mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-23 14:59:55 +00:00
72 lines
3.2 KiB
Groovy
Executable file
72 lines
3.2 KiB
Groovy
Executable file
//
|
|
// 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)
|
|
}
|
|
}
|
|
}
|