Merge pull request #240 from luisas/update_citation

Update citation

Author: JoseEspinosa

CHANGELOG.md

@@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Enhancements & fixes
 
+- [[#240](https://github.com/nf-core/multiplesequencealign/pull/240)] - Update publication citation.
 - [[PR #248](https://github.com/nf-core/multiplesequencealign/pull/248)] - Updated pipeline template to [nf-core/tools 4.0.2](https://github.com/nf-core/tools/releases/tag/4.0.2)
 
 ### Parameters

CITATIONS.md

@@ -1,5 +1,9 @@
 # nf-core/multiplesequencealign: Citations
 
+## [nf-core/multiplesequencealign](https://pubmed.ncbi.nlm.nih.gov/40746377/)
+
+> Santus L, Espinosa-Carrasco J, Rauschning L, Mir-Pedrol J, Trujnara I, Vignoli A, Mansouri L, Baltzis A, Floden EW, Di Tommaso P, Garriga E, Gudyś A, Deorowicz S, Gilchrist C, Steinegger M, Notredame C. An nf-core framework for the systematic comparison of alternative modeling tools: the multiple sequence alignment case study. NAR Genom Bioinform. 2025 Jul 31;7(3):lqaf104. doi: 10.1093/nargab/lqaf104. PubMed PMID: 40746377.
+
 ## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)
 
 > Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031.

README.md

@@ -260,7 +260,13 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 
 ## Citations
 
-If you use nf-core/multiplesequencealign for your analysis, please cite it using the following doi: [10.5281/zenodo.13889386](https://doi.org/10.5281/zenodo.13889386)
+If you use nf-core/multiplesequencealign for your analysis, please cite:
+
+> **An nf-core framework for the systematic comparison of alternative modeling tools: The multiple sequence alignment case study**
+>
+> Luisa Santus, Jose Espinosa-Carrasco, Leon Rauschning, Júlia Mir-Pedrol, Igor Trujnara, Alessio Vignoli, Leila Mansouri, Athanasios Baltzis, Evan W. Floden, Paolo Di Tommaso, Edgar Garriga, Adam Gudyś, Sebastian Deorowicz, Cameron Gilchrist, Martin Steinegger, Cedric Notredame.
+>
+> _NAR Genomics and Bioinformatics_ 2025 Jul 31. doi: [10.1093/nargab/lqaf104](https://doi.org/10.1093/nargab/lqaf104).
 
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.