nf-core_modules/modules/gatk4/gatherbqsrreports/main.nf

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process GATK4_GATHERBQSRREPORTS {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
container "${ 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(table)
output:
tuple val(meta), path("*.table"), emit: table
path "versions.yml" , emit: versions
2022-02-04 08:53:32 +00:00
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def input_list = table.collect{"--input $it"}.join(' ')
def avail_mem = 3
if (!task.memory) {
log.info '[GATK GatherBQSRReports] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
} else {
avail_mem = task.memory.giga
}
"""
gatk --java-options "-Xmx${avail_mem}g" GatherBQSRReports \\
$input_list \\
--output ${prefix}.table \\
--tmp-dir . \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
}