
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@ -51,6 +51,7 @@ process KRAKEN2_KRAKEN2 {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo \$(kraken2 --version 2>&1) | sed 's/^.*Kraken version //; s/ .*\$//')
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pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
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END_VERSIONS
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"""
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}
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@ -4,6 +4,8 @@ include { initOptions; saveFiles; getSoftwareName; getProcessName } from './func
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params.options = [:]
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options = initOptions(params.options)
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def VERSION = '2.3.2' // No version information printed
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process RAPIDNJ {
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label 'process_medium'
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publishDir "${params.outdir}",
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@ -23,7 +25,7 @@ process RAPIDNJ {
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output:
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path "*.sth" , emit: stockholm_alignment
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path "*.tre" , emit: phylogeny
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path "versions.yml" , emit: version
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path "versions.yml", emit: version
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script:
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def software = getSoftwareName(task.process)
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@ -38,10 +40,10 @@ process RAPIDNJ {
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-c $task.cpus \\
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-x rapidnj_phylogeny.tre
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# Doesn't appear to be a way of getting the version number
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo 2.3.2)
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${getSoftwareName(task.process)}: \$(echo $VERSION)
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biopython: \$(python -c "import Bio; print(Bio.__version__)")
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END_VERSIONS
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"""
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}
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@ -59,6 +59,7 @@ process RSEM_CALCULATEEXPRESSION {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g")
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star: \$(STAR --version | sed -e "s/STAR_//g")
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END_VERSIONS
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"""
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}
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@ -53,6 +53,7 @@ process RSEM_PREPAREREFERENCE {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g")
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star: \$(STAR --version | sed -e "s/STAR_//g")
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END_VERSIONS
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"""
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} else {
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@ -67,6 +68,7 @@ process RSEM_PREPAREREFERENCE {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g")
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star: \$(STAR --version | sed -e "s/STAR_//g")
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END_VERSIONS
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"""
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}
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@ -23,7 +23,7 @@ process SAMTOOLS_FAIDX {
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output:
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path "*.fai" , emit: fai
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path "versions.yml" , emit: version
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path "versions.yml", emit: version
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script:
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def software = getSoftwareName(task.process)
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@ -40,6 +40,8 @@ process SEACR_CALLPEAK {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo $VERSION)
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bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
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r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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@ -7,13 +7,11 @@ options = initOptions(params.options)
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process SEQKIT_SPLIT2 {
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tag "$meta.id"
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label 'process_medium'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? 'bioconda::seqkit=0.16.1' : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/seqkit:0.16.1--h9ee0642_0"
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} else {
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@ -24,41 +22,39 @@ process SEQKIT_SPLIT2 {
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tuple val(meta), path(reads)
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output:
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tuple val(meta), path("*.split/*.gz"), emit: reads
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path("versions.yml") , emit: version
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tuple val(meta), path("*${prefix}/*.gz"), emit: reads
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path "versions.yml" , emit: version
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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if(meta.single_end){
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"""
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seqkit \
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split2 \
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$options.args \
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--threads $task.cpus \
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-1 ${reads} \
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--out-dir ${prefix}.split
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seqkit \\
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split2 \\
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$options.args \\
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--threads $task.cpus \\
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-1 $reads \\
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--out-dir $prefix
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(seqkit --version 2>&1 | sed 's/^.*seqkit //; s/Using.*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(seqkit 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
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END_VERSIONS
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"""
