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6bb4a6a7ee
* Implement PLINK_EXTRACT module * fix plink version number * Update main.nf * Update test_data.config * Update modules/plink/extract/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * just use one channel * fix test with new channel input Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
47 lines
1.7 KiB
Text
47 lines
1.7 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 PLINK_EXTRACT {
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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::plink=1.90b6.21" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/plink:1.90b6.21--h779adbc_1"
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} else {
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container "quay.io/biocontainers/plink:1.90b6.21--h779adbc_1"
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}
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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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script:
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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if( "$bed" == "${prefix}.bed" ) error "Input and output names are the same, use the suffix option to disambiguate"
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"""
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plink \\
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--bfile ${meta.id} \\
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$options.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 $prefix
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(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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