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80 lines
3.4 KiB
Groovy
80 lines
3.4 KiB
Groovy
//
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// This file holds several functions specific to the workflow/taxprofiler.nf in the nf-core/taxprofiler pipeline
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//
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import nextflow.Nextflow
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import groovy.text.SimpleTemplateEngine
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class WorkflowTaxprofiler {
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//
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// Check and validate parameters
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//
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public static void initialise(params, log) {
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genomeExistsError(params, log)
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if (!params.fasta) {
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Nextflow.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file."
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}
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}
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//
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// Get workflow summary for MultiQC
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//
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public static String paramsSummaryMultiqc(workflow, summary) {
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String summary_section = ''
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for (group in summary.keySet()) {
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def group_params = summary.get(group) // This gets the parameters of that particular group
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if (group_params) {
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summary_section += " <p style=\"font-size:110%\"><b>$group</b></p>\n"
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summary_section += " <dl class=\"dl-horizontal\">\n"
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for (param in group_params.keySet()) {
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summary_section += " <dt>$param</dt><dd><samp>${group_params.get(param) ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>\n"
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}
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summary_section += " </dl>\n"
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}
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}
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String yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n"
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yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n"
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yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n"
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yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n"
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yaml_file_text += "plot_type: 'html'\n"
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yaml_file_text += "data: |\n"
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yaml_file_text += "${summary_section}"
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return yaml_file_text
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}
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public static String methodsDescriptionText(run_workflow, mqc_methods_yaml) {
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// Convert to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file
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def meta = [:]
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meta.workflow = run_workflow.toMap()
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meta["manifest_map"] = run_workflow.manifest.toMap()
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meta["doi_text"] = meta.manifest_map.doi ? "(doi: <a href=\'https://doi.org/${meta.manifest_map.doi}\'>${meta.manifest_map.doi}</a>)" : ""
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meta["nodoi_text"] = meta.manifest_map.doi ? "": "<li>If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. </li>"
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def methods_text = mqc_methods_yaml.text
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def engine = new SimpleTemplateEngine()
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def description_html = engine.createTemplate(methods_text).make(meta)
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return description_html
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}
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//
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// Exit pipeline if incorrect --genome key provided
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//
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private static void genomeExistsError(params, log) {
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if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) {
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def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
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" Genome '${params.genome}' not found in any config files provided to the pipeline.\n" +
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" Currently, the available genome keys are:\n" +
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" ${params.genomes.keySet().join(", ")}\n" +
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"~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
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Nextflow.error(error_string)
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}
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}
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}
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