nf-core_modules/deprecated/umi_tools/main.nf
2020-08-05 16:09:25 +01:00

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#!/usr/bin/env nextflow
// Specify DSL2
nextflow.preview.dsl = 2
// Process definition
process umitools_dedup {
publishDir "${params.outdir}/umitools/dedup",
mode: "copy", overwrite: true
container 'luslab/nf-modules-umitools:latest'
input:
tuple val(sample_id), path(bam)
output:
tuple val(sample_id), path("${sample_id}.dedup.bam"), emit: dedupBam
tuple val(sample_id), path("${sample_id}.dedup.bam.bai"), emit: dedupBai
path "*.dedup.log", emit: report
script:
// Init
args = "--log=${sample_id}.dedup.log"
// Check main args string exists and strip whitespace
if(params.umitools_dedup_args) {
ext_args = params.umitools_dedup_args
args += " " + ext_args.trim()
}
// Contruct CL line
dedup_command = "umi_tools dedup ${args} -I ${bam[0]} -S ${sample_id}.dedup.bam --output-stats=${sample_id}"
// Log
if (params.verbose){
println ("[MODULE] umi_tools/dedup command: " + dedup_command)
}
//SHELL
"""
${dedup_command}
samtools index ${sample_id}.dedup.bam
"""
}