nf-core_modules/modules/plink/extract/main.nf

process PLINK_EXTRACT {
    tag "$meta.id"
    label 'process_low'

    conda (params.enable_conda ? "bioconda::plink=1.90b6.21" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
        'https://depot.galaxyproject.org/singularity/plink:1.90b6.21--h779adbc_1' :
        'quay.io/biocontainers/plink:1.90b6.21--h779adbc_1' }"

    input:
    tuple val(meta), path(bed), path(bim), path(fam), path(variants)

    output:
    tuple val(meta), path("*.bed"), emit: bed
    tuple val(meta), path("*.bim"), emit: bim
    tuple val(meta), path("*.fam"), emit: fam
    path "versions.yml"           , emit: versions

    when:
    task.ext.when == null || task.ext.when

    script:
    def args = task.ext.args ?: ''
    def prefix = task.ext.prefix ?: "${meta.id}"
    if( "$bed" == "${prefix}.bed" ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
    """
    plink \\
        --bfile ${meta.id} \\
        $args \\
        --extract $variants \\
        --threads $task.cpus \\
        --make-bed \\
        --out $prefix

    cat <<-END_VERSIONS > versions.yml
    "${task.process}":
        plink: \$(echo \$(plink --version) | sed 's/^PLINK v//;s/64.*//')
    END_VERSIONS
    """
}