process PICARD_ADDORREPLACEREADGROUPS { tag "$meta.id" label 'process_low' conda (params.enable_conda ? "bioconda::picard=2.27.2" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' : 'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }" input: tuple val(meta), path(bam) output: tuple val(meta), path("*.bam"), emit: bam path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def ID = task.ext.id ?: "id" def LIBRARY= task.ext.library ?: "library" def PLATFORM= task.ext.platform ?: "illumina" def BARCODE= task.ext.barcode ?: "barcode" def SAMPLE= task.ext.sample ?: "sample" def INDEX= task.ext.index ?: "index" def avail_mem = 3 if (!task.memory) { log.info '[Picard AddOrReplaceReadGroups] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' } else { avail_mem = task.memory.giga } """ picard \\ AddOrReplaceReadGroups \\ -Xmx${avail_mem}g \\ --INPUT ${bam} \\ --OUTPUT ${prefix}.bam \\ --RGID ${ID} \\ --RGLB ${LIBRARY} \\ --RGPL ${PLATFORM} \\ --RGPU ${BARCODE} \\ --RGSM ${SAMPLE} \\ --CREATE_INDEX true cat <<-END_VERSIONS > versions.yml "${task.process}": picard: \$(picard AddOrReplaceReadGroups --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:) END_VERSIONS """ }