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chore(#336): Update reference text
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edmundmiller committed Oct 17, 2023
1 parent d2d652f commit fdf9c6b
Showing 1 changed file with 11 additions and 8 deletions.
19 changes: 11 additions & 8 deletions lib/WorkflowMethylseq.groovy
Original file line number Diff line number Diff line change
Expand Up @@ -74,13 +74,17 @@ class WorkflowMethylseq {

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
// FIXME Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "<li>Author (2023) Pub name, Journal, DOI</li>" : "",
def reference_text = [
"<li>Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).",
"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('</li> <li>').trim()
"<li>Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).",
"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",
"https://www.bioinformatics.babraham.ac.uk/projects/trim_galore",
"Felix Krueger, Simon R. Andrews, Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications, Bioinformatics, Volume 27, Issue 11, 1 June 2011, Pages 1571–1572, doi: /10.1093/bioinformatics/btr167",
"Pedersen, Brent S. and Eyring, Kenneth and De, Subhajyoti and Yang, Ivana V. and Schwartz, David A. Fast and accurate alignment of long bisulfite-seq reads, arXiv:1401.1129, doi: 10.48550/arXiv.1401.1129"
"Picard Tools, Broad Institute. <http://broadinstitute.github.io/picard/>"
"Konstantin Okonechnikov, Ana Conesa, Fernando García-Alcalde, Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data, Bioinformatics, Volume 32, Issue 2, 15 January 2016, Pages 292–294, doi: 10.1093/bioinformatics/btv566",
"Daley, T., Smith, A. Predicting the molecular complexity of sequencing libraries. Nat Methods 10, 325–327 (2013). doi: 10.1038/nmeth.2375</li>",
].join('</li> <li>').trim()

return reference_text
}
Expand All @@ -99,9 +103,8 @@ class WorkflowMethylseq {
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)
meta["tool_bibliography"] = toolBibliographyText(params)


def methods_text = mqc_methods_yaml.text
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