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} else {
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"""
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seqkit \
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split2 \
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$options.args \
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--threads $task.cpus \
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-1 ${reads[0]} \
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-2 ${reads[1]} \
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--out-dir ${prefix}.split
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seqkit \\
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split2 \\
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$options.args \\
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--threads $task.cpus \\
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-1 ${reads[0]} \\
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-2 ${reads[1]} \\
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--out-dir $prefix
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(seqkit --version 2>&1 | sed 's/^.*seqkit //; s/Using.*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(seqkit 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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@ -40,7 +40,7 @@ process SEQTK_SAMPLE {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(seqtk 2>&1 | sed 's/^.*Version: //; s/ .*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
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END_VERSIONS
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"""
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} else {
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@ -64,7 +64,7 @@ process SEQTK_SAMPLE {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(seqtk 2>&1 | sed 's/^.*Version: //; s/ .*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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@ -43,7 +43,7 @@ process SEQTK_SUBSEQ {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(seqtk 2>&1 | sed 's/^.*Version: //; s/ .*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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@ -24,7 +24,7 @@ process SEQUENZAUTILS_BAM2SEQZ {
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path wigfile
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output:
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tuple val(meta), path("*.seqz.gz"), emit: seqz
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tuple val(meta), path("*.gz"), emit: seqz
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path "versions.yml" , emit: version
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script:
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@ -38,11 +38,11 @@ process SEQUENZAUTILS_BAM2SEQZ {
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-t $tumourbam \\
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--fasta $fasta \\
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-gc $wigfile \\
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-o ${prefix}.seqz.gz
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-o ${prefix}.gz
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(sequenzautils --version 2>&1 | sed 's/^.*sequenzautils //; s/Using.*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(sequenza-utils 2>&1) | sed 's/^.*is version //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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@ -37,7 +37,7 @@ process SEQUENZAUTILS_GCWIGGLE {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(sequenzautils --version 2>&1 | sed 's/^.*sequenzautils //; s/Using.*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(sequenza-utils 2>&1) | sed 's/^.*is version //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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@ -44,7 +44,7 @@ process SHOVILL {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(shovill --version 2>&1 | sed 's/^.*shovill //' )
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${getSoftwareName(task.process)}: \$(echo \$(shovill --version 2>&1) | sed 's/^.*shovill //')
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END_VERSIONS
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"""
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}
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@ -46,6 +46,8 @@ process STAR_GENOMEGENERATE {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(STAR --version | sed -e "s/STAR_//g")
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
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END_VERSIONS
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"""
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} else {
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@ -67,6 +69,8 @@ process STAR_GENOMEGENERATE {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(STAR --version | sed -e "s/STAR_//g")
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
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END_VERSIONS
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"""
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}
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@ -35,14 +35,15 @@ process TIDDIT_SV {
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def reference = fasta == "dummy_file.txt" ? "--ref $fasta" : ""
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"""
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tiddit \\
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--sv $options.args \\
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--sv \\
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$options.args \\
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--bam $bam \\
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$reference \\
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-o $prefix
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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||||
${getSoftwareName(task.process)}: \$(tiddit -h 2>&1 | sed 's/^.*Version: //; s/(.*\$//')
|
||||
${getSoftwareName(task.process)}: \$(echo \$(tiddit 2>&1) | sed 's/^.*TIDDIT-//; s/ .*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -32,7 +32,11 @@ process UCSC_BEDGRAPHTOBIGWIG {
|
|||
def software = getSoftwareName(task.process)
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
"""
|
||||
bedGraphToBigWig $bedgraph $sizes ${prefix}.bigWig
|
||||
bedGraphToBigWig \\
|
||||
$bedgraph \\
|
||||
$sizes \\
|
||||
${prefix}.bigWig
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(echo $VERSION)
|
||||
|
|
|
|||
|
|
@ -4,6 +4,8 @@ include { initOptions; saveFiles; getSoftwareName; getProcessName } from './func
|
|||
params.options = [:]
|
||||
options = initOptions(params.options)
|
||||
|
||||
def VERSION = '377'
|
||||
|
||||
process UCSC_BIGWIGAVERAGEOVERBED {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
|
@ -23,7 +25,7 @@ process UCSC_BIGWIGAVERAGEOVERBED {
|
|||
path bigwig
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.tab") , emit: tab
|
||||
tuple val(meta), path("*.tab"), emit: tab
|
||||
path "versions.yml" , emit: version
|
||||
|
||||
script:
|
||||
|
|
@ -31,11 +33,15 @@ process UCSC_BIGWIGAVERAGEOVERBED {
|
|||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
"""
