nf-core_modules/modules/gatk4/mergevcfs/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
options = initOptions(params.options)
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process GATK4_MERGEVCFS {
tag "$meta.id"
label 'process_medium'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
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} else {
container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
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}
input:
tuple val(meta), path(vcfs)
path ref_dict
val use_ref_dict
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output:
tuple val(meta), path('*.vcf.gz'), emit: vcf
path "versions.yml" , emit: versions
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script:
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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// Make list of VCFs to merge
def input = ""
for (vcf in vcfs) {
input += " I=${vcf}"
}
def ref = use_ref_dict ? "D=${ref_dict}" : ""
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"""
gatk MergeVcfs \\
$input \\
O=${prefix}.vcf.gz \\
$ref \\
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$options.args
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
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"""
}