mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 13:43:09 +00:00
43 lines
1.4 KiB
Text
43 lines
1.4 KiB
Text
process UMITOOLS_DEDUP {
|
|
tag "$meta.id"
|
|
label "process_medium"
|
|
|
|
conda (params.enable_conda ? "bioconda::umi_tools=1.1.2" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/umi_tools:1.1.2--py38h4a8c8d9_0' :
|
|
'quay.io/biocontainers/umi_tools:1.1.2--py38h4a8c8d9_0' }"
|
|
|
|
input:
|
|
tuple val(meta), path(bam), path(bai)
|
|
val get_output_stats
|
|
|
|
output:
|
|
tuple val(meta), path("*.bam") , emit: bam
|
|
tuple val(meta), path("*edit_distance.tsv"), optional:true, emit: tsv_edit_distance
|
|
tuple val(meta), path("*per_umi.tsv") , optional:true, emit: tsv_per_umi
|
|
tuple val(meta), path("*per_position.tsv") , optional:true, emit: tsv_umi_per_position
|
|
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 paired = meta.single_end ? "" : "--paired"
|
|
def stats = get_output_stats ? "--output-stats $prefix" : ""
|
|
"""
|
|
umi_tools \\
|
|
dedup \\
|
|
-I $bam \\
|
|
-S ${prefix}.bam \\
|
|
$stats \\
|
|
$paired \\
|
|
$args
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
umitools: \$(umi_tools --version 2>&1 | sed 's/^.*UMI-tools version://; s/ *\$//')
|
|
END_VERSIONS
|
|
"""
|
|
}
|