nf-core_modules/modules/manta/germline/main.nf
Ramprasad Neethiraj fd5f6f5f4f
Revert recent changes made to some of the modules (#1463)
* revert changes to modules

* fix tests

* fix kraken2

* fix untar

* fix cat

* add blank lines

* fix typo
2022-03-30 20:21:06 +02:00

78 lines
2.8 KiB
Text

process MANTA_GERMLINE {
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), path(index)
path fasta
path fasta_fai
tuple 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
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 input_files = input.collect{"--bam ${it}"}.join(' ')
def options_manta = target_bed ? "--callRegions $target_bed" : ""
"""
configManta.py \
${input_files} \
--reference $fasta \
--runDir manta \
$options_manta \
$args
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 \
${prefix}.diploid_sv.vcf.gz.tbi
cat <<-END_VERSIONS > versions.yml
"${task.process}":
manta: \$( configManta.py --version )
END_VERSIONS
"""
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.candidate_small_indels.vcf.gz
touch ${prefix}.candidate_small_indels.vcf.gz.tbi
touch ${prefix}.candidate_sv.vcf.gz
touch ${prefix}.candidate_sv.vcf.gz.tbi
touch ${prefix}.diploid_sv.vcf.gz
touch ${prefix}.diploid_sv.vcf.gz.tbi
cat <<-END_VERSIONS > versions.yml
"${task.process}":
manta: \$( configManta.py --version )
END_VERSIONS
"""
}