process IDR { tag "$prefix" label 'process_low' conda (params.enable_conda ? "bioconda::idr=2.0.4.2" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/idr:2.0.4.2--py39hcbe4a3b_5' : 'quay.io/biocontainers/idr:2.0.4.2--py38h9af456f_5' }" input: path peaks val peak_type val prefix output: path "*idrValues.txt", emit: idr path "*log.txt" , emit: log path "*.png" , emit: png path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' if (peaks.toList().size < 2) { log.error "[ERROR] idr needs at least two replicates only one provided." } def peak_types = ['narrowPeak', 'broadPeak', 'bed'] if (!peak_types.contains(peak_type)) { log.error "[ERROR] Invalid option: '${peak_type}'. Valid options for 'peak_type': ${peak_types.join(', ')}." } def idr_vals = prefix ? "${prefix}.idrValues.txt" : "idrValues.txt" def log_file = prefix ? "${prefix}.log.txt" : "log.txt" """ idr \\ --samples $peaks \\ --input-file-type $peak_type \\ --output-file $idr_vals \\ --log-output-file $log_file \\ --plot \\ $args cat <<-END_VERSIONS > versions.yml "${task.process}": idr: \$(echo \$(idr --version 2>&1) | sed 's/^.*IDR //; s/ .*\$//') END_VERSIONS """ }