// 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: 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 """ }