mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 15:52:05 +00:00
41 lines
1.4 KiB
Text
41 lines
1.4 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
|
|
|
params.options = [:]
|
|
def options = initOptions(params.options)
|
|
|
|
process UMITOOLS_DEDUP {
|
|
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), publish_id:meta.id) }
|
|
|
|
conda (params.enable_conda ? "bioconda::umi_tools=1.1.1=py38h0213d0e_1" : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container "https://depot.galaxyproject.org/singularity/umi_tools:1.1.1--py38h0213d0e_1"
|
|
} else {
|
|
container "quay.io/biocontainers/umi_tools:1.1.1--py38h0213d0e_1"
|
|
}
|
|
|
|
input:
|
|
tuple val(meta), path(bam), path(bai)
|
|
|
|
output:
|
|
tuple val(meta), path("*.bam"), emit: bam
|
|
tuple val(meta), path("*.tsv"), emit: tsv
|
|
path "*.version.txt" , emit: version
|
|
|
|
script:
|
|
def software = getSoftwareName(task.process)
|
|
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
|
"""
|
|
umi_tools dedup \\
|
|
-I $bam \\
|
|
-S ${prefix}.bam \\
|
|
--output-stats=$prefix \\
|
|
$options.args \\
|
|
|
|
umi_tools --version | sed -e "s/UMI-tools version: //g" > ${software}.version.txt
|
|
"""
|
|
}
|