// Import generic module functions include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) process GATK4_BASERECALIBRATOR { tag "$meta.id" label 'process_low' publishDir "${params.outdir}", mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0" } else { container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0" } input: tuple val(meta), path(input), path(input_index) path fasta path fastaidx path dict path intervalsBed path knownSites path knownSites_tbi output: tuple val(meta), path("*.table"), emit: table path "versions.yml" , emit: versions script: def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def intervalsCommand = intervalsBed ? "-L ${intervalsBed}" : "" def sitesCommand = knownSites.collect{"--known-sites ${it}"}.join(' ') if (!task.memory) { log.info '[GATK BaseRecalibrator] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' } else { avail_mem = task.memory.giga } """ gatk BaseRecalibrator \ -R $fasta \ -I $input \ $sitesCommand \ $intervalsCommand \ --tmp-dir . \ $options.args \ -O ${prefix}.table cat <<-END_VERSIONS > versions.yml ${getProcessName(task.process)}: ${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ }