Empowering bioinformatics communities with Nextflow and nf-core

Björn E Langer¹, Andreia Amaral^{2

3}, Marie-Odile Baudement⁴, Franziska Bonath⁵, Mathieu Charles^{6

7}, Praveen Krishna Chitneedi⁸, Emily L Clark⁹, Paolo Di Tommaso¹⁰, Sarah Djebali¹¹, Philip A Ewels¹⁰, Sonia Eynard¹², James A Fellows Yates^{13

14

15}, Daniel Fischer¹⁶, Evan W Floden¹⁰, Sylvain Foissac¹², Gisela Gabernet¹⁷, Maxime U Garcia¹⁰, Gareth Gillard⁴, Manu Kumar Gundappa⁹, Cervin Guyomar¹², Christopher Hakkaart¹⁰, Friederike Hanssen^{18

19

20}, Peter W Harrison²¹, Matthias Hörtenhuber^{22

23}, Cyril Kurylo¹², Christa Kühn^{8

24}, Sandrine Lagarrigue²⁵, Delphine Lallias⁶, Daniel J Macqueen⁹, Edmund Miller²⁶, Júlia Mir-Pedrol¹⁹, Gabriel Costa Monteiro Moreira²⁷, Sven Nahnsen^{18

19

20

28}, Harshil Patel¹⁰, Alexander Peltzer²⁹, Frederique Pitel¹², Yuliaxis Ramayo-Caldas³⁰, Marcel da Câmara Ribeiro-Dantas^{10

31}, Dominique Rocha⁶, Mazdak Salavati^{9

32}, Alexey Sokolov²¹, Jose Espinosa-Carrasco³³, Cedric Notredame^{34

35}, The Nf-Core Community

Affiliations

¹ Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.
² MED. University of Évora, Polo da Mitra, Évora, 7002-554, Portugal.
³ Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Lisbon, 1300-477, Portugal.
⁴ Centre for Integrative Genetics (CIGENE), Faculty of Biosciences, Norwegian University of Life Sciences, Ås, 1430, Norway.
⁵ Kungliga Techniska Högskolan, School of Engineering Sciences in Chemistry, Biotechnology and Health at the Department of Gene Technology, Stockholm, Sweden.
⁶ INRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, F-78350, France.
⁷ SIGENAE, INRAE, Jouy-en-Josas, F-78350, France.
⁸ Research Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, Dummerstorf, 18196, Germany.
⁹ The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Roslin, UK.
¹⁰ Seqera, Carrer de Marià Aguiló, 28, Barcelona, 08005, Spain.
¹¹ IRSD, Université de Toulouse, INSERM, INRAE, ENVT, Univ Toulouse III - Paul Sabatier (UPS), Toulouse, France.
¹² GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, 31326, France.
¹³ Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, Leipzig, Saxony, 04103, Germany.
¹⁴ Current address: Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Adolf-Reichwein-Straße 23, Jena, Thuringia, 07745, Germany.
¹⁵ Current Address: Associated Research Group of Archaeogenetics, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Adolf-Reichwein-Straße 23, 07745, Jena, Thuringia, Germany.
¹⁶ Natural Resources Institute Finland (Luke), Applied Statistical Methods, Myllytie 1, Jokioinen, 31600, Finland.
¹⁷ Department of Pathology, Yale School of Medicine, New Haven, CT, 06511, USA.
¹⁸ Biomedical Data Science, Department of Computer Science, University of Tübingen, Tübingen, Germany.
¹⁹ Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany.
²⁰ M3 Research Center, Faculty of Medicine, University of Tübingen, Tübingen, Germany.
²¹ European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
²² Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
²³ SciLifeLab, Uppsala University, Uppsala, Sweden.
²⁴ Friedrich-Loeffler-Institut (FLI), Greifswald-Riems, 17493, Germany.
²⁵ PEGASE, INRAE, Institut Agro, Saint Gilles, 35590, France.
²⁶ Department of Biological Sciences and Center for Systems Biology, The University of Texas at Dallas, Richardson, TX, 75205, USA.
²⁷ Unit of Animal Genomics, GIGA & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium.
²⁸ Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Tübingen, Germany.
²⁹ Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorfer Straße 65, Biberach/Riss, 88400, Germany.
³⁰ Animal Breeding and Genetics Program, Institute of Agrifood Research and Technology (IRTA), Caldes de Montbui, Barcelona, Spain.
³¹ Postgraduate Program in Biotechnology at Universidade Potiguar (UnP), Natal/RN, Brazil.
³² Dairy Research Innovation Centre, South and West Faculty, Scotland's Rural College, Dumfries, DG1 3NE, UK.
³³ Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain. joseantonio.espinosa@crg.eu.
³⁴ Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain. cedric.notredame@crg.eu.
³⁵ Universitat Pompeu Fabra (UPF), Barcelona, Spain. cedric.notredame@crg.eu.

PMID: 40731283
PMCID: PMC12309086
DOI: 10.1186/s13059-025-03673-9

Review

Empowering bioinformatics communities with Nextflow and nf-core

Björn E Langer et al. Genome Biol. 2025.

