mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 13:43:09 +00:00
46 lines
1.4 KiB
Text
46 lines
1.4 KiB
Text
|
process GATK4_GATHERPILEUPSUMMARIES {
|
||
|
|
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(pileup)
|
||
|
|
path dict
|
||
|
|
|
||
|
|
output:
|
||
|
|
tuple val(meta), path("*.pileupsummaries.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 input = pileup.collect{ "-I ${it} " }.join(' ')
|
||
|
|
|
||
|
|
def avail_mem = 3
|
||
|
|
if (!task.memory) {
|
||
|
|
log.info '[GATK GatherPileupSummaries] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
|
||
|
|
} else {
|
||
|
|
avail_mem = task.memory.giga
|
||
|
|
}
|
||
|
|
"""
|
||
|
|
gatk --java-options "-Xmx${avail_mem}g" \
|
||
|
|
GatherPileupSummaries \
|
||
|
|
--sequence-dictionary ${dict} \
|
||
|
|
${input} \
|
||
|
|
-O ${prefix}.pileupsummaries.table
|
||
|
|
|
||
|
|
cat <<-END_VERSIONS > versions.yml
|
||
|
|
"${task.process}":
|
||
|
|
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
|
||
|
|
END_VERSIONS
|
||
|
|
"""
|
||
|
|
}
|