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44 lines
1.4 KiB
Text
44 lines
1.4 KiB
Text
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// 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 PLINK2_VCF {
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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::plink2=2.00a2.3" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/plink2:2.00a2.3--h712d239_1"
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} else {
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container "quay.io/biocontainers/plink2:2.00a2.3--h712d239_1"
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}
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input:
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tuple val(meta), path(vcf)
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output:
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tuple val(meta), path("*.pgen"), emit: pgen
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tuple val(meta), path("*.psam"), emit: psam
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tuple val(meta), path("*.pvar"), emit: pvar
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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}" : "${meta.id}"
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"""
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plink2 \\
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$options.args \\
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--vcf $vcf \\
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--out ${prefix}
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(plink2 --version 2>&1 | sed 's/^PLINK v//; s/ 64.*\$//' )
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END_VERSIONS
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"""
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}
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