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WorkflowNascent.groovy
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WorkflowNascent.groovy
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//
// This file holds several functions specific to the workflow/nascent.nf in the nf-core/nascent pipeline
//
import nextflow.Nextflow
import groovy.text.SimpleTemplateEngine
class WorkflowNascent {
//
// Check and validate parameters
//
public static void initialise(params, log) {
genomeExistsError(params, log)
if (!params.fasta) {
Nextflow.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file."
}
}
//
// Function to validate channels from input samplesheet
//
public static ArrayList validateInput(input) {
def (metas, fastqs) = input[1..2]
// Check that multiple runs of the same sample are of the same strandedness
def strandedness_ok = metas.collect{ it.strandedness }.unique().size == 1
if (!strandedness_ok) {
Nextflow.error("Please check input samplesheet -> Multiple runs of a sample must have the same strandedness!: ${metas[0].id}")
}
// Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end
def endedness_ok = metas.collect{ it.single_end }.unique().size == 1
if (!endedness_ok) {
Nextflow.error("Please check input samplesheet -> Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end: ${metas[0].id}")
}
return [ metas[0], fastqs ]
}
//
// Get workflow summary for MultiQC
//
public static String paramsSummaryMultiqc(workflow, summary) {
String summary_section = ''
for (group in summary.keySet()) {
def group_params = summary.get(group) // This gets the parameters of that particular group
if (group_params) {
summary_section += " <p style=\"font-size:110%\"><b>$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
}
//
// Generate methods description for MultiQC
//
public static String toolCitationText(params) {
// TODO nf-core: Optionally add in-text citation tools to this list.
// Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "",
// Uncomment function in methodsDescriptionText to render in MultiQC report
def citation_text = [
"Tools used in the workflow included:",
"FastQC (Andrews 2010),",
"MultiQC (Ewels et al. 2016)",
"."
].join(' ').trim()
return citation_text
}
public static String toolBibliographyText(params) {
// TODO Optionally add bibliographic entries to this list.
// Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "<li>Author (2023) Pub name, Journal, DOI</li>" : "",
// Uncomment function in methodsDescriptionText to render in MultiQC report
def reference_text = [
"<li>Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).</li>",
"<li>Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354</li>"
].join(' ').trim()
return reference_text
}
public static String methodsDescriptionText(run_workflow, mqc_methods_yaml, params) {
// Convert to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file
def meta = [:]
meta.workflow = run_workflow.toMap()
meta["manifest_map"] = run_workflow.manifest.toMap()
// Pipeline DOI
meta["doi_text"] = meta.manifest_map.doi ? "(doi: <a href=\'https://doi.org/${meta.manifest_map.doi}\'>${meta.manifest_map.doi}</a>)" : ""
meta["nodoi_text"] = meta.manifest_map.doi ? "": "<li>If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. </li>"
// Tool references
meta["tool_citations"] = ""
meta["tool_bibliography"] = ""
// TODO Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
//meta["tool_citations"] = toolCitationText(params).replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".")
//meta["tool_bibliography"] = toolBibliographyText(params)
def methods_text = mqc_methods_yaml.text
def engine = new SimpleTemplateEngine()
def description_html = engine.createTemplate(methods_text).make(meta)
return description_html
}
//
// Exit pipeline if incorrect --genome key provided
//
private static void genomeExistsError(params, log) {
if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) {
def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
" Genome '${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" +
"~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
Nextflow.error(error_string)
}
}
}