nf-core_modules/modules/gatk4/collectreadcounts/main.nf

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process GATK4_COLLECTREADCOUNTS {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
container "${ 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(intervals)
path(fasta)
path(fai)
path(dict)
output:
tuple val(meta), path("*.hdf5"), optional: true, emit: hdf5
tuple val(meta), path("*.tsv") , optional: true, emit: tsv
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 reference = fasta ? "--reference $fasta" : ""
def extension = args.contains("--format HDF5") ? "hdf5" :
args.contains("--format TSV") ? "tsv" :
"hdf5"
def avail_mem = 3
if (!task.memory) {
log.info '[GATK COLLECTREADCOUNTS] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
} else {
avail_mem = task.memory.giga
}
"""
gatk --java-options "-Xmx${avail_mem}g" CollectReadCounts \\
--input $input \\
--intervals $intervals \\
--output ${prefix}.$extension \\
$reference \\
--tmp-dir . \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
}