nf-core_modules/modules/gatk4/mutect2/main.nf
FriederikeHanssen 7389963d5c
Add memory stuff to all gatk4 modules (#1122)
* Add memory stuff to all gatj4 modules

* Add removed input line back in

* revert script section
2021-12-07 15:22:24 +01:00

76 lines
2.4 KiB
Text

process GATK4_MUTECT2 {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_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 fai
path dict
path germline_resource
path germline_resource_tbi
path panel_of_normals
path panel_of_normals_tbi
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 args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${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 ${prefix}.f1r2.tar.gz"
normals_command = '-normal ' + which_norm.join( ' -normal ')
}
def avail_mem = 3
if (!task.memory) {
log.info '[GATK Mutect2] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
} else {
avail_mem = task.memory.giga
}
"""
gatk --java-options "-Xmx${avail_mem}g" Mutect2 \\
-R ${fasta} \\
${inputs_command} \\
${normals_command} \\
${panels_command} \\
-O ${prefix}.vcf.gz \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
}