nf-core_modules/modules/gatk4/gatherbqsrreports/main.nf
FriederikeHanssen 967fb22ded
Update versions (#1292)
* Update versions

* update checksums + remove variables as input for applyvqsr

* sneak in removal of values and provide them via modules.config

* update another checksum

* more checksums

* move vairable to config

* remove controlfreec, wrong branch

* add line break
2022-02-15 11:29:36 +01:00

44 lines
1.3 KiB
Text

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(recal_table)
output:
tuple val(meta), path("*.table"), emit: table
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 input = recal_table.collect{"-I ${it}"}.join(' ')
def avail_mem = 3
if (!task.memory) {
log.info '[GATK GatherBQSRReports] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
} else {
avail_mem = task.memory.giga
}
"""
gatk --java-options "-Xmx${avail_mem}g" \\
GatherBQSRReports \
${input} \
--tmp-dir . \
$args \
--output ${prefix}.table
cat <<-END_VERSIONS > versions.yml
"${task.process}":
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
}