Empowering bioinformatics communities with Nextflow and nf-core

Indexed in

License and use

Citations

Altmetrics

Grant support

The EuroFAANG genomics communities have received funding from the European Union's Horizon 2020 research and innovation programme under Grant Agreement Numbers 817923 (AQUA-FAANG), 815668 (BovReg), 817998 (GENE-SWitCH), 101000226 (RUMIGEN), 101000236 (GEroNIMO), 101000213 (HoloRuminant), and the Horizon Europe programme under Grant Agreement Number 101094718 (EuroFAANG Research Infrastructure). Views and opinions expressed are, however, those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Executive Agency (REA). Neither the European Union nor the granting authority can be held responsible for them.Horizon 2020 research and innovation programme,European Union,815668 (BovReg),815668 (BovReg),817923 (AQUA-FAANG),815668 (BovReg),815668 (BovReg),815668 (BovReg),817998 (GENE-SWitCH),101000236 (GEroNIMO),815668 (BovReg),817998 (GENE-SWitCH),817923 (AQUA-FAANG),817923 (AQUA-FAANG),817998 (GENE-SWitCH),815668 (BovReg),817998 (GENE-SWitCH),815668 (BovReg),817998 (GENE-SWitCH),817923 (AQUA-FAANG),817923 (AQUA-FAANG),815668 (BovReg),101000236 (GEroNIMO),101000213 (HoloRuminant),815668 (BovReg),815668 (BovReg),815668 (BovReg),815668 (BovReg),815668 (BovReg),Spanish Ministry of Science and Innovation,Generalitat de Catalunya,Werner Siemens-Stiftung,Palaeobiotechnology,Horizon Europe programme,European Union,101094718 (EuroFAANG Research Infrastructure),101094718 (EuroFAANG Research Infrastructure),Carl-Zeiss-Stiftung,Certification and Foundations of Safe Machine Learning Systems in Healthcare,Deutsche Forschungsgemeinschaft,EXC 2180-390900677 (iFIT)CN, BL and JEC have received funding from the Spanish Ministry of Science and Innovation. They acknowledge support from the Spanish Ministry of Science and Innovation through the Centro de Excelencia Severo Ochoa (CEX2020-001049-S, MCIN/AEI/https://doi.org/10.13039/501100011033), and the Generalitat de Catalunya through the CERCA programme. This project has received funding from the European Union's Horizon 2020 research and innovation programme under the grant agreement 815,668 (BovReg). They are grateful to the CRG Core Technologies Programme for their support and assistance in this work.SN acknowledges support by the Carl Zeiss Foundation, project "Certification and Foundations of Safe Machine Learning Systems in Healthcare." SN is "gefoerdert durch die Deutsche Forschungsgemeinschaft (DFG) im Rahmen der Exzellenzstrategie des Bundes und der Laender-EXC 2180-390,900,677 (iFIT)." SN is "gefoerdert durch die Deutsche Forschungsgemeinschaft (DFG) im Rahmen der Exzellenzstrategie des Bundes und der Laender-EXC 2124-390,838,134 (CMFI)." This study was funded by Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) via the project NFDI 1/1 "GHGA-German Human Genome-Phenome Archive" (#441,914,366 to SN).J.A.F.Y. was supported by Max Planck Society and the Werner Siemens Foundation grant "Palaeobiotechnology" (awarded to Profs. Pierre Stallforth and Christina Warinner).

Analysis of institutional authors

Ramayo-Caldas, YuliaxisAuthor

August 6, 2025

Publications

Review

Publicated to:Genome Biology. 26 (1): 228- - 2025-07-29 26(1), DOI: 10.1186/s13059-025-03673-9

Authors: Langer, Bjoern E; Amaral, Andreia; Baudement, Marie-Odile; Bonath, Franziska; Charles, Mathieu; Chitneedi, Praveen Krishna; Clark, Emily L; Di Tommaso, Paolo; Djebali, Sarah; Ewels, Philip A; Eynard, Sonia; Fellows Yates, James A; Fischer, Daniel; Floden, Evan W; Foissac, Sylvain; Gabernet, Gisela; Garcia, Maxime U; Gillard, Gareth; Gundappa, Manu Kumar; Guyomar, Cervin; Hakkaart, Christopher; Hanssen, Friederike; Harrison, Peter W; Hoertenhuber, Matthias; Kurylo, Cyril; Kuehn, Christa; Lagarrigue, Sandrine; Lallias, Delphine; Macqueen, Daniel J; Miller, Edmund; Mir-Pedrol, Julia; Moreira, Gabriel Costa Monteiro; Nahnsen, Sven; Patel, Harshil; Peltzer, Alexander; Pitel, Frederique; Ramayo-Caldas, Yuliaxis; Ribeiro-Dantas, Marcel da Camara; Rocha, Dominique; Salavati, Mazdak; Sokolov, Alexey; Espinosa-Carrasco, Jose; Notredame, Cedric

