nf-core_modules/modules/manta/somatic/main.nf
nickhsmith 979e57b7ac
Manta consistancy (#1407)
* update tests

* update

* update

* make the manta inputs consistant for germline/somatic/tumoronly

* match chromosomes to cram file (chr21)

* undo genotypegvfs

* undo genotypegvfs

* update manta input structure to match strelka. tuple(relevant input), path(fasta), path(fai)

* update tests

* fix typos

* fix typos

Co-authored-by: Smith Nicholas <smith@in.tum.de>
2022-03-18 13:30:03 +01:00

58 lines
2.7 KiB
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process MANTA_SOMATIC {
tag "$meta.id"
label 'process_high'
conda (params.enable_conda ? "bioconda::manta=1.6.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/manta:1.6.0--h9ee0642_1' :
'quay.io/biocontainers/manta:1.6.0--h9ee0642_1' }"
input:
tuple val(meta), path(input_normal), path(input_index_normal), path(input_tumor), path(input_index_tumor), path(target_bed), path(target_bed_tbi)
path fasta
path fai
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
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def options_manta = target_bed ? "--exome --callRegions $target_bed" : ""
"""
configManta.py \
--tumorBam $input_tumor \
--normalBam $input_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 ${prefix}.somatic_sv.vcf.gz.tbi
cat <<-END_VERSIONS > versions.yml
"${task.process}":
manta: \$( configManta.py --version )
END_VERSIONS
"""
}