include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] options = initOptions(params.options) process MASH_SKETCH { 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::mash=2.3" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { container "https://depot.galaxyproject.org/singularity/mash:2.3--he348c14_1" } else { container "quay.io/biocontainers/mash:2.3--he348c14_1" } input: tuple val(meta), path(reads) output: tuple val(meta), path("*.msh") , emit: mash tuple val(meta), path("*.mash_stats") , emit: stats path "*.version.txt" , emit: version script: def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ mash \\ sketch \\ $options.args \\ -p $task.cpus \\ -o ${prefix} \\ -r $reads \\ 2> ${prefix}.mash_stats echo \$(mash --version 2>&1) > ${software}.version.txt """ }