|
||||
# there is a bug that bigWigAverageOverBed can not handle ensembl seqlevels style.
|
||||
bigWigAverageOverBed ${options.args} $bigwig $bed ${bed.getSimpleName()}.tab
|
||||
bigWigAverageOverBed \\
|
||||
$options.args \\
|
||||
$bigwig \\
|
||||
$bed \\
|
||||
${prefix}.tab
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(bigWigAverageOverBed 2>&1 | sed 's/bigWigAverageOverBed v//; s/ - Compute.*\$//')
|
||||
${getSoftwareName(task.process)}: \$(echo $VERSION)
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -44,7 +44,7 @@ process UNICYCLER {
|
|||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(unicycler --version 2>&1 | sed 's/^.*Unicycler v//; s/ .*\$//')
|
||||
${getSoftwareName(task.process)}: \$(echo \$(unicycler --version 2>&1) | sed 's/^.*Unicycler v//; s/ .*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -22,21 +22,25 @@ process YARA_INDEX {
|
|||
path fasta
|
||||
|
||||
output:
|
||||
path "yara", emit: index
|
||||
path "versions.yml" , emit: version
|
||||
path "yara" , emit: index
|
||||
path "versions.yml", emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
|
||||
"""
|
||||
mkdir yara
|
||||
yara_indexer $fasta -o "yara"
|
||||
|
||||
yara_indexer \\
|
||||
$fasta \\
|
||||
-o "yara"
|
||||
|
||||
mv *.{lf,rid,sa,txt}.* yara
|
||||
cp $fasta yara/yara.fasta
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(yara_indexer --help 2>&1 | grep -e "yara_indexer version:" | sed 's/yara_indexer version: //g')
|
||||
${getSoftwareName(task.process)}: \$(echo \$(yara_indexer --version 2>&1) | sed 's/^.*yara_indexer version: //; s/ .*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -29,26 +29,39 @@ process YARA_MAPPER {
|
|||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
|
||||
if(meta.single_end) {
|
||||
if (meta.single_end) {
|
||||
"""
|
||||
yara_mapper $options.args -t ${task.cpus} -f bam ${index}/yara $reads | samtools view -@ ${task.cpus} -hb -F4 > ${prefix}.mapped.bam
|
||||
yara_mapper \\
|
||||
$options.args \\
|
||||
-t $task.cpus \\
|
||||
-f bam \\
|
||||
${index}/yara \\
|
||||
$reads | samtools view -@ $task.cpus -hb -F4 > ${prefix}.mapped.bam
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(yara_mapper --help 2>&1)
|
||||
${getSoftwareName(task.process)}: \$(echo \$(yara_mapper --version 2>&1) | sed 's/^.*yara_mapper version: //; s/ .*\$//')
|
||||
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
} else {
|
||||
"""
|
||||
yara_mapper $options.args -t ${task.cpus} -f bam ${index}/yara ${reads[0]} ${reads[1]} > output.bam
|
||||
samtools view -@ ${task.cpus} -hF 4 -f 0x40 -b output.bam > ${prefix}_1.mapped.bam
|
||||
samtools view -@ ${task.cpus} -hF 4 -f 0x80 -b output.bam > ${prefix}_2.mapped.bam
|
||||
yara_mapper \\
|
||||
$options.args \\
|
||||
-t ${task.cpus} \\
|
||||
-f bam \\
|
||||
${index}/yara \\
|
||||
${reads[0]} \\
|
||||
${reads[1]} > output.bam
|
||||
|
||||
