nf-core_modules/modules/macs2/callpeak/main.nf

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

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

process MACS2_CALLPEAK {
    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::macs2=2.2.7.1" : null)
    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
        container "https://depot.galaxyproject.org/singularity/macs2:2.2.7.1--py38h4a8c8d9_3"
    } else {
        container "quay.io/biocontainers/macs2:2.2.7.1--py38h4a8c8d9_3"
    }

    input:
    tuple val(meta), path(ipbam), path(controlbam)
    val   macs2_gsize

    output:
    tuple val(meta), path("*.{narrowPeak,broadPeak}"), emit: peak
    tuple val(meta), path("*.xls")                   , emit: xls
    path  "versions.yml"                             , emit: versions

    tuple val(meta), path("*.gappedPeak"), optional:true, emit: gapped
    tuple val(meta), path("*.bed")       , optional:true, emit: bed
    tuple val(meta), path("*.bdg")       , optional:true, emit: bdg

    script:
    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
    def args     = options.args.tokenize()
    def format   = meta.single_end ? 'BAM' : 'BAMPE'
    def control  = controlbam ? "--control $controlbam" : ''
    if(args.contains('--format')){
        def id = args.findIndexOf{it=='--format'}
        format = args[id+1]
        args.remove(id+1)
        args.remove(id)
    }
    """
    macs2 \\
        callpeak \\
        ${args.join(' ')} \\
        --gsize $macs2_gsize \\
        --format $format \\
        --name $prefix \\
        --treatment $ipbam \\
        $control

    cat <<-END_VERSIONS > versions.yml
    ${getProcessName(task.process)}:
        ${getSoftwareName(task.process)}: \$(macs2 --version | sed -e "s/macs2 //g")
    END_VERSIONS
    """
}