Citationtools

CITATIONS.md

@@ -26,6 +26,9 @@
 
   > <https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/>
 
+  <!-- TODO https://github.com/FelixKrueger/TrimGalore/issues/25 -->
+  <!-- https://zenodo.org/records/7598955 -->
+
 - [Bismark](https://doi.org/10.1093/bioinformatics/btr167)
 
   > 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](https://doi.org/10.1093/bioinformatics/btr167)

assets/citations.bib

@@ -0,0 +1,41 @@
+@misc{bwa-meth,
+    title        = {Fast and accurate alignment of long bisulfite-seq reads},
+    author       = {Brent S. Pedersen and Kenneth Eyring and Subhajyoti De and Ivana V. Yang and David A. Schwartz},
+    year         = 2014,
+    eprint       = {1401.1129},
+    archiveprefix = {arXiv},
+    primaryclass = {q-bio.GN}
+}
+@misc{Picard,
+    title        = {Picard toolkit},
+    year         = 2019,
+    journal      = {Broad Institute, GitHub repository},
+    publisher    = {Broad Institute},
+    howpublished = {\url{https://broadinstitute.github.io/picard/}}
+}
+@article{Qualimap,
+    title        = {{Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data}},
+    author       = {Okonechnikov, Konstantin and Conesa, Ana and García-Alcalde, Fernando},
+    year         = 2015,
+    month        = 10,
+    journal      = {Bioinformatics},
+    volume       = 32,
+    number       = 2,
+    pages        = {292--294},
+    doi          = {10.1093/bioinformatics/btv566},
+    issn         = {1367-4803},
+    url          = {https://doi.org/10.1093/bioinformatics/btv566},
+    abstract     = {{Motivation: Detection of random errors and systematic biases is a crucial step of a robust pipeline for processing high-throughput sequencing (HTS) data. Bioinformatics software tools capable of performing this task are available, either for general analysis of HTS data or targeted to a specific sequencing technology. However, most of the existing QC instruments only allow processing of one sample at a time.Results: Qualimap 2 represents a next step in the QC analysis of HTS data. Along with comprehensive single-sample analysis of alignment data, it includes new modes that allow simultaneous processing and comparison of multiple samples. As with the first version, the new features are available via both graphical and command line interface. Additionally, it includes a large number of improvements proposed by the user community.Availability and implementation: The implementation of the software along with documentation is freely available at http://www.qualimap.org.Contact:  [email protected] information:  Supplementary data are available at Bioinformatics online.}},
+    eprint       = {https://academic.oup.com/bioinformatics/article-pdf/32/2/292/49016552/bioinformatics\_32\_2\_292.pdf}
+}
+@article{Preseq,
+    title        = {Predicting the molecular complexity of sequencing libraries},
+    author       = {Daley, Timothy and Smith, Andrew D},
+    year         = 2013,
+    journal      = {Nature methods},
+    publisher    = {Nature Publishing Group US New York},
+    volume       = 10,
+    number       = 4,
+    pages        = {325--327},
+    doi          = {10.1038/nmeth.2375}
+}

lib/WorkflowMethylseq.groovy

@@ -55,12 +55,16 @@ class WorkflowMethylseq {
 
     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
+        // FIXME Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "",
         def citation_text = [
                 "Tools used in the workflow included:",
                 "FastQC (Andrews 2010),",
+                "Trim Galore! (Krueger)",
+                "Bismark (Krueger 2011)",
+                "bwa-meth (Pedersen 2014)",
+                "Picard (Broad Institute 2019)",
+                "Qualimap (Okonechnikov 2015)",
+                "Preseq (Daley 2013)",
                 "MultiQC (Ewels et al. 2016)",
                 "."
             ].join(' ').trim()
@@ -70,13 +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/).</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()
+            "<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
     }
@@ -95,9 +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_citations"] = toolCitationText(params).replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".")
+        meta["tool_bibliography"] = toolBibliographyText(params)
 
 
         def methods_text = mqc_methods_yaml.text

main.nf

@@ -17,9 +17,6 @@ nextflow.enable.dsl = 2
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-// TODO nf-core: Remove this line if you don't need a FASTA file
-//   This is an example of how to use getGenomeAttribute() to fetch parameters
-//   from igenomes.config using `--genome`
 params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta')
 params.fasta_index = WorkflowMain.getGenomeAttribute(params, 'fasta_index')
 params.bismark_index = WorkflowMain.getGenomeAttribute(params, 'bismark')