mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 07:42:05 +00:00
36 lines
1.2 KiB
Text
36 lines
1.2 KiB
Text
process BIOBAMBAM_BAMMARKDUPLICATES2 {
|
|
tag "$meta.id"
|
|
label 'process_medium'
|
|
|
|
conda (params.enable_conda ? "bioconda::biobambam=2.0.183" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/biobambam:2.0.183--h9f5acd7_1' : 'quay.io/biocontainers/biobambam:2.0.183--h9f5acd7_1'}"
|
|
|
|
input:
|
|
tuple val(meta), path(bam)
|
|
|
|
output:
|
|
tuple val(meta), path("*.bam") , emit: bam
|
|
tuple val(meta), path("*.metrics.txt"), emit: metrics
|
|
path "versions.yml" , emit: versions
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
|
"""
|
|
bammarkduplicates2 \\
|
|
$args \\
|
|
I=$bam \\
|
|
O=${prefix}.bam \\
|
|
M=${prefix}.metrics.txt \\
|
|
tmpfile=$prefix \\
|
|
markthreads=$task.cpus
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
bammarkduplicates2: \$(echo \$(bammarkduplicates2 --version 2>&1) | sed 's/^This is biobambam2 version //; s/..biobambam2 is .*\$//' )
|
|
END_VERSIONS
|
|
"""
|
|
}
|