Empowering bioinformatics communities with Nextflow and nf-core

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

doi:10.1186/s13059-025-03673-9

Empowering bioinformatics communities with Nextflow and nf-core

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

Research output: Contribution to journal › Review article › peer-review

3 Citations (Scopus)

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.

Original language	English
Article number	228
Pages (from-to)	228
Number of pages	14
Journal	BMC Genome Biology
Volume	26
Issue number	1
DOIs	https://doi.org/10.1186/s13059-025-03673-9
Publication status	Print publication - 29 Jul 2025

Bibliographical note

Empowering bioinformatics communities with Nextflow and nf-core
Authors: Björn E. Langer1, Andreia Amaral2,3, Marie-Odile Baudement4, Franziska Bonath5, Mathieu Charles6,7, Praveen Krishna Chitneedi8, Emily L. Clark9, Paolo Di Tommaso10, Sarah Djebali11, Philip A. Ewels10, Sonia Eynard12, James A. Fellows Yates13,14,15, Daniel Fischer16, Evan W. Floden10, Sylvain Foissac12, Gisela Gabernet17, Maxime U. Garcia10, Gareth Gillard4, Manu Kumar Gundappa9, Cervin Guyomar12, Christopher Hakkaart10, Friederike Hanssen18,19,20, Peter W. Harrison21, Matthias Hörtenhuber22,23, Cyril Kurylo12, Christa Kühn8,24, Sandrine Lagarrigue25, Delphine Lallias6, Daniel J. Macqueen9, Edmund Miller26, Júlia Mir-Pedrol19, Gabriel Costa Monteiro Moreira27, Sven Nahnsen18,19,20,28, Harshil Patel10, Alexander Peltzer29, Frederique Pitel12, Yuliaxis Ramayo-Caldas30, Marcel da Câmara Ribeiro-Dantas10,31, Dominique Rocha6, Mazdak Salavati9,32, Alexey Sokolov21, Jose Espinosa-Carrasco1*, Cedric Notredame1,33* and 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, 7002-554 Évora, Portugal
3 Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, 1300-477, Lisbon Portugal
4 Centre for Integrative Genetics (CIGENE), Faculty of Biosciences, Norwegian University of Life Sciences, 1430 Ås, Norway
5 Kungliga Techniska Högskolan, School of Engineering Sciences in Chemistry, Biotechnology and Health at the Department of Gene Technology
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, 18196 Dummerstorf, Germany
9 The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, 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, 31326 Castanet-Tolosan, France
13 Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, Leipzig, Saxony, 4103, Germany
14 Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Adolf-Reichwein-Straße 23, Jena, Thuringia, 07745, Germany (Current Address)
15 Associated Research Group of Archaeogenetics, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Adolf-Reichwein-Straße 23, Jena, Thuringia, 07745, Germany (Current Address)
16 Natural Resources Institute Finland (Luke), Applied Statistical Methods, Myllytie 1, 31600 Jokioinen, 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, Germany
19 Quantitative Biology Center (QBiC), University of Tübingen, Germany
20 M3 Research Center, Faculty of Medicine, University of Tübingen
21 European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK.
22 Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
23 SciLifeLab, Uppsala University, Uppsala, Sweden
24 Friedrich-Loeffler-Institut (FLI), 17493 Greifswald-Riems, Germany
25 PEGASE, INRAE, Institut Agro, 35590, Saint Gilles, France
26 Department of Biological Sciences and Center for Systems Biology, The University of Texas at Dallas, Richardson, TX 75205, United States
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
29 Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorfer Straße 65, 88400 Biberach/Riss, 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, United Kingdom DG1 3NE
33 Universitat Pompeu Fabra (UPF), Barcelona, Spain

*To whom correspondence should be addressed.

