mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 15:52:05 +00:00
51 lines
1.7 KiB
Text
51 lines
1.7 KiB
Text
process GATK4_APPLYBQSR_SPARK {
|
|
tag "$meta.id"
|
|
label 'process_low'
|
|
|
|
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
|
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
|
|
|
input:
|
|
tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals)
|
|
path fasta
|
|
path fai
|
|
path dict
|
|
|
|
output:
|
|
tuple val(meta), path("*.bam") , emit: bam, optional: true
|
|
tuple val(meta), path("*.cram"), emit: cram, optional: true
|
|
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 interval_command = intervals ? "--intervals $intervals" : ""
|
|
|
|
def avail_mem = 3
|
|
if (!task.memory) {
|
|
log.info '[GATK ApplyBQSRSpark] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
|
|
} else {
|
|
avail_mem = task.memory.giga
|
|
}
|
|
"""
|
|
gatk --java-options "-Xmx${avail_mem}g" ApplyBQSRSpark \\
|
|
--input $input \\
|
|
--output ${prefix}.${input.getExtension()} \\
|
|
--reference $fasta \\
|
|
--bqsr-recal-file $bqsr_table \\
|
|
$interval_command \\
|
|
--spark-master local[${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
|
|
"""
|
|
}
|