process MACS2_CALLPEAK { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::macs2=2.2.7.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/macs2:2.2.7.1--py38h4a8c8d9_3' : '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 args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def args_list = args.tokenize() def format = meta.single_end ? 'BAM' : 'BAMPE' def control = controlbam ? "--control $controlbam" : '' if(args_list.contains('--format')){ def id = args_list.findIndexOf{it=='--format'} format = args_list[id+1] args_list.remove(id+1) args_list.remove(id) } """ macs2 \\ callpeak \\ ${args_list.join(' ')} \\ --gsize $macs2_gsize \\ --format $format \\ --name $prefix \\ --treatment $ipbam \\ $control cat <<-END_VERSIONS > versions.yml "${task.process}": macs2: \$(macs2 --version | sed -e "s/macs2 //g") END_VERSIONS """ }