process GATK4_APPLYBQSR_SPARK { tag "$meta.id" label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) container "${ 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(bqsr_table), path(intervals) path fasta path fai path dict output: tuple val(meta), path("*.bam") , emit: bam, optional: true tuple val(meta), path("*.cram"), emit: cram, optional: true 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 interval_command = intervals ? "--intervals $intervals" : "" def avail_mem = 3 if (!task.memory) { log.info '[GATK ApplyBQSRSpark] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' } else { avail_mem = task.memory.giga } """ gatk --java-options "-Xmx${avail_mem}g" ApplyBQSRSpark \\ --input $input \\ --output ${prefix}.${input.getExtension()} \\ --reference $fasta \\ --bqsr-recal-file $bqsr_table \\ $interval_command \\ --spark-master local[${task.cpus}] \\ --tmp-dir . \\ $args cat <<-END_VERSIONS > versions.yml "${task.process}": gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ }