nf-core_modules/tools/umi_tools/main.nf

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#!/usr/bin/env nextflow
// Specify DSL2
nextflow.preview.dsl = 2
// Local default params
params.internal_process_name = 'umitools_dedup'
// Process definition
process umitools_dedup {
publishDir "${params.outdir}/${params.internal_process_name}",
mode: "copy", overwrite: true
container 'luslab/nf-modules-umitools:latest'
input:
tuple val(sample_id), path(bai), path(bam)
output:
tuple val(sample_id), path("*.dedup.bam"), emit: dedupBam
path "*.dedup.log", emit: report
script:
// Init
internal_prog = "umi_tools dedup"
args = "--log=${sample_id}.dedup.log"
// Check main args string exists and strip whitespace
if(params.umitools_dedup_args) {
ext_args = params.umitools_dedup_args
internal_args += " " + ext_args.trim()
}
// Contruct CL line
command = "${internal_prog} ${internal_args} -I $bam -S ${sample_id}.dedup.bam --output-stats=${sample_id}"
// Log
if (params.verbose){
println ("[MODULE] umi_tools/dedup exec: " + internal_cl)
}
//SHELL
"""
${internal_cl}
"""
}