mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
acb1a12a56
* Re-organise all test data * Fix ECLint * Fix ECLint agaaainn * Now is not the time EClint
55 lines
2.1 KiB
Text
55 lines
2.1 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName } 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), publish_id: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
|
|
|
|
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 "*.version.txt" , emit: version
|
|
|
|
script:
|
|
def software = getSoftwareName(task.process)
|
|
def ioptions = initOptions(options)
|
|
def prefix = ioptions.suffix ? "strelka_${meta.id}${ioptions.suffix}" : "strelka_${meta.id}"
|
|
def options_strelka = params.target_bed ? "--exome --callRegions ${target_bed}" : ""
|
|
"""
|
|
configureStrelkaGermlineWorkflow.py \\
|
|
--bam $bam \\
|
|
--referenceFasta $fasta \\
|
|
$options_strelka \\
|
|
$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
|
|
|
|
echo configureStrelkaGermlineWorkflow.py --version &> ${software}.version.txt #2>&1
|
|
"""
|
|
}
|