mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
7389963d5c
* Add memory stuff to all gatj4 modules * Add removed input line back in * revert script section
49 lines
1.5 KiB
Text
49 lines
1.5 KiB
Text
process GATK4_BASERECALIBRATOR {
|
|
tag "$meta.id"
|
|
label 'process_low'
|
|
|
|
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
|
|
container "${ 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)
|
|
path fasta
|
|
path fai
|
|
path dict
|
|
path intervalsBed
|
|
path knownSites
|
|
path knownSites_tbi
|
|
|
|
output:
|
|
tuple val(meta), path("*.table"), emit: table
|
|
path "versions.yml" , emit: versions
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
|
def intervalsCommand = intervalsBed ? "-L ${intervalsBed}" : ""
|
|
def sitesCommand = knownSites.collect{"--known-sites ${it}"}.join(' ')
|
|
def avail_mem = 3
|
|
if (!task.memory) {
|
|
log.info '[GATK BaseRecalibrator] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
|
|
} else {
|
|
avail_mem = task.memory.giga
|
|
}
|
|
"""
|
|
gatk --java-options "-Xmx${avail_mem}g" BaseRecalibrator \
|
|
-R $fasta \
|
|
-I $input \
|
|
$sitesCommand \
|
|
$intervalsCommand \
|
|
--tmp-dir . \
|
|
$args \
|
|
-O ${prefix}.table
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
|
|
END_VERSIONS
|
|
"""
|
|
}
|