process DEEPTOOLS_PLOTFINGERPRINT { tag "$meta.id" label 'process_high' conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0' : 'quay.io/biocontainers/deeptools:3.5.1--py_0' }" input: tuple val(meta), path(bams), path(bais) output: tuple val(meta), path("*.pdf") , emit: pdf tuple val(meta), path("*.raw.txt") , emit: matrix tuple val(meta), path("*.qcmetrics.txt"), emit: metrics path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def extend = (meta.single_end && params.fragment_size > 0) ? "--extendReads ${params.fragment_size}" : '' """ plotFingerprint \\ $args \\ $extend \\ --bamfiles ${bams.join(' ')} \\ --plotFile ${prefix}.plotFingerprint.pdf \\ --outRawCounts ${prefix}.plotFingerprint.raw.txt \\ --outQualityMetrics ${prefix}.plotFingerprint.qcmetrics.txt \\ --numberOfProcessors $task.cpus cat <<-END_VERSIONS > versions.yml "${task.process}": deeptools: \$(plotFingerprint --version | sed -e "s/plotFingerprint //g") END_VERSIONS """ }