mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-26 04:18:17 +00:00
59 lines
2.4 KiB
Text
59 lines
2.4 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process STRELKA_SOMATIC {
|
|
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--h9ee0642_1"
|
|
} else {
|
|
container "quay.io/biocontainers/strelka:2.9.10--h9ee0642_1"
|
|
}
|
|
|
|
input:
|
|
tuple val(meta), path(cram_normal), path(crai_normal), path(cram_tumor), path(crai_tumor)
|
|
path fasta
|
|
path fai
|
|
path target_bed
|
|
path target_bed_tbi
|
|
|
|
output:
|
|
tuple val(meta), path("*.somatic_indels.vcf.gz") , emit: vcf_indels
|
|
tuple val(meta), path("*.somatic_indels.vcf.gz.tbi"), emit: vcf_indels_tbi
|
|
tuple val(meta), path("*.somatic_snvs.vcf.gz") , emit: vcf_snvs
|
|
tuple val(meta), path("*.somatic_snvs.vcf.gz.tbi") , emit: vcf_snvs_tbi
|
|
path "versions.yml" , emit: versions
|
|
|
|
script:
|
|
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
|
def options_strelka = params.target_bed ? "--exome --callRegions ${target_bed}" : ""
|
|
"""
|
|
configureStrelkaSomaticWorkflow.py \\
|
|
--tumor $cram_tumor \\
|
|
--normal $cram_normal \\
|
|
--referenceFasta $fasta \\
|
|
$options_strelka \\
|
|
$options.args \\
|
|
--runDir strelka
|
|
|
|
python strelka/runWorkflow.py -m local -j $task.cpus
|
|
|
|
mv strelka/results/variants/somatic.indels.vcf.gz ${prefix}.somatic_indels.vcf.gz
|
|
mv strelka/results/variants/somatic.indels.vcf.gz.tbi ${prefix}.somatic_indels.vcf.gz.tbi
|
|
mv strelka/results/variants/somatic.snvs.vcf.gz ${prefix}.somatic_snvs.vcf.gz
|
|
mv strelka/results/variants/somatic.snvs.vcf.gz.tbi ${prefix}.somatic_snvs.vcf.gz.tbi
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
${getProcessName(task.process)}:
|
|
${getSoftwareName(task.process)}: \$( configureStrelkaSomaticWorkflow.py --version )
|
|
END_VERSIONS
|
|
"""
|
|
}
|