process GATK4_BASERECALIBRATOR { tag "$meta.id" label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' : 'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }" input: tuple val(meta), path(input), path(input_index) path fasta path fai path dict path intervalsBed path knownSites path knownSites_tbi output: tuple val(meta), path("*.table"), emit: table path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def intervalsCommand = intervalsBed ? "-L ${intervalsBed}" : "" def sitesCommand = knownSites.collect{"--known-sites ${it}"}.join(' ') def avail_mem = 3 if (!task.memory) { log.info '[GATK BaseRecalibrator] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' } else { avail_mem = task.memory.giga } """ gatk --java-options "-Xmx${avail_mem}g" BaseRecalibrator \ -R $fasta \ -I $input \ $sitesCommand \ $intervalsCommand \ --tmp-dir . \ $args \ -O ${prefix}.table cat <<-END_VERSIONS > versions.yml "${task.process}": gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ }