// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'

params.options = [:]
options        = initOptions(params.options)

process PLINK_VCF {
    tag "$meta.id"
    label 'process_medium'
    publishDir "${params.outdir}",
        mode: params.publish_dir_mode,
        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }

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

    input:
    tuple val(meta), path(vcf)

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

    path "versions.yml" , emit: version

    script:
    def software = getSoftwareName(task.process)
    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"

    """
    plink \\
        --vcf ${vcf} \\
        $options.args \\
        --threads $task.cpus \\
        --out ${prefix}

    cat <<-END_VERSIONS > versions.yml
    ${getProcessName(task.process)}:
        plink: \$(echo \$(plink --version 2>&1) | sed 's/^PLINK v//' | sed 's/..-bit.*//' )
    END_VERSIONS
    """
}