updated citations

CITATIONS.md

@@ -30,6 +30,18 @@
 
   > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
 
+- [seqkit](https://bioinf.shenwei.me/seqkit/)
+
+  > Shen, W., Le, S., Li, Y., & Hu, F. (2016). SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation. In Q. Zou (Ed.), PLOS ONE (Vol. 11, Issue 10, p. e0163962). Public Library of Science (PLoS). doi:10.1371/journal.pone.0163962
+
+## Python
+
+- [Python](https://www.python.org/)
+
+- [biopython](https://biopython.org/)
+
+  > Cock, P. J. A., Antao, T., Chang, J. T., Chapman, B. A., Cox, C. J., Dalke, A., Friedberg, I., Hamelryck, T., Kauff, F., Wilczynski, B., & de Hoon, M. J. L. (2009). Biopython: freely available Python tools for computational molecular biology and bioinformatics. In Bioinformatics (Vol. 25, Issue 11, pp. 1422–1423). Oxford University Press (OUP). doi:10.1093/bioinformatics/btp163
+
 ## Software packaging/containerisation tools
 
 - [Anaconda](https://anaconda.com)

README.md

@@ -86,8 +86,6 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 <!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
 <!-- If you use nf-core/detaxizer for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
 
-<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
-
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
 
 You can cite the `nf-core` publication as follows:

assets/methods_description_template.yml

@@ -3,8 +3,6 @@ description: "Suggested text and references to use when describing pipeline usag
 section_name: "nf-core/detaxizer Methods Description"
 section_href: "https://github.com/nf-core/detaxizer"
 plot_type: "html"
-## TODO nf-core: Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
-## You inject any metadata in the Nextflow '${workflow}' object
 data: |
   <h4>Methods</h4>
   <p>Data was processed using nf-core/detaxizer v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>), utilising reproducible software environments from the Bioconda (<a href="https://doi.org/10.1038/s41592-018-0046-7">Grüning <em>et al.</em>, 2018</a>) and Biocontainers (<a href="https://doi.org/10.1093/bioinformatics/btx192">da Veiga Leprevost <em>et al.</em>, 2017</a>) projects.</p>

lib/WorkflowDetaxizer.groovy

@@ -53,13 +53,14 @@ class WorkflowDetaxizer {
 
     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)",
+                "MultiQC (Ewels et al. 2016),",
+                "Kraken2 (Wood et al. 2019),",
+                !params["skip_blastn"] ? "BLAST (Altschul et al. 1990)," : "",
+                !params["skip_blastn"] | params["enable_filter"] ? "seqkit (Shen et al. 2016)," : "",
+                "fastp (Chen et al. 2018)",
                 "."
             ].join(' ').trim()
 
@@ -68,12 +69,13 @@ class WorkflowDetaxizer {
 
     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>"
+                "<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>",
+                "<li>Wood, D. E., Lu, J. & Langmead, B. (2019) Improved metagenomic analysis with Kraken 2. Genome Biol 20, 257. doi: 10.1186/s13059-019-1891-0</li>",
+                !params["skip_blastn"] ? "<li>Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. (1990) Basic local alignment search tool. Journal of Molecular Biology 215, 403–410. doi: 10.1016/s0022-2836(05)80360-2.</li>" : "",
+                !params["skip_blastn"] | params["enable_filter"] ? "<li>Shen, W., Le, S., Li, Y., & Hu, F. (2016). SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation. In Q. Zou (Ed.), PLOS ONE (Vol. 11, Issue 10, p. e0163962). Public Library of Science (PLoS). doi: 10.1371/journal.pone.0163962</li>" : "",
+                "<li>Chen, S., Zhou, Y., Chen, Y. & Gu, J. (2018) fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884–i890. doi: 10.1093/bioinformatics/bty560</li>"
             ].join(' ').trim()
 
         return reference_text
@@ -93,9 +95,8 @@ class WorkflowDetaxizer {
         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