nf-core_modules/modules/gatk4/mutect2/main.nf

78 lines
2.5 KiB
Text
Raw Normal View History

// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process GATK4_MUTECT2 {
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), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
} else {
container "quay.io/biocontainers/gatk4:4.2.0.0--0"
}
input:
tuple val(meta) , path(bam) , path(bai) , val(which_norm)
val run_single
val run_pon
path fasta
path fastaidx
path dict
path germline_resource
path germline_resource_idx
path panel_of_normals
path panel_of_normals_idx
output:
tuple val(meta), path("*.vcf.gz") , emit: vcf
tuple val(meta), path("*.tbi") , emit: tbi
tuple val(meta), path("*.stats") , emit: stats
tuple val(meta), path("*.f1r2.tar.gz"), optional:true, emit: f1r2
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def inputsList = []
def normalsList = []
def inputsCommand = ''
def panelsCommand = ''
def normalsCommand = ''
bam.each() {a -> inputsList.add(" -I " + a ) }
inputsCommand = inputsList.join( ' ')
if(run_pon) {
panelsCommand = ''
normalsCommand = ''
} else if(run_single) {
panelsCommand = " --germline-resource $germline_resource --panel-of-normals $panel_of_normals"
normalsCommand = ''
} else {
panelsCommand = " --germline-resource $germline_resource --panel-of-normals $panel_of_normals --f1r2-tar-gz ${prefix}.f1r2.tar.gz"
which_norm.each() {a -> normalsList.add(" -normal " + a ) }
normalsCommand = normalsList.join( ' ')
}
"""
gatk Mutect2 \\
-R ${fasta} \\
${inputsCommand} \\
${normalsCommand} \\
${panelsCommand} \\
-O ${prefix}.vcf.gz \\
$options.args
echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//' > ${software}.version.txt
"""
}