nf-core_modules/modules/strelka/germline/main.nf
FriederikeHanssen 5e7b1ef9a5
Reduce resource requests (#2021)
use process_single

Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
2022-09-07 10:33:05 +02:00

48 lines
1.8 KiB
Text

process STRELKA_GERMLINE {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::strelka=2.9.10" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/strelka:2.9.10--h9ee0642_1' :
'quay.io/biocontainers/strelka:2.9.10--h9ee0642_1' }"
input:
tuple val(meta), path(input), path(input_index), path (target_bed), path (target_bed_tbi)
path fasta
path fai
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
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def regions = target_bed ? "--callRegions ${target_bed}" : ""
"""
configureStrelkaGermlineWorkflow.py \\
--bam $input \\
--referenceFasta $fasta \\
$regions \\
$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 ${prefix}.variants.vcf.gz.tbi
cat <<-END_VERSIONS > versions.yml
"${task.process}":
strelka: \$( configureStrelkaGermlineWorkflow.py --version )
END_VERSIONS
"""
}