nf-core_modules/modules/picard/addorreplacereadgroups/main.nf

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process PICARD_ADDORREPLACEREADGROUPS {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
input:
tuple val(meta), path(bam)
output:
tuple val(meta), path("*.bam"), emit: bam
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def ID = task.ext.id ?: "id"
def LIBRARY= task.ext.library ?: "library"
def PLATFORM= task.ext.platform ?: "illumina"
def BARCODE= task.ext.barcode ?: "barcode"
def SAMPLE= task.ext.sample ?: "sample"
def INDEX= task.ext.index ?: "index"
def avail_mem = 3
if (!task.memory) {
log.info '[Picard AddOrReplaceReadGroups] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
} else {
avail_mem = task.memory.giga
}
"""
picard \\
AddOrReplaceReadGroups \\
-Xmx${avail_mem}g \\
--INPUT ${bam} \\
--OUTPUT ${prefix}.bam \\
--RGID ${ID} \\
--RGLB ${LIBRARY} \\
--RGPL ${PLATFORM} \\
--RGPU ${BARCODE} \\
--RGSM ${SAMPLE} \\
--CREATE_INDEX true
cat <<-END_VERSIONS > versions.yml
"${task.process}":
picard: \$(picard AddOrReplaceReadGroups --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:)
END_VERSIONS
"""
}