nf-core_modules/modules/gatk4/getpileupsummaries/main.nf
FriederikeHanssen f5d5926516
Update intervals (#1278)
* Match target bed to input files

* Intervals in getpileupsumamries

* more interval updates

* change targets in strelka

* remove leftover channel

* fix checksums

* add new test vcfs

* add new test vcfs

* Update modules/freebayes/main.nf

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-02-10 10:34:22 +01:00

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process GATK4_GETPILEUPSUMMARIES {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input:
tuple val(meta), path(input), path(index), path(intervals)
path fasta
path fai
path dict
path variants
path variants_tbi
output:
tuple val(meta), path('*.pileups.table'), emit: table
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 sitesCommand = intervals ? " -L ${intervals} " : " -L ${variants} "
def reference = fasta ? " -R ${fasta}" :""
def avail_mem = 3
if (!task.memory) {
log.info '[GATK GetPileupSummaries] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
} else {
avail_mem = task.memory.giga
}
"""
gatk --java-options "-Xmx${avail_mem}g" GetPileupSummaries \\
-I $input \\
-V $variants \\
$sitesCommand \\
${reference} \\
-O ${prefix}.pileups.table \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
}