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42 lines
1.4 KiB
Text
42 lines
1.4 KiB
Text
process PLINK2_EXTRACT {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::plink2=2.00a2.3" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/plink2:2.00a2.3--h712d239_1' :
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'quay.io/biocontainers/plink2:2.00a2.3--h712d239_1' }"
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input:
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tuple val(meta), path(pgen), path(psam), path(pvar), path(variants)
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output:
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tuple val(meta), path("*.pgen") , emit: extract_pgen
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tuple val(meta), path("*.psam") , emit: extract_psam
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tuple val(meta), path("*.pvar.zst"), emit: extract_pvar
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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 prefix = task.ext.prefix ?: "${meta.id}"
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if( "$pgen" == "${prefix}.pgen" ) error "Input and output names are the same, use \"task.ext.prefix\" in modules.config to disambiguate!"
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def mem_mb = task.memory.toMega()
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"""
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plink2 \\
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--threads $task.cpus \\
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--memory $mem_mb \\
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--pfile ${pgen.baseName} \\
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$args \\
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--extract $variants \\
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--make-pgen vzs \\
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--out ${prefix}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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plink2: \$(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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