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906577873b
* New functions.nf * Convert code to create versions.yml * Update meta.yml * update output channel * Fix more meta.yml * Manually update remaining modules * remove superflous echo * Fix misformatted meta.yml files * Fix yaml, was list instead of dict * fix version for bcftools Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
48 lines
1.8 KiB
Text
48 lines
1.8 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName; getProcessName } 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 "versions.yml" , 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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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(msisensor 2>&1 | sed -nE 's/Version:\\sv([0-9]\\.[0-9])/\\1/ p')
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END_VERSIONS
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"""
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}
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