nf-core_modules/modules/gatk4/applyvqsr/main.nf
2022-02-04 09:53:32 +01:00

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process GATK4_APPLYVQSR {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input:
tuple val(meta), path(vcf), path(tbi), path(recal), path(recalidx), path(tranches)
path fasta
path fai
path dict
val allelespecific
val truthsensitivity
val mode
output:
tuple val(meta), path("*.vcf.gz") , emit: vcf
tuple val(meta), path("*.tbi") , emit: tbi
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}"
refCommand = fasta ? "-R ${fasta} " : ''
alleleSpecificCommand = allelespecific ? '-AS' : ''
truthSensitivityCommand = truthsensitivity ? "--truth-sensitivity-filter-level ${truthsensitivity}" : ''
modeCommand = mode ? "--mode ${mode} " : 'SNP'
def avail_mem = 3
if (!task.memory) {
log.info '[GATK ApplyVQSR] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
} else {
avail_mem = task.memory.giga
}
"""
gatk --java-options "-Xmx${avail_mem}g" ApplyVQSR \\
${refCommand} \\
-V ${vcf} \\
-O ${prefix}.vcf.gz \\
${alleleSpecificCommand} \\
${truthSensitivityCommand} \\
--tranches-file $tranches \\
--recal-file $recal \\
${modeCommand} \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
}