nf-core_modules/modules/manta/somatic/main.nf
FriederikeHanssen ac1e6df076
Update to allow cram + update needed to use the gatk4 modules in sarek (#976)
* Make samtools/merge cram compliant

* samtools/stats cram compliance

* update yml file

* samtools/view to deal with crams

* Update tests to make sure cram works

* also fix tmp dir and min mem in one go

* basequalityrecal test for cram + min mem + tmpdir

* update haplotypecaller for sarek

* update haplotype yml

* update markdup to allow multiple bams, take out params to be passed with options.args

* remove TODO statement

* Remove variable md5sum

* add emtpy input to stats module in subworkflows

* subworkflows seem to work now on my side

* Apply code review

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>

* replace bam with input to be more inclusive

* rename everywhere

* rename input

* remove variable checksum

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2021-10-29 13:01:05 +02:00

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3.1 KiB
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// 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(input_normal), path(input_index_normal), path(input_tumor), path(input_index_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 $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
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$( configManta.py --version )
END_VERSIONS
"""
}