mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
967fb22ded
* Update versions * update checksums + remove variables as input for applyvqsr * sneak in removal of values and provide them via modules.config * update another checksum * more checksums * move vairable to config * remove controlfreec, wrong branch * add line break
50 lines
1.4 KiB
Text
50 lines
1.4 KiB
Text
process GATK4_MERGEVCFS {
|
|
tag "$meta.id"
|
|
label 'process_medium'
|
|
|
|
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
|
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
|
|
|
input:
|
|
tuple val(meta), path(vcfs)
|
|
path ref_dict
|
|
val use_ref_dict
|
|
|
|
output:
|
|
tuple val(meta), path('*.vcf.gz'), emit: vcf
|
|
path "versions.yml" , emit: versions
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
|
|
|
// Make list of VCFs to merge
|
|
def input = ""
|
|
for (vcf in vcfs) {
|
|
input += " I=${vcf}"
|
|
}
|
|
def ref = use_ref_dict ? "D=${ref_dict}" : ""
|
|
def avail_mem = 3
|
|
if (!task.memory) {
|
|
log.info '[GATK MergeVcfs] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
|
|
} else {
|
|
avail_mem = task.memory.giga
|
|
}
|
|
"""
|
|
gatk --java-options "-Xmx${avail_mem}g" MergeVcfs \\
|
|
$input \\
|
|
O=${prefix}.vcf.gz \\
|
|
$ref \\
|
|
$args
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
|
|
END_VERSIONS
|
|
"""
|
|
}
|