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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
45 lines
1.7 KiB
Text
45 lines
1.7 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 MSISENSOR_MSI {
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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::msisensor=0.5" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/msisensor:0.5--hb3646a4_2"
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} else {
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container "quay.io/biocontainers/msisensor:0.5--hb3646a4_2"
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}
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input:
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tuple val(meta), path(normal_bam), path(normal_bai), path(tumor_bam), path(tumor_bai), val(metascan), path(homopolymers)
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output:
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tuple val(meta), path("${prefix}") , emit: output
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tuple val(meta), path("${prefix}_dis") , emit: output_dis
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tuple val(meta), path("${prefix}_germline"), emit: output_germline
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tuple val(meta), path("${prefix}_somatic") , emit: output_somatic
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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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"""
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msisensor \\
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msi \\
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-d $homopolymers \\
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-n $normal_bam \\
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-t $tumor_bam \\
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-o $prefix \\
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$options.args
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echo \$(msisensor 2>&1) | sed -nE 's/Version:\\sv([0-9]\\.[0-9])/\\1/ p' > ${software}.version.txt
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"""
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}
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