Merge pull request #427 from nf-core/patch-release-dump

Bump version for patch release

Author: jfy133

CHANGELOG.md

@@ -3,11 +3,25 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## Unreleased
+## v1.1.3 - Augmented Akita Patch [2024-01-12]
+
+### `Added`
+
+- [#424](https://github.com/nf-core/taxprofiler/pull/424) Updated to nf-core pipeline template v2.11.1 (added by @LilyAnderssonLee & @sofstam)
 
 ### `Fixed`
 
+- [#419](https://github.com/nf-core/taxprofiler/pull/419) Added improved syntax highlighting for tables in documentation (fix by @mashehu)
 - [#421](https://github.com/nf-core/taxprofiler/pull/421) Updated the krakenuniq/preloadedkrakenuniq module that contained a fix for saving the output reads (❤️ to @SannaAb for reporting, fix by @Midnighter)
+- [#427](https://github.com/nf-core/taxprofiler/pull/427) Fixed preprint information in the recommended methods text (fix by @jfy133)
+
+### `Dependencies`
+
+| Tool          | Previous version | New version |
+| ------------- | ---------------- | ----------- |
+| multiqc       | 1.15             | 1.19        |
+| fastqc        | 11.9             | 12.1        |
+| nf-validation | unpinned         | 1.1.3       |
 
 ## v1.1.2 - Augmented Akita Patch [2023-10-27]
 

assets/methods_description_template.yml

@@ -3,8 +3,6 @@ description: "Suggested text and references to use when describing pipeline usag
 section_name: "nf-core/taxprofiler Methods Description"
 section_href: "https://github.com/nf-core/taxprofiler"
 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 '${workflow}' object
 data: |
   <h4>Methods</h4>
   <p>Data was processed using nf-core/taxprofiler v${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>
@@ -17,12 +15,13 @@ data: |
     <li>Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: <a href="https://doi.org/10.1038/s41587-020-0439-x">10.1038/s41587-020-0439-x</a></li>
     <li>Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: <a href="https://doi.org/10.1038/s41592-018-0046-7">10.1038/s41592-018-0046-7</a></li>
     <li>da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: <a href="https://doi.org/10.1093/bioinformatics/btx192">10.1093/bioinformatics/btx192</a></li>
+    <li>Stamouli, S., Beber, M. E., Normark, T., Christensen, T. A., Andersson-Li, L., Borry, M., Jamy, M., nf-core community, & Fellows Yates, J. A. (2023). nf-core/taxprofiler: Highly parallelised and flexible pipeline for metagenomic taxonomic classification and profiling. (Preprint). bioRxiv 2023.10.20.563221. doi: <a href="https://doi.org/10.1101/2023.10.20.563221">10.1101/2023.10.20.563221</a></li>
     ${tool_bibliography}
   </ul>
   <div class="alert alert-info">
     <h5>Notes:</h5>
     <ul>
-      ${nodoi_text}
+      ${doi_text}
       <li>The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!</li>
       <li>You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.</li>
     </ul>

assets/multiqc_config.yml

@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/taxprofiler/tree/dev" target="_blank">nf-core/taxprofiler</a>
+  This report has been generated by the <a href="https://github.com/nf-core/taxprofiler/releases/tag/1.1.3" target="_blank">nf-core/taxprofiler</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/taxprofiler/dev/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/taxprofiler/1.1.3/docs/output" target="_blank">documentation</a>.
 
 report_section_order:
   "nf-core-taxprofiler-methods-description":

lib/WorkflowTaxprofiler.groovy

@@ -216,7 +216,7 @@ class WorkflowTaxprofiler {
         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["doi_text"] = meta.manifest_map.doi ? "(doi: <a href=\'https://doi.org/${meta.manifest_map.doi}\'>Stamouli et al. 2023</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>"
 
         meta["tool_citations"] = ""

main.nf

@@ -17,10 +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`
-
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     VALIDATE & PRINT PARAMETER SUMMARY

nextflow.config

@@ -372,7 +372,7 @@ manifest {
     description     = """Taxonomic classification and profiling of shotgun short- and long-read metagenomic data"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '1.1.3dev'
+    version         = '1.1.3'
     doi             = '10.1101/2023.10.20.563221'
 }