nf-core_modules/modules/gatk4/markduplicatesspark/main.nf
2022-06-09 15:16:11 +02:00

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process GATK4_MARKDUPLICATES_SPARK {
tag "$meta.id"
label 'process_high'
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1 conda-forge::openjdk=8.0.312" : null)
container 'broadinstitute/gatk:4.2.6.1'
input:
tuple val(meta), path(bam)
path fasta
path fasta_fai
path dict
output:
tuple val(meta), path("${prefix}"), emit: output
tuple val(meta), path("*.metrics"), emit: metrics, optional: true
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
def input_list = bam.collect{"--input $it"}.join(' ')
def avail_mem = 3
if (!task.memory) {
log.info '[GATK MarkDuplicatesSpark] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
} else {
avail_mem = task.memory.giga
}
"""
gatk --java-options "-Xmx${avail_mem}g" MarkDuplicatesSpark \\
$input_list \\
--output $prefix \\
--reference $fasta \\
--spark-master local[${task.cpus}] \\
--tmp-dir . \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
openjdk: \$(echo \$(java -version 2>&1) | grep version | sed 's/\"//g' | cut -f3 -d ' ')
END_VERSIONS
"""
}