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60 lines
1.9 KiB
Text
60 lines
1.9 KiB
Text
process QUALIMAP_BAMQCCRAM {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::qualimap=2.2.2d bioconda::samtools=1.12" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:4bf11d12f2c3eccf1eb585097c0b6fd31c18c418-0' :
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'quay.io/biocontainers/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:4bf11d12f2c3eccf1eb585097c0b6fd31c18c418-0' }"
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input:
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tuple val(meta), path(cram), path(crai)
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path gff
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path fasta
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path fasta_fai
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output:
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tuple val(meta), path("${prefix}"), emit: results
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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prefix = task.ext.prefix ?: "${meta.id}"
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def collect_pairs = meta.single_end ? '' : '--collect-overlap-pairs'
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def memory = task.memory.toGiga() + "G"
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def regions = gff ? "--gff $gff" : ''
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def strandedness = 'non-strand-specific'
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if (meta.strandedness == 'forward') {
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strandedness = 'strand-specific-forward'
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} else if (meta.strandedness == 'reverse') {
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strandedness = 'strand-specific-reverse'
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}
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"""
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unset DISPLAY
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mkdir tmp
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export _JAVA_OPTIONS=-Djava.io.tmpdir=./tmp
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samtools view -hb -T ${fasta} ${cram} |
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qualimap \\
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--java-mem-size=$memory \\
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bamqc \\
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$args \\
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-bam /dev/stdin \\
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$regions \\
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-p $strandedness \\
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$collect_pairs \\
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-outdir $prefix \\
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-nt $task.cpus
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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qualimap: \$(echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//')
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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END_VERSIONS
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"""
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}
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