mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 13:43:09 +00:00
009f7c691c
* Added: gatk4/leftalignandtrimvariants Additions: - GATK4/LeftAlignAndTrimVariants module - Use sars-ncov2 test data as this normalises a larger INDEL correctly. Fixes #1801 * fixup: Added index to output spec * fixup: Pattern of tbi output corrected to 'tbi' * gatk4/leftalignandtrimvariants: Added intervals Changes: - gatk4/leftalignandtrimvariants now supports optional interval as BED file - Tests added with and without interval. Not test BED file excludes all variants so no variants are actually normalised. Fixes #1801 * fixup: leftalignandtrimvariants vcf->tbi fix * fixup: gatk4/leftalignandtrimvariants Intervals added to meta.yml
48 lines
1.6 KiB
Text
48 lines
1.6 KiB
Text
process GATK4_LEFTALIGNANDTRIMVARIANTS {
|
|
tag "$meta.id"
|
|
label 'process_low'
|
|
|
|
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
|
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
|
|
|
input:
|
|
tuple val(meta), path(vcf), path(tbi), path(intervals)
|
|
path fasta
|
|
path fai
|
|
path dict
|
|
|
|
output:
|
|
tuple val(meta), path("*.vcf.gz"), emit: vcf
|
|
tuple val(meta), path("*.tbi") , emit: 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 interval_command = intervals ? "--intervals $intervals" : ""
|
|
def avail_mem = 3
|
|
if (!task.memory) {
|
|
log.info '[GATK LeftAlignAndTrimVariants] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
|
|
} else {
|
|
avail_mem = task.memory.toGiga()
|
|
}
|
|
"""
|
|
gatk --java-options "-Xmx${avail_mem}G" LeftAlignAndTrimVariants \\
|
|
$interval_command \\
|
|
--variant $vcf \\
|
|
--output ${prefix}.vcf.gz \\
|
|
--reference $fasta \\
|
|
--tmp-dir . \\
|
|
$args
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
|
|
END_VERSIONS
|
|
"""
|
|
}
|