mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-15 07:43:09 +00:00
60 lines
2.6 KiB
Groovy
Executable file
60 lines
2.6 KiB
Groovy
Executable file
//
|
|
// 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 += " <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 += "${summary_section}"
|
|
return yaml_file_text
|
|
}
|
|
|
|
//
|
|
// Exit pipeline if incorrect --genome key provided
|
|
//
|
|
private static void genomeExistsError(params, log) {
|
|
if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) {
|
|
log.error "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
|
|
" Genome '${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)
|
|
}
|
|
}
|
|
}
|