process GENRICH { tag "$meta.id" label 'process_high' conda (params.enable_conda ? "bioconda::genrich=0.6.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/genrich:0.6.1--h5bf99c6_1' : 'quay.io/biocontainers/genrich:0.6.1--h5bf99c6_1' }" input: tuple val(meta), path(treatment_bam) path control_bam path blacklist_bed val save_pvalues val save_pileup val save_bed val save_duplicates output: tuple val(meta), path("*narrowPeak") , emit: peaks tuple val(meta), path("*pvalues.bedGraph"), optional:true, emit: bedgraph_pvalues tuple val(meta), path("*pileup.bedGraph") , optional:true, emit: bedgraph_pileup tuple val(meta), path("*intervals.bed") , optional:true, emit: bed_intervals tuple val(meta), path("*duplicates.txt") , optional:true, emit: duplicates path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def control = control_bam ? "-c $control_bam" : '' def blacklist = blacklist_bed ? "-E $blacklist_bed" : "" def pvalues = save_pvalues ? "-f ${prefix}.pvalues.bedGraph" : "" def pileup = save_pileup ? "-k ${prefix}.pileup.bedGraph" : "" def bed = save_bed ? "-b ${prefix}.intervals.bed" : "" def duplicates = "" if (save_duplicates) { if (args.contains('-r')) { duplicates = "-R ${prefix}.duplicates.txt" } else { log.info '[Genrich] Duplicates can only be saved if they are filtered, defaulting to -r option (Remove PCR duplicates).' duplicates = "-r -R ${prefix}.duplicates.txt" } } """ Genrich \\ -t $treatment_bam \\ $args \\ $control \\ $blacklist \\ -o ${prefix}.narrowPeak \\ $pvalues \\ $pileup \\ $bed \\ $duplicates \\ $control cat <<-END_VERSIONS > versions.yml "${task.process}": genrich: \$(echo \$(Genrich --version 2>&1) | sed 's/^Genrich, version //; s/ .*\$//') END_VERSIONS """ }