mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
68 lines
3.1 KiB
Text
68 lines
3.1 KiB
Text
|
// Import generic module functions
|
||
|
|
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
|
||
|
|
|
||
|
|
params.options = [:]
|
||
|
|
options = initOptions(params.options)
|
||
|
|
|
||
|
|
process MANTA_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::manta=1.6.0" : null)
|
||
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||
|
|
container "https://depot.galaxyproject.org/singularity/manta:1.6.0--h9ee0642_1"
|
||
|
|
} else {
|
||
|
|
container "quay.io/biocontainers/manta:1.6.0--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("*.candidate_small_indels.vcf.gz") , emit: candidate_small_indels_vcf
|
||
|
|
tuple val(meta), path("*.candidate_small_indels.vcf.gz.tbi") , emit: candidate_small_indels_vcf_tbi
|
||
|
|
tuple val(meta), path("*.candidate_sv.vcf.gz") , emit: candidate_sv_vcf
|
||
|
|
tuple val(meta), path("*.candidate_sv.vcf.gz.tbi") , emit: candidate_sv_vcf_tbi
|
||
|
|
tuple val(meta), path("*.diploid_sv.vcf.gz") , emit: diploid_sv_vcf
|
||
|
|
tuple val(meta), path("*.diploid_sv.vcf.gz.tbi") , emit: diploid_sv_vcf_tbi
|
||
|
|
tuple val(meta), path("*.somatic_sv.vcf.gz") , emit: somatic_sv_vcf
|
||
|
|
tuple val(meta), path("*.somatic_sv.vcf.gz.tbi") , emit: somatic_sv_vcf_tbi
|
||
|
|
path "versions.yml" , emit: versions
|
||
|
|
|
||
|
|
script:
|
||
|
|
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||
|
|
def options_manta = target_bed ? "--exome --callRegions $target_bed" : ""
|
||
|
|
|
||
|
|
"""
|
||
|
|
configManta.py \
|
||
|
|
--tumorBam $cram_tumor \
|
||
|
|
--normalBam $cram_normal \
|
||
|
|
--reference $fasta \
|
||
|
|
$options_manta \
|
||
|
|
--runDir manta
|
||
|
|
|
||
|
|
python manta/runWorkflow.py -m local -j $task.cpus
|
||
|
|
|
||
|
|
mv manta/results/variants/candidateSmallIndels.vcf.gz ${prefix}.candidate_small_indels.vcf.gz
|
||
|
|
mv manta/results/variants/candidateSmallIndels.vcf.gz.tbi ${prefix}.candidate_small_indels.vcf.gz.tbi
|
||
|
|
mv manta/results/variants/candidateSV.vcf.gz ${prefix}.candidate_sv.vcf.gz
|
||
|
|
mv manta/results/variants/candidateSV.vcf.gz.tbi ${prefix}.candidate_sv.vcf.gz.tbi
|
||
|
|
mv manta/results/variants/diploidSV.vcf.gz ${prefix}.diploid_sv.vcf.gz
|
||
|
|
mv manta/results/variants/diploidSV.vcf.gz.tbi ${prefix}.diploid_sv.vcf.gz.tbi
|
||
|
|
mv manta/results/variants/somaticSV.vcf.gz ${prefix}.somatic_sv.vcf.gz
|
||
|
|
mv manta/results/variants/somaticSV.vcf.gz.tbi ${prefix}.somatic_sv.vcf.gz.tbi
|
||
|
|
|
||
|
|
cat <<-END_VERSIONS > versions.yml
|
||
|
|
${getProcessName(task.process)}:
|
||
|
|
${getSoftwareName(task.process)}: \$( configManta.py --version )
|
||
|
|
END_VERSIONS
|
||
|
|
"""
|
||
|
|
}
|