nf-core_modules/modules/gatk4/variantrecalibrator/main.nf
GCJMackenzie 54e0ac4ed9
add module: Variantrecalibrator (#1088)
* committing to pull updated nf-core files

* saving changes to checout other branch

* committing progress so far, difficulty with test data

* uploading to be used as draft PR

* fix linting error in meta.yml

* attempt to group reference inputs together

* updated input format for resources

* meta.yml updated with new resource names

* added output channel for recal index

* module only takes single vcf file input now

* committing to checkout

* update to new syntax, remove indel test for now

* updated to use memory options and new test data

* Update modules/gatk4/variantrecalibrator/main.nf

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>

* Update main.nf

* Update modules/gatk4/variantrecalibrator/main.nf

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>

* remove duplicate test keys from test_data.config

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-12-16 10:54:49 +00:00

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process GATK4_VARIANTRECALIBRATOR {
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(vcf) , path(tbi)
path fasta
path fai
path dict
val allelespecific
tuple path(resvcfs), path(restbis), val(reslabels)
val annotation
val mode
val create_rscript
output:
tuple val(meta), path("*.recal") , emit: recal
tuple val(meta), path("*.idx") , emit: idx
tuple val(meta), path("*.tranches"), emit: tranches
tuple val(meta), path("*plots.R") , emit: plots, optional:true
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
refCommand = fasta ? "-R ${fasta} " : ''
alleleSpecificCommand = allelespecific ? '-AS' : ''
resourceCommand = '--resource:' + reslabels.join( ' --resource:')
annotationCommand = '-an ' + annotation.join( ' -an ')
modeCommand = mode ? "--mode ${mode} " : 'SNP'
rscriptCommand = create_rscript ? "--rscript-file ${prefix}.plots.R" : ''
def avail_mem = 3
if (!task.memory) {
log.info '[GATK VariantRecalibrator] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
} else {
avail_mem = task.memory.giga
}
"""
gatk --java-options "-Xmx${avail_mem}g" VariantRecalibrator \\
${refCommand} \\
-V ${vcf} \\
${alleleSpecificCommand} \\
${resourceCommand} \\
${annotationCommand} \\
${modeCommand} \\
-O ${prefix}.recal \\
--tranches-file ${prefix}.tranches \\
${rscriptCommand}\\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
}