Empowering bioinformatics communities with Nextflow and nf-core

作者：Björn E. Langer, Andreia Neves do Amaral, Marie-Odile Baudement, Franziska Bonath, Mathieu Charles, Praveen Chitneedi, Emily L. Clark, Paolo Di Tommaso, Sarah Djebali, Philip Ewels, Sonia E Eynard, James A. Fellows Yates, Daniel Fischer, Evan Floden, Sylvain Foissac, Gisela Gabernet, Maxime Garcia, Gareth Gillard, Manu Kumar Gundappa, Cervin Guyomar, Christopher Hakkaart, Friederike Hanssen, Peter W. Harrison, Matthias Hörtenhuber, Cyril Kurylo, Christa Kuehn, Sandrine Lagarrigue, Delphine Lallias, Daniel J. Macqueen, E. Miller, Júlia Mir-Pedrol, Gabriel Costa Monteiro Moreira, Sven Nahnsen, Harshil Patel, Alexander Peltzer, Frédérique Pitel, Yuliaxis Ramayo‐Caldas, Marcel da Câmara Ribeiro-Dantas, Dominique Rocha, Mazdak Salavati, Alexey Sokolov, Jose Espinosa‐Carrasco, Cédric Notredame, The Nf-Core Community · 发表于：Genome biology · 年份：2025 · DOI：10.1186/s13059-025-03673-9 · 被引用次数：35 · 研究领域：Scientific Computing and Data Management、Research Data Management Practices、Cell Image Analysis Techniques

Standardized analysis pipelines contribute to making data bioinformatics research compliant with the paradigm of Findability, Accessibility, Interoperability, and Reusability (FAIR), and facilitate collaboration. Nextflow and Snakemake, two popular command-line solutions, are increasingly adopted by users, complementing GUI-based platforms such as Galaxy. We report recent developments of the nf-core framework with the new Nextflow Domain-Specific Language (DSL2). An extensive library of modules and subworkflows enables research communities to adopt common standards progressively, as resources and needs allow. We present an overview of some of the research communities built around nf-core and showcase its adoption by six EuroFAANG farmed animal research consortia.