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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).

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Empowering bioinformatics communities with Nextflow and nf-core

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

Autores: 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

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Resumen

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.

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