nf-core_modules/modules/gatk4/applybqsr/main.nf
Maxime U. Garcia 409af2f27c
Improve syntax/logic coherence in all gatk4 plugins (#1459)
* feat: code polishing

* Apply suggestions from code review

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>

* code polishing

* more code polishing

* code polishing

* tests for applybqsrspark

* fix typo

* no need to check md5sum for versions.yml

* fix: use correct syntax

* code polishing again

* add tests for markduplicatesspark

* simplify mergevcfs tests

* add tests for baserecalibratorspark

* fix: path to entry

* code polishing

* fix linting

* simplify module

* update meta.yml

* fix pair mode

* fix: MITO mode

* more tests

* fix command

* bad copy paste

* fix typos

* fix tests

* fix test

* update meta.yml

* correct versions.yml in all test.yml

* code polishing

* code polishing

* more code polishing

* fix args

* add tmpdir for all

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-04-12 17:15:39 +02:00

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process GATK4_APPLYBQSR {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
input:
tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals)
path fasta
path fai
path dict
output:
tuple val(meta), path("*.bam") , emit: bam, optional: true
tuple val(meta), path("*.cram"), emit: cram, optional: true
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 interval_command = intervals ? "--intervals $intervals" : ""
def avail_mem = 3
if (!task.memory) {
log.info '[GATK ApplyBQSR] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
} else {
avail_mem = task.memory.giga
}
"""
gatk --java-options "-Xmx${avail_mem}g" ApplyBQSR \\
--input $input \\
--output ${prefix}.${input.getExtension()} \\
--reference $fasta \\
--bqsr-recal-file $bqsr_table \\
$interval_command \\
--tmp-dir . \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
}