mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 13:43:09 +00:00
36 lines
1.1 KiB
Text
36 lines
1.1 KiB
Text
process BISMARK_DEDUPLICATE {
|
|
tag "$meta.id"
|
|
label 'process_high'
|
|
|
|
conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/bismark:0.23.0--0' :
|
|
'quay.io/biocontainers/bismark:0.23.0--0' }"
|
|
|
|
input:
|
|
tuple val(meta), path(bam)
|
|
|
|
output:
|
|
tuple val(meta), path("*.deduplicated.bam") , emit: bam
|
|
tuple val(meta), path("*.deduplication_report.txt"), emit: report
|
|
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}"
|
|
def seqtype = meta.single_end ? '-s' : '-p'
|
|
"""
|
|
deduplicate_bismark \\
|
|
$args \\
|
|
$seqtype \\
|
|
--bam $bam
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
|
|
END_VERSIONS
|
|
"""
|
|
}
|