nf-core_modules/modules/gatk4/applybqsr/main.nf
FriederikeHanssen 598d7abdb2
Log4j again (#1202)
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2022-01-12 13:55:54 +01:00

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process GATK4_APPLYBQSR {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.1--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
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def interval = intervals ? "-L ${intervals}" : ""
def file_type = input.getExtension()
def avail_mem = 3
if (!task.memory) {
log.info '[GATK ApplyBQSR] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
} else {
avail_mem = task.memory.giga
}
"""
gatk --java-options "-Xmx${avail_mem}g" ApplyBQSR \\
-R $fasta \\
-I $input \\
--bqsr-recal-file $bqsr_table \\
$interval \\
--tmp-dir . \\
-O ${prefix}.${file_type} \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
}