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55 lines
1.6 KiB
Text
55 lines
1.6 KiB
Text
process CNVKIT_BATCH {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? 'bioconda::cnvkit=0.9.9' : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0' :
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'quay.io/biocontainers/cnvkit:0.9.9--pyhdfd78af_0' }"
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input:
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tuple val(meta), path(tumor), path(normal)
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path fasta
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path targets
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path reference
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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, optional: true
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tuple val(meta), path("*.cnr"), emit: cnr, optional: true
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tuple val(meta), path("*.cns"), emit: cns, optional: true
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def normal_args = normal ? "--normal $normal" : ""
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def fasta_args = fasta ? "--fasta $fasta" : ""
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def reference_args = reference ? "--reference $reference" : ""
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def target_args = ""
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if (args.contains("--method wgs") || args.contains("-m wgs")) {
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target_args = targets ? "--targets $targets" : ""
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}
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else {
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target_args = "--targets $targets"
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}
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"""
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cnvkit.py \\
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batch \\
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$tumor \\
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$normal_args \\
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$fasta_args \\
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$reference_args \\
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$target_args \\
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--processes $task.cpus \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
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END_VERSIONS
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"""
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}
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