// // This file holds several functions specific to the workflow/taxprofiler.nf in the nf-core/taxprofiler pipeline // class WorkflowTaxprofiler { // // Check and validate parameters // public static void initialise(params, log) { genomeExistsError(params, log) // TODO update as necessary //if (!params.fasta) { // log.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file." // System.exit(1) //} } // // Get workflow summary for MultiQC // public static String paramsSummaryMultiqc(workflow, summary) { String summary_section = '' for (group in summary.keySet()) { def group_params = summary.get(group) // This gets the parameters of that particular group if (group_params) { summary_section += "

$group

\n" summary_section += "
\n" for (param in group_params.keySet()) { summary_section += "
$param
${group_params.get(param) ?: 'N/A'}
\n" } summary_section += "
\n" } } String yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" yaml_file_text += "plot_type: 'html'\n" yaml_file_text += "data: |\n" yaml_file_text += "${summary_section}" return yaml_file_text } // // Exit pipeline if incorrect --genome key provided // private static void genomeExistsError(params, log) { if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) { log.error "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + " Genome '${params.genome}' not found in any config files provided to the pipeline.\n" + " Currently, the available genome keys are:\n" + " ${params.genomes.keySet().join(", ")}\n" + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" System.exit(1) } } }