nf-core_modules/modules/gatk4/mutect2/main.nf
GCJMackenzie 71945a5b5f
Mutect2 add mitochondria mode and update tests (#967)
* new mitochondria mode added, tests updated to allow for temp fix for test data

* add cram test

* bam/bam_idx renamed to input and input_index

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
2021-10-29 11:27:56 +01:00

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } 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(input) , path(input_index) , val(which_norm)
val run_single
val run_pon
val run_mito
val interval_label
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 "versions.yml" , emit: versions
script:
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def panels_command = ''
def normals_command = ''
def inputs_command = '-I ' + input.join( ' -I ')
if(run_pon) {
panels_command = ''
normals_command = ''
} else if(run_single) {
panels_command = " --germline-resource $germline_resource --panel-of-normals $panel_of_normals"
normals_command = ''
} else if(run_mito){
panels_command = "-L ${interval_label} --mitochondria-mode"
normals_command = ''
} else {
panels_command = " --germline-resource $germline_resource --panel-of-normals $panel_of_normals --f1r2-tar-gz ${prefix}.f1r2.tar.gz"
normals_command = '-normal ' + which_norm.join( ' -normal ')
}
"""
gatk Mutect2 \\
-R ${fasta} \\
${inputs_command} \\
${normals_command} \\
${panels_command} \\
-O ${prefix}.vcf.gz \\
$options.args
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
}