samtools view -@ $task.cpus -hF 4 -f 0x40 -b output.bam > ${prefix}_1.mapped.bam
|
||||
samtools view -@ $task.cpus -hF 4 -f 0x80 -b output.bam > ${prefix}_2.mapped.bam
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
${getProcessName(task.process)}:
|
||||
${getSoftwareName(task.process)}: \$(yara_mapper --version 2>&1 | grep -e "yara_mapper version:" | sed 's/yara_mapper version: //g')
|
||||
${getSoftwareName(task.process)}: \$(echo \$(yara_mapper --version 2>&1) | sed 's/^.*yara_mapper version: //; s/ .*\$//')
|
||||
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -5,9 +5,10 @@ nextflow.enable.dsl = 2
|
|||
include { SEACR_CALLPEAK } from '../../../../modules/seacr/callpeak/main.nf' addParams( options: [ args:'norm stringent' ] )
|
||||
|
||||
workflow test_seacr_callpeak {
|
||||
input = [ [ id:'test_1'],
|
||||
file("${launchDir}/tests/data/generic/bedgraph/K27me3_1_to_chr20.bedgraph", checkIfExists: true),
|
||||
file("${launchDir}/tests/data/generic/bedgraph/IgG_1_to_chr20.bedgraph", checkIfExists: true)
|
||||
input = [
|
||||
[ id:'test_1'],
|
||||
file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/bedgraph/K27me3_1_to_chr20.bedgraph", checkIfExists: true),
|
||||
file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/bedgraph/IgG_1_to_chr20.bedgraph", checkIfExists: true)
|
||||
]
|
||||
|
||||
SEACR_CALLPEAK ( input )
|
||||
|
|
|
|||
|
|
@ -4,9 +4,9 @@
|
|||
- seqkit
|
||||
- seqkit/split2
|
||||
files:
|
||||
- path: output/seqkit/test.split/test_1.part_001.fastq.gz
|
||||
- path: output/seqkit/test/test_1.part_001.fastq.gz
|
||||
md5sum: 6f7d58ba35c254c0817fe9a7c69862e4
|
||||
- path: output/seqkit/test.split/test_1.part_002.fastq.gz
|
||||
- path: output/seqkit/test/test_1.part_002.fastq.gz
|
||||
md5sum: cf38c51506e45380fe25abdd1bd5ccc6
|
||||
|
||||
- name: seqkit split2 single-end size
|
||||
|
|
@ -15,9 +15,9 @@
|
|||
- seqkit
|
||||
- seqkit/split2
|
||||
files:
|
||||
- path: output/seqkit/test.split/test_1.part_001.fastq.gz
|
||||
- path: output/seqkit/test/test_1.part_001.fastq.gz
|
||||
md5sum: bf835e685d597fc1ab5e5ac7dd689619
|
||||
- path: output/seqkit/test.split/test_1.part_002.fastq.gz
|
||||
- path: output/seqkit/test/test_1.part_002.fastq.gz
|
||||
md5sum: 703d95ff4fbb5b7fb4da8a164ba9aa54
|
||||
|
||||
- name: seqkit split2 single-end part
|
||||
|
|
@ -26,11 +26,11 @@
|
|||
- seqkit
|
||||
- seqkit/split2
|
||||
files:
|
||||
- path: output/seqkit/test.split/test_1.part_001.fastq.gz
|
||||
- path: output/seqkit/test/test_1.part_001.fastq.gz
|
||||
md5sum: fa25951435471238d5567fd2cae31f55
|
||||
- path: output/seqkit/test.split/test_1.part_002.fastq.gz
|
||||
- path: output/seqkit/test/test_1.part_002.fastq.gz
|
||||
md5sum: 1dcf631aaaa5e7e0bd6c9668fbc6e04a
|
||||
- path: output/seqkit/test.split/test_1.part_003.fastq.gz
|
||||
- path: output/seqkit/test/test_1.part_003.fastq.gz
|
||||
md5sum: 8bc86ba83a611c54f592f4eae19b680f
|
||||
|
||||
- name: seqkit split2 paired-end length
|
||||
|
|
@ -39,13 +39,13 @@
|
|||
- seqkit
|
||||
- seqkit/split2
|
||||
files:
|
||||
- path: output/seqkit/test.split/test_1.part_001.fastq.gz
|
||||
- path: output/seqkit/test/test_1.part_001.fastq.gz
|
||||
md5sum: 6f7d58ba35c254c0817fe9a7c69862e4
|
||||
- path: output/seqkit/test.split/test_1.part_002.fastq.gz
|
||||
- path: output/seqkit/test/test_1.part_002.fastq.gz
|
||||
md5sum: cf38c51506e45380fe25abdd1bd5ccc6
|
||||
- path: output/seqkit/test.split/test_2.part_001.fastq.gz
|
||||
- path: output/seqkit/test/test_2.part_001.fastq.gz
|
||||
md5sum: 6b094b1ba7c439fe44c1bb5e99a02ba4
|
||||
- path: output/seqkit/test.split/test_2.part_002.fastq.gz
|
||||
- path: output/seqkit/test/test_2.part_002.fastq.gz
|
||||
md5sum: 927097c6ac7522199a9e016333181a8e
|
||||
|
||||
- name: seqkit split2 paired-end size
|
||||
|
|
@ -54,13 +54,13 @@
|
|||
- seqkit
|
||||
- seqkit/split2
|
||||
files:
|
||||
- path: output/seqkit/test.split/test_1.part_001.fastq.gz
|
||||
- path: output/seqkit/test/test_1.part_001.fastq.gz
|
||||
md5sum: bf835e685d597fc1ab5e5ac7dd689619
|
||||
- path: output/seqkit/test.split/test_1.part_002.fastq.gz
|
||||
- path: output/seqkit/test/test_1.part_002.fastq.gz
|
||||
md5sum: 703d95ff4fbb5b7fb4da8a164ba9aa54
|
||||
- path: output/seqkit/test.split/test_2.part_001.fastq.gz
|
||||
- path: output/seqkit/test/test_2.part_001.fastq.gz
|
||||
md5sum: 09d0dd83b5b1b9b95d316eeed79ea5ba
|
||||
- path: output/seqkit/test.split/test_2.part_002.fastq.gz
|
||||
- path: output/seqkit/test/test_2.part_002.fastq.gz
|
||||
md5sum: 8796c3f327b1094244bfcdb36d536526
|
||||
|
||||
- name: seqkit split2 paired-end part
|
||||
|
|
@ -69,15 +69,15 @@
|
|||
- seqkit
|
||||
- seqkit/split2
|
||||
files:
|
||||
- path: output/seqkit/test.split/test_1.part_001.fastq.gz
|
||||
- path: output/seqkit/test/test_1.part_001.fastq.gz
|
||||
md5sum: fa25951435471238d5567fd2cae31f55
|
||||
- path: output/seqkit/test.split/test_1.part_002.fastq.gz
|
||||
- path: output/seqkit/test/test_1.part_002.fastq.gz
|
||||
md5sum: 1dcf631aaaa5e7e0bd6c9668fbc6e04a
|
||||
- path: output/seqkit/test.split/test_1.part_003.fastq.gz
|
||||
- path: output/seqkit/test/test_1.part_003.fastq.gz
|
||||
md5sum: 8bc86ba83a611c54f592f4eae19b680f
|
||||
- path: output/seqkit/test.split/test_2.part_001.fastq.gz
|
||||
- path: output/seqkit/test/test_2.part_001.fastq.gz
|
||||
md5sum: f0055c99cd193fd97466b3cde9dd1b8f
|
||||
- path: output/seqkit/test.split/test_2.part_002.fastq.gz
|
||||
- path: output/seqkit/test/test_2.part_002.fastq.gz
|
||||
md5sum: 8a90df768201785f7a7cd5dbb41e846a
|
||||
- path: output/seqkit/test.split/test_2.part_003.fastq.gz
|
||||
- path: output/seqkit/test/test_2.part_003.fastq.gz
|
||||
md5sum: 890b90083e8e1606bd13ba34149cedd7
|
||||
|
|
|
|||
|
|
@ -4,5 +4,5 @@
|
|||
- sequenzautils
|
||||
- sequenzautils/bam2seqz
|
||||
files:
|
||||
- path: output/sequenzautils/test.seqz.gz
|
||||
