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e937c7950a
* Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
61 lines
1.9 KiB
Text
61 lines
1.9 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process QUALIMAP_BAMQC {
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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::qualimap=2.2.2d" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/qualimap:2.2.2d--1"
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} else {
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container "quay.io/biocontainers/qualimap:2.2.2d--1"
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}
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input:
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tuple val(meta), path(bam)
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path gff
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val use_gff
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output:
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tuple val(meta), path("${prefix}"), emit: results
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def collect_pairs = meta.single_end ? '' : '--collect-overlap-pairs'
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def memory = task.memory.toGiga() + "G"
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def regions = use_gff ? "--gff $gff" : ''
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def strandedness = 'non-strand-specific'
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if (meta.strandedness == 'forward') {
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strandedness = 'strand-specific-forward'
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} else if (meta.strandedness == 'reverse') {
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strandedness = 'strand-specific-reverse'
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}
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"""
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unset DISPLAY
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mkdir tmp
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export _JAVA_OPTIONS=-Djava.io.tmpdir=./tmp
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qualimap \\
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--java-mem-size=$memory \\
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bamqc \\
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$options.args \\
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-bam $bam \\
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$regions \\
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-p $strandedness \\
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$collect_pairs \\
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-outdir $prefix \\
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-nt $task.cpus
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echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//' > ${software}.version.txt
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"""
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}
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