mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 21:53:10 +00:00
50 lines
1.5 KiB
Text
50 lines
1.5 KiB
Text
process GATK4_MARKDUPLICATES_SPARK {
|
|
tag "$meta.id"
|
|
label 'process_high'
|
|
|
|
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
|
|
'broadinstitute/gatk:4.2.3.0' }"
|
|
|
|
input:
|
|
tuple val(meta), path(bam)
|
|
path fasta
|
|
path fasta_fai
|
|
path dict
|
|
|
|
output:
|
|
tuple val(meta), path("${prefix}"), emit: output
|
|
path "versions.yml" , emit: versions
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
prefix = task.ext.prefix ?: "${meta.id}"
|
|
def input_list = bam.collect{"--input $it"}.join(' ')
|
|
|
|
def avail_mem = 3
|
|
if (!task.memory) {
|
|
log.info '[GATK MarkDuplicatesSpark] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
|
|
} else {
|
|
avail_mem = task.memory.giga
|
|
}
|
|
"""
|
|
export SPARK_USER=spark3
|
|
|
|
gatk --java-options "-Xmx${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/ .*\$//')
|
|
END_VERSIONS
|
|
"""
|
|
}
|