process GATK4_SAMTOFASTQ { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' : 'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }" input: tuple val(meta), path(bam) output: tuple val(meta), path('*.fastq.gz'), emit: fastq path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def output = meta.single_end ? "FASTQ=${prefix}.fastq.gz" : "FASTQ=${prefix}_1.fastq.gz SECOND_END_FASTQ=${prefix}_2.fastq.gz" def avail_mem = 3 if (!task.memory) { log.info '[GATK SamToFastq] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' } else { avail_mem = task.memory.giga } """ gatk --java-options "-Xmx${avail_mem}g" SamToFastq \\ I=$bam \\ $output \\ $args cat <<-END_VERSIONS > versions.yml "${task.process}": gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ }