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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
46 lines
1.4 KiB
Text
Executable file
46 lines
1.4 KiB
Text
Executable file
// 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 CNVKIT {
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tag "$meta.id"
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label 'process_low'
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publishDir "${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::cnvkit=0.9.8" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/cnvkit:0.9.8--py_0"
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} else {
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container "quay.io/biocontainers/cnvkit:0.9.8--py_0"
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}
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input:
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tuple val(meta), path(tumourbam), path(normalbam)
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path fasta
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path targetfile
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output:
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tuple val(meta), path("*.bed"), emit: bed
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tuple val(meta), path("*.cnn"), emit: cnn
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tuple val(meta), path("*.cnr"), emit: cnr
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tuple val(meta), path("*.cns"), emit: cns
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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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"""
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cnvkit.py \\
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batch \\
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$tumourbam \\
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--normal $normalbam\\
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--fasta $fasta \\
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--targets $targetfile \\
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$options.args
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echo \$(cnvkit.py version) | sed -e "s/cnvkit v//g" > ${software}.version.txt
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"""
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}
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