Affiliations

Barcelona Inst Sci & Technol, Ctr Genom Regulat CRG, Dr Aiguader 88, Barcelona 08003, Spain - Author

Boehringer Ingelheim Pharm GmbH & Co KG, Birkendorfer Str 65, D-88397 Biberach, Germany - Author

European Bioinformat Inst, European Mol Biol Lab, Wellcome Genome Campus, Cambridge CB10 1SD, England - Author

Friedrich Loeffler Inst FLI, D-17493 Greifswald, Germany - Author

INRAE, SIGENAE, F-78350 Jouy En Josas, France - Author

Inst Agrifood Res & Technol IRTA, Anim Breeding & Genet Program, Caldes De Montbui 08140, Barcelona, Spain - Author

Inst Agro, PEGASE, INRAE, F-35590 St Gilles, France - Author

Kungliga Tekn Hgsk, Sch Engn Sci Chem Biotechnol & Hlth, Dept Gene Technol, Stockholm, Sweden - Author

Leibniz Inst Nat Prod Res & Infect Biol, Hans Knoll Inst, Beutenbergstr 11a, D-07745 Jena, Germany - Author

Leibniz Inst Nat Prod Res & Infect Biol, Hans Knoll Inst, D-07745 Jena, Germany - Author

Max Planck Inst Evolutionary Anthropol, Dept Archaeogenet, Deutsch Pl 6, D-04103 Leipzig, Germany - Author

MED Univ Evora, P-7002554 Evora, Portugal - Author

Nat Resources Inst Finland Luke, Appl Stat Methods, Myllytie 1, Jokioinen 31600, Finland - Author

Norwegian Univ Life Sci, Fac Biosci, Ctr Integrat Genet CIGENE, N-1430 As, Norway - Author

Res Inst Biol Farm Anim, FBN, D-18196 Dummerstorf, Germany - Author

Scotlands Rural Coll, Dairy Res & Innovat Ctr, Dumfries DG1 3NE, England - Author

Univ Clin Tubingen UKT, Med Fac, Res Ctr M3, Tubingen, Germany - Author

Univ Edinburgh, Royal Dick Sch Vet Studies, Easter Bush Campus, Roslin, Midlothian, Scotland - Author

Univ Liege, GIGA & Fac Vet Med, Unit Anim Genom, Liege, Belgium - Author

Univ Lisbon, Fac Vet Med, Ctr Interdisciplinary Res Anim Hlth CIISA, P-1300477 Lisbon, Portugal - Author

Univ Paris Saclay, INRAE, AgroParisTech, GABI, F-78350 Jouy En Josas, France - Author

Univ Pompeu Fabra UPF, Barcelona, Spain - Author

Univ Potiguar UnP, Biotechnol Postgrad Program, Natal, RN, Brazil - Author

Univ Texas Dallas, Ctr Syst Biol, Richardson, TX 75083 USA - Author

Univ Toulouse III Paul Sabatier UPS, Univ Toulouse, INRAE, IRSD,INSERM,ENVT, Toulouse, France - Author

Univ Toulouse, GenPhySE, INRAE, ENVT, F-31326 Castanet Tolosan, France - Author

Univ Tubingen, Dept Comp Sci, Biomed data Sci, Tubingen, Germany - Author

Univ Tubingen, Inst Bioinformat & Med Informat IBMI, Tubingen, Germany - Author

Univ Tubingen, Quant Biol Ctr QB, Tubingen, Germany - Author

UPF, Barcelona 08005, Spain - Author

Uppsala Univ, Dept Immunol Genet & Pathol, Uppsala, Sweden - Author

Uppsala Univ, SciLifeLab, Uppsala, Sweden - Author

Yale Sch Med, Dept Pathol, New Haven, CT 06511 USA - Author

Abstract

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.

Keywords

GalaxPlatform

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Genome Biology due to its progression and the good impact it has achieved in recent years, according to the agency WoS (JCR), it has become a reference in its field. In the year of publication of the work, 2025, it was in position 10/177, thus managing to position itself as a Q1 (Primer Cuartil), in the category Biotechnology & Applied Microbiology. Notably, the journal is positioned above the 90th percentile.

Impact and social visibility

Leadership analysis of institutional authors