process QUALIMAP_BAMQCCRAM { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::qualimap=2.2.2d bioconda::samtools=1.15.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:61f6d4658ac88635fc37623af50bba77561988ab-0' : 'quay.io/biocontainers/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:61f6d4658ac88635fc37623af50bba77561988ab-0' }" input: tuple val(meta), path(cram), path(crai) path gff path fasta path fasta_fai output: tuple val(meta), path("${prefix}"), emit: results path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" def collect_pairs = meta.single_end ? '' : '--collect-overlap-pairs' def memory = task.memory.toGiga() + "G" def regions = 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 samtools view -hb -T ${fasta} ${cram} | qualimap \\ --java-mem-size=$memory \\ bamqc \\ $args \\ -bam /dev/stdin \\ $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.*\$//') samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ }