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taxprofiler/lib/WorkflowTaxprofiler.groovy

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//
// This file holds several functions specific to the workflow/taxprofiler.nf in the nf-core/taxprofiler pipeline
//
import groovy.text.SimpleTemplateEngine
class WorkflowTaxprofiler {
//
// Check and validate parameters
//
public static void initialise(params, log) {
genomeExistsError(params, log)
}
//
// 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 += " <p style=\"font-size:110%\"><b>$group</b></p>\n"
summary_section += " <dl class=\"dl-horizontal\">\n"
for (param in group_params.keySet()) {
summary_section += " <dt>$param</dt><dd><samp>${group_params.get(param) ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>\n"
}
summary_section += " </dl>\n"
}
}
String yaml_file_text = "id: '${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
}
public static String methodsDescriptionText(run_workflow, mqc_methods_yaml) {
// Convert to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file
def meta = [:]
meta.workflow = run_workflow.toMap()
meta["manifest_map"] = run_workflow.manifest.toMap()
meta["doi_text"] = meta.manifest_map.doi ? "(doi: <a href=\'https://doi.org/${meta.manifest_map.doi}\'>${meta.manifest_map.doi}</a>)" : ""
meta["nodoi_text"] = meta.manifest_map.doi ? "": "<li>If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. </li>"
def methods_text = mqc_methods_yaml.text
def engine = new SimpleTemplateEngine()
def description_html = engine.createTemplate(methods_text).make(meta)
return description_html
}//
// Exit pipeline if incorrect --genome key provided
//
private static void genomeExistsError(params, log) {
if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) {
log.error "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
" Genome '${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)
}
}
}