mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
53 lines
1.5 KiB
Text
53 lines
1.5 KiB
Text
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
|
|
"""
|
|
}
|