- path: output/sequenzautils/test.gz
|
||||
md5sum: 12b41979a498ac10c0aff162b12e6a6e
|
||||
|
|
|
|||
|
|
@ -5,7 +5,8 @@ nextflow.enable.dsl = 2
|
|||
include { UCSC_BIGWIGAVERAGEOVERBED } from '../../../../modules/ucsc/bigwigaverageoverbed/main.nf' addParams( options: [:] )
|
||||
|
||||
workflow test_ucsc_bigwigaverageoverbed {
|
||||
input = [ [ id: 'test' ], // meta map
|
||||
input = [
|
||||
[ id: 'test' ], // meta map
|
||||
[ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true ) ]
|
||||
]
|
||||
bigwig = file(params.test_data['sarscov2']['illumina']['test_bigwig'], checkIfExists: true)
|
||||
|
|
|
|||
|
|
@ -2,11 +2,11 @@
|
|||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { YARA_INDEX } from '../../../../modules/yara/index/main.nf' addParams( options: [:] )
|
||||
include { YARA_INDEX } from '../../../../modules/yara/index/main.nf' addParams( options: [publish_dir:'yara'] )
|
||||
|
||||
workflow test_yara_index {
|
||||
|
||||
def input = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
|
||||
input = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
||||
|
||||
YARA_INDEX ( input )
|
||||
}
|
||||
|
|
|
|||
|
|
@ -4,27 +4,27 @@
|
|||
- yara/index
|
||||
- yara
|
||||
files:
|
||||
- path: output/index/yara/yara.rid.limits
|
||||
- path: output/yara/yara/yara.rid.limits
|
||||
md5sum: 8b814661f30a0c9e350bfbcb454930ce
|
||||
- path: output/index/yara/yara.sa.len
|
||||
- path: output/yara/yara/yara.sa.len
|
||||
md5sum: 45677f66c28c79c02250ceb8b58645e8
|
||||
- path: output/index/yara/yara.sa.ind
|
||||
- path: output/yara/yara/yara.sa.ind
|
||||
md5sum: 464314583efb5f07260b0efecc29a1ce
|
||||
- path: output/index/yara/yara.lf.drp
|
||||
- path: output/yara/yara/yara.lf.drp
|
||||
md5sum: 3ef99a87a4e44513f46d42f4261f7842
|
||||
- path: output/index/yara/yara.txt.size
|
||||
- path: output/yara/yara/yara.txt.size
|
||||
md5sum: 063987b3c3f747be7d2b8043c9d91000
|
||||
- path: output/index/yara/yara.rid.concat
|
||||
- path: output/yara/yara/yara.rid.concat
|
||||
md5sum: 1e4e4c88ddeaf907a12f02f0d88367c5
|
||||
- path: output/index/yara/yara.txt.concat
|
||||
- path: output/yara/yara/yara.txt.concat
|
||||
md5sum: 6074d1933c9e7e5ab05fa0def5ce28c0
|
||||
- path: output/index/yara/yara.lf.drs
|
||||
- path: output/yara/yara/yara.lf.drs
|
||||
md5sum: 55a54008ad1ba589aa210d2629c1df41
|
||||
- path: output/index/yara/yara.txt.limits
|
||||
- path: output/yara/yara/yara.txt.limits
|
||||
md5sum: 4480a068db603e4c9a27bc4fa9ceaf14
|
||||
- path: output/index/yara/yara.sa.val
|
||||
- path: output/yara/yara/yara.sa.val
|
||||
md5sum: ce57cc82e2d3ae7b9824210f54168ce9
|
||||
- path: output/index/yara/yara.lf.pst
|
||||
- path: output/yara/yara/yara.lf.pst
|
||||
md5sum: e8daba34298e99e42942435286f9b3f0
|
||||
- path: output/index/yara/yara.lf.drv
|
||||
- path: output/yara/yara/yara.lf.drv
|
||||
md5sum: cf6408307fe9fd7f99c33f521bf95550
|
||||
|
|
|
|||
Loading…
Reference in a new issue