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40 lines
1.3 KiB
Text
40 lines
1.3 KiB
Text
process PLINK_EXTRACT {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::plink=1.90b6.21" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/plink:1.90b6.21--h779adbc_1' :
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'quay.io/biocontainers/plink:1.90b6.21--h779adbc_1' }"
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input:
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tuple val(meta), path(bed), path(bim), path(fam), path(variants)
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output:
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tuple val(meta), path("*.bed"), emit: bed
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tuple val(meta), path("*.bim"), emit: bim
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tuple val(meta), path("*.fam"), emit: fam
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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 ?: "${meta.id}"
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if( "$bed" == "${prefix}.bed" ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
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"""
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plink \\
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--bfile ${meta.id} \\
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$args \\
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--extract $variants \\
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--threads $task.cpus \\
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--make-bed \\
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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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plink: \$(echo \$(plink --version) | sed 's/^PLINK v//;s/64.*//')
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END_VERSIONS
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"""
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}
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