. 2025 Jul 29;26(1):228.

doi: 10.1186/s13059-025-03673-9.

Authors

Affiliations

¹ Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.
² MED. University of Évora, Polo da Mitra, Évora, 7002-554, Portugal.
³ Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Lisbon, 1300-477, Portugal.
⁴ Centre for Integrative Genetics (CIGENE), Faculty of Biosciences, Norwegian University of Life Sciences, Ås, 1430, Norway.
⁵ Kungliga Techniska Högskolan, School of Engineering Sciences in Chemistry, Biotechnology and Health at the Department of Gene Technology, Stockholm, Sweden.
⁶ INRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, F-78350, France.
⁷ SIGENAE, INRAE, Jouy-en-Josas, F-78350, France.
⁸ Research Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, Dummerstorf, 18196, Germany.
⁹ The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Roslin, UK.
¹⁰ Seqera, Carrer de Marià Aguiló, 28, Barcelona, 08005, Spain.
¹¹ IRSD, Université de Toulouse, INSERM, INRAE, ENVT, Univ Toulouse III - Paul Sabatier (UPS), Toulouse, France.
¹² GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, 31326, France.
¹³ Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, Leipzig, Saxony, 04103, Germany.
¹⁴ Current address: Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Adolf-Reichwein-Straße 23, Jena, Thuringia, 07745, Germany.
¹⁵ Current Address: Associated Research Group of Archaeogenetics, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Adolf-Reichwein-Straße 23, 07745, Jena, Thuringia, Germany.
¹⁶ Natural Resources Institute Finland (Luke), Applied Statistical Methods, Myllytie 1, Jokioinen, 31600, Finland.
¹⁷ Department of Pathology, Yale School of Medicine, New Haven, CT, 06511, USA.
¹⁸ Biomedical Data Science, Department of Computer Science, University of Tübingen, Tübingen, Germany.
¹⁹ Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany.
²⁰ M3 Research Center, Faculty of Medicine, University of Tübingen, Tübingen, Germany.
²¹ European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
²² Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
²³ SciLifeLab, Uppsala University, Uppsala, Sweden.
²⁴ Friedrich-Loeffler-Institut (FLI), Greifswald-Riems, 17493, Germany.
²⁵ PEGASE, INRAE, Institut Agro, Saint Gilles, 35590, France.
²⁶ Department of Biological Sciences and Center for Systems Biology, The University of Texas at Dallas, Richardson, TX, 75205, USA.
²⁷ Unit of Animal Genomics, GIGA & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium.
²⁸ Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Tübingen, Germany.
²⁹ Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorfer Straße 65, Biberach/Riss, 88400, Germany.
³⁰ Animal Breeding and Genetics Program, Institute of Agrifood Research and Technology (IRTA), Caldes de Montbui, Barcelona, Spain.
³¹ Postgraduate Program in Biotechnology at Universidade Potiguar (UnP), Natal/RN, Brazil.
³² Dairy Research Innovation Centre, South and West Faculty, Scotland's Rural College, Dumfries, DG1 3NE, UK.
³³ Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain. joseantonio.espinosa@crg.eu.
³⁴ Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain. cedric.notredame@crg.eu.
³⁵ Universitat Pompeu Fabra (UPF), Barcelona, Spain. cedric.notredame@crg.eu.

PMID: 40731283
PMCID: PMC12309086
DOI: 10.1186/s13059-025-03673-9

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.

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Conflict of interest statement

Declarations. Competing interests: Several Seqera employees are active promoters of nf-core. Seqera also provides direct infrastructure support (e.g. Wave) to the nf-core project as well as direct support to Nextflow and nf-core development. The Centre for Genomic Regulation and CN hold Seqera stocks and phantom stocks respectively. The CN lab at the Centre for Genomic Regulation receives support from Seqera.

Figures

**Fig. 1**
Google Scholar citation counts for bioinformatics workflow management systems. Sum of citations of the major publications of Galaxy, Nextflow, and Snakemake between 2018 and 2024 (Data in Additional File 1: Supp. Table 1)

**Fig. 2**
Pipeline maintenance and usage. A Major contributions to the nf-core/smrnaseq pipeline over time by different academic institutions or private companies. Data for individual contributors is collapsed to their institution (SciLifeLab: 3; QBiC: 2; Boehringer Ingelheim: 3; Seqera: 4; all the others: 1) B Nextflow analysis pipelines used in the EuroFAANG consortia for the functional annotation of various species’ genomes

See this image and copyright information in PMC

References

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1. ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489(7414):57–74. - PMC - PubMed
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1. Deelman E, Peterka T, Altintas I, Carothers CD, Van Dam KK, Moreland K, et al. The future of scientific workflows. Int J High Perform Comput Appl. 2018;32(1):159–75.

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Empowering bioinformatics communities with Nextflow and nf-core

Affiliations

Empowering bioinformatics communities with Nextflow and nf-core

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

References

Publication types

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources