process GATK4_GETPILEUPSUMMARIES { 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(bam), path(bai) path variants path variants_tbi path sites output: tuple val(meta), path('*.pileups.table'), emit: table path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def sitesCommand = '' sitesCommand = sites ? " -L ${sites} " : " -L ${variants} " def avail_mem = 3 if (!task.memory) { log.info '[GATK GetPileupSummaries] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' } else { avail_mem = task.memory.giga } """ gatk --java-options "-Xmx${avail_mem}g" GetPileupSummaries \\ -I $bam \\ -V $variants \\ $sitesCommand \\ -O ${prefix}.pileups.table \\ $args cat <<-END_VERSIONS > versions.yml "${task.process}": gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ }