nf-core_modules/modules/qualimap/rnaseq/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
options = initOptions(params.options)
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process QUALIMAP_RNASEQ {
tag "$meta.id"
label 'process_medium'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::qualimap=2.2.2d" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/qualimap:2.2.2d--1"
} else {
container "quay.io/biocontainers/qualimap:2.2.2d--1"
}
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input:
tuple val(meta), path(bam)
path gtf
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output:
tuple val(meta), path("${prefix}"), emit: results
path "versions.yml" , emit: versions
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script:
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prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def paired_end = meta.single_end ? '' : '-pe'
def memory = task.memory.toGiga() + "G"
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=$memory \\
rnaseq \\
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$options.args \\
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-bam $bam \\
-gtf $gtf \\
-p $strandedness \\
$paired_end \\
-outdir $prefix
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//')
END_VERSIONS
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"""
}