mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
71945a5b5f
* 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>
80 lines
2.6 KiB
Text
80 lines
2.6 KiB
Text
// 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
|
|
"""
|
|
}
|