process QUALIMAP_BAMQC { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::qualimap=2.2.2d" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/qualimap:2.2.2d--1' : 'quay.io/biocontainers/qualimap:2.2.2d--1' }" input: tuple val(meta), path(bam) path gff val use_gff output: tuple val(meta), path("${prefix}"), emit: results path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" def collect_pairs = meta.single_end ? '' : '--collect-overlap-pairs' def memory = task.memory.toGiga() + "G" def regions = use_gff ? "--gff $gff" : '' def strandedness = 'non-strand-specific' if (meta.strandedness == 'forward') { strandedness = 'strand-specific-forward' } else if (meta.strandedness == 'reverse') { strandedness = 'strand-specific-reverse' } """ unset DISPLAY mkdir tmp export _JAVA_OPTIONS=-Djava.io.tmpdir=./tmp qualimap \\ --java-mem-size=$memory \\ bamqc \\ $args \\ -bam $bam \\ $regions \\ -p $strandedness \\ $collect_pairs \\ -outdir $prefix \\ -nt $task.cpus cat <<-END_VERSIONS > versions.yml "${task.process}": qualimap: \$(echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//') END_VERSIONS """ }