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

64 lines
2 KiB
Text
Raw Normal View History

2021-02-17 16:34:51 +00:00
// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
2021-02-17 16:34:51 +00:00
params.options = [:]
options = initOptions(params.options)
2021-02-17 16:34:51 +00:00
process QUALIMAP_BAMQC {
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']) }
2021-02-17 16:34:51 +00:00
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"
}
input:
tuple val(meta), path(bam)
path gff
val use_gff
output:
tuple val(meta), path("${prefix}"), emit: results
path "versions.yml" , emit: versions
2021-02-17 16:34:51 +00:00
script:
prefix = options.suffix ? "${meta.id}${options.suffix}" : "${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 \\
$options.args \\
-bam $bam \\
$regions \\
-p $strandedness \\
$collect_pairs \\
-outdir $prefix \\
-nt $task.cpus
2021-02-17 16:34:51 +00:00
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//')
END_VERSIONS
2021-02-17 16:34:51 +00:00
"""
}