chore(#336): Update reference text

nf-core · Oct 17, 2023 · a8bb3b4 · a8bb3b4
1 parent d2d652f
commit a8bb3b4
Showing 1 changed file with 11 additions and 8 deletions.
diff --git a/lib/WorkflowMethylseq.groovy b/lib/WorkflowMethylseq.groovy
@@ -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
     }
@@ -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