nf-core_modules/modules/gatk4/getpileupsummaries/main.nf
FriederikeHanssen 50eafb19c6
Update version for log4j vulnerability (#1176)
* Update version for log4j vulnerability

* update checksums

* update checksums

* update checksums

* Remove todo string

* remove werid output paths

* remove werid output paths

* remove werid output paths

* Update various checksums

* Update various checksums

* Remove unstable md5sums

* Update md5sums

* Fix pileupsummary

* Fix genotypegvcfs

* Update test files mutect2

* hm genotypevcf updated again

* Update some mutect checksums and whatnot

* Fix last mutect checksum

* Apply suggestion to use mtochondria data instead
2021-12-20 17:10:49 +01:00

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process GATK4_GETPILEUPSUMMARIES {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
input:
tuple val(meta), path(bam), path(bai)
path variants
path variants_tbi
path sites
output:
tuple val(meta), path('*.pileups.table'), emit: table
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def sitesCommand = ''
sitesCommand = sites ? " -L ${sites} " : " -L ${variants} "
def avail_mem = 3
if (!task.memory) {
log.info '[GATK GetPileupSummaries] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
} else {
avail_mem = task.memory.giga
}
"""
gatk --java-options "-Xmx${avail_mem}g" GetPileupSummaries \\
-I $bam \\
-V $variants \\
$sitesCommand \\
-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
"""
}