nf-core_modules/software/gatk/createsequencedictionary/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
def options = initOptions(params.options)
process GATK_CREATESEQUENCEDICTIONARY {
tag "$fasta"
label 'process_medium'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
conda (params.enable_conda ? "bioconda::gatk4=4.1.9.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/gatk4:4.1.9.0--py39_0"
} else {
container "quay.io/biocontainers/gatk4:4.1.9.0--py39_0"
}
input:
path fasta
output:
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path "*.dict" , emit: dict
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def avail_mem = 6
if (!task.memory) {
log.info '[GATK] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.'
} else {
avail_mem = task.memory.giga
}
"""
gatk --java-options "-Xmx${avail_mem}g" \\
CreateSequenceDictionary \\
--REFERENCE $fasta \\
--URI $fasta
$options.args
echo \$(gatk CreateSequenceDictionary --version 2>&1) | sed 's/^.*(GATK) v//; s/ HTSJDK.*\$//' > ${software}.version.txt
"""
}