nf-core_modules/modules/strelka/germline/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
process STRELKA_GERMLINE {
tag "$meta.id"
label 'process_high'
publishDir "${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']) }
conda (params.enable_conda ? "bioconda::strelka=2.9.10" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/strelka:2.9.10--0"
} else {
container "quay.io/biocontainers/strelka:2.9.10--0"
}
input:
tuple val(meta), path(bam), path(bai)
path fasta
path fai
path target_bed
path target_bed_tbi
output:
tuple val(meta), path("*variants.vcf.gz") , emit: vcf
tuple val(meta), path("*variants.vcf.gz.tbi"), emit: vcf_tbi
tuple val(meta), path("*genome.vcf.gz") , emit: genome_vcf
tuple val(meta), path("*genome.vcf.gz.tbi") , emit: genome_vcf_tbi
path "versions.yml" , emit: versions
script:
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def regions = target_bed ? "--exome --callRegions ${target_bed}" : ""
"""
configureStrelkaGermlineWorkflow.py \\
--bam $bam \\
--referenceFasta $fasta \\
$regions \\
$options.args \\
--runDir strelka
python strelka/runWorkflow.py -m local -j $task.cpus
mv strelka/results/variants/genome.*.vcf.gz ${prefix}.genome.vcf.gz
mv strelka/results/variants/genome.*.vcf.gz.tbi ${prefix}.genome.vcf.gz.tbi
mv strelka/results/variants/variants.vcf.gz ${prefix}.variants.vcf.gz
mv strelka/results/variants/variants.vcf.gz.tbi ${prefix}.variants.vcf.gz.tbi
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$( configureStrelkaGermlineWorkflow.py --version )
END_VERSIONS
"""
}