// Import generic module functions include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) process PICARD_MERGESAMFILES { tag "$meta.id" label 'process_medium' publishDir "${params.outdir}", mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } conda (params.enable_conda ? 'bioconda::picard=2.25.7' : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { container "https://depot.galaxyproject.org/singularity/picard:2.25.7--hdfd78af_0" } else { container "quay.io/biocontainers/picard:2.25.7--hdfd78af_0" } input: tuple val(meta), path(bams) output: tuple val(meta), path("*.bam"), emit: bam path "versions.yml" , emit: version script: def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def bam_files = bams.sort() def avail_mem = 3 if (!task.memory) { log.info '[Picard MergeSamFiles] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' } else { avail_mem = task.memory.giga } if (bam_files.size() > 1) { """ picard \\ -Xmx${avail_mem}g \\ MergeSamFiles \\ $options.args \\ ${'INPUT='+bam_files.join(' INPUT=')} \\ OUTPUT=${prefix}.bam cat <<-END_VERSIONS > versions.yml ${getProcessName(task.process)}: ${getSoftwareName(task.process)}: \$(picard MergeSamFiles --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:) END_VERSIONS """ } else { """ ln -s ${bam_files[0]} ${prefix}.bam cat <<-END_VERSIONS > versions.yml ${getProcessName(task.process)}: ${getSoftwareName(task.process)}: \$(picard MergeSamFiles --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:) END_VERSIONS """ } }