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Langer BE, Amaral A, Baudement MO, Bonath F, Charles M, Chitneedi PK, Clark EL, Di Tommaso P, Djebali S, Ewels PA, Eynard S, Fellows Yates JA, Fischer D, Floden EW, Foissac S, Gabernet G, Garcia MU, Gillard G, Gundappa MK, Guyomar C, Hakkaart C, Hanssen F, Harrison PW, Hörtenhuber M, Kurylo C, Kühn C, Lagarrigue S, Lallias D, Macqueen DJ, Miller E, Mir-Pedrol J, Moreira GCM, Nahnsen S, Patel H, Peltzer A, Pitel F, Ramayo-Caldas Y, Ribeiro-Dantas MDC, Rocha D, Salavati M, Sokolov A, Espinosa-Carrasco J, Notredame C, Community TN
Genome Biol. 26 (1) 228 [2025-07-29; online 2025-07-29]
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.
PubMed 40731283
DOI 10.1186/s13059-025-03673-9
Crossref 10.1186/s13059-025-03673-9
pmc: PMC12309086
pii: 10.1186/s13059-025-03673-9