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https://github.com/MillironX/nf-core_modules.git
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3df4fe6085
* add freebayes/somatic and update freebayes/germline to new syntax and cram * add pytest * update with new freebayes/germline path
80 lines
2.6 KiB
Text
80 lines
2.6 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getProcessName; getSoftwareName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process FREEBAYES_GERMLINE {
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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::freebayes=1.3.5" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/freebayes:1.3.5--py38ha193a2f_3"
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} else {
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container "quay.io/biocontainers/freebayes:1.3.5--py38ha193a2f_3"
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}
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input:
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tuple val(meta), path(input), path(input_index)
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path fasta
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path fai
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path targets
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path samples
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path populations
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path cnv
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output:
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tuple val(meta), path("*.vcf.gz") , emit: vcf
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path "versions.yml" , emit: versions
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script:
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def targets_file = targets ? "--target ${targets}" : ""
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def samples_file = samples ? "--samples ${samples}" : ""
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def populations_file = populations ? "--populations ${populations}" : ""
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def cnv_file = cnv ? "--cnv-map ${cnv}" : ""
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if (task.cpus > 1) {
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"""
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freebayes-parallel \\
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<(fasta_generate_regions.py ${fasta}.fai 10000) ${task.cpus} \\
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-f $fasta \\
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$targets_file \\
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$samples_file \\
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$populations_file \\
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$cnv_file \\
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$options.args \\
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$input > ${prefix}.vcf
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gzip --no-name ${prefix}.vcf
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo \$(freebayes --version 2>&1) | sed 's/version:\s*v//g' )
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END_VERSIONS
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"""
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} else {
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"""
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freebayes \\
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-f $fasta \\
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$targets_file \\
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$samples_file \\
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$populations_file \\
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$cnv_file \\
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$options.args \\
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$input > ${prefix}.vcf
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gzip --no-name ${prefix}.vcf
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo \$(freebayes --version 2>&1) | sed 's/version:\s*v//g' )
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END_VERSIONS
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"""
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}
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}
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