Keywords

Animals
Computational Biology/methods
Software

Access to Document

10.1186/s13059-025-03673-9Licence: CC BY-NC

Empowering bioinformatics communities with Nextflow and nf-coreFinal published version, 272 KBLicence: CC BY-NC-ND

Embargoed Document

V2.1 (rev1) - Manuscript_Empowering_bioinformatics_communities_with_Nextflow_and_nf-core
869 KB

Embargoed Document

Citation Level of Bioinformatics Workflow Managers (Google Scholar)
27.3 KB

Embargoed Document

Citation Level of Bioinformatics Workflow Managers (Scopus)
28.8 KB

Cite this

Langer, B. E., Amaral, A., Baudement, M.-O., Bonath, F., Charles, M., Chitneedi, P. K., Clark, E. L., Tommaso, P. D., Djebali, S., Ewels, P. A., Eynard, S., Yates, J. A. F., Fischer, D., Floden, E. W., Foissac, S., Gabernet, G., Garcia, M. U., Gillard, G., Gundappa, M. K., ... Notredame, C. (2025). Empowering bioinformatics communities with Nextflow and nf-core. BMC Genome Biology, 26(1), 228. Article 228. https://doi.org/10.1186/s13059-025-03673-9

@article{d7731e0b60ae4239aa21d993e72b7504,

title = "Empowering bioinformatics communities with Nextflow and nf-core",

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 = "Animals, Computational Biology/methods, Software",

author = "Langer, \{Bj{\"o}rn E.\} and Andreia Amaral and Marie-Odile Baudement and Franziska Bonath and Mathieu Charles and Chitneedi, \{Praveen Krishna\} and Clark, \{Emily L\} and Tommaso, \{Paolo Di\} and Sarah Djebali and Ewels, \{Philip A.\} and Sonia Eynard and Yates, \{James A. Fellows\} and Daniel Fischer and Floden, \{Evan W.\} and Sylvain Foissac and Gisela Gabernet and Garcia, \{Maxime U.\} and Gareth Gillard and Gundappa, \{Manu Kumar\} and Cervin Guyomar and Christopher Hakkaart and Friederike Hanssen and Harrison, \{Peter W.\} and Matthias H{\"o}rtenhuber and Cyril Kurylo and Christa K{\"u}hn and Sandrine Lagarrigue and Delphine Lallias and Macqueen, \{Daniel J.\} and Edmund Miller and J{\'u}lia Mir-Pedrol and Moreira, \{Gabriel Costa Monteiro\} and Sven Nahnsen and Harshil Patel and Alexander Peltzer and Frederique Pitel and Yuliaxis Ramayo-Caldas and Ribeiro-Dantas, \{Marcel da C{\^a}mara\} and Dominique Rocha and M Salavati and Alexey Sokolov and Jose Espinosa-Carrasco and Cedric Notredame",

note = "Empowering bioinformatics communities with Nextflow and nf-core Authors: Bj{\"o}rn E. Langer1, Andreia Amaral2,3, Marie-Odile Baudement4, Franziska Bonath5, Mathieu Charles6,7, Praveen Krishna Chitneedi8, Emily L. Clark9, Paolo Di Tommaso10, Sarah Djebali11, Philip A. Ewels10, Sonia Eynard12, James A. Fellows Yates13,14,15, Daniel Fischer16, Evan W. Floden10, Sylvain Foissac12, Gisela Gabernet17, Maxime U. Garcia10, Gareth Gillard4, Manu Kumar Gundappa9, Cervin Guyomar12, Christopher Hakkaart10, Friederike Hanssen18,19,20, Peter W. Harrison21, Matthias H{\"o}rtenhuber22,23, Cyril Kurylo12, Christa K{\"u}hn8,24, Sandrine Lagarrigue25, Delphine Lallias6, Daniel J. Macqueen9, Edmund Miller26, J{\'u}lia Mir-Pedrol19, Gabriel Costa Monteiro Moreira27, Sven Nahnsen18,19,20,28, Harshil Patel10, Alexander Peltzer29, Frederique Pitel12, Yuliaxis Ramayo-Caldas30, Marcel da C{\^a}mara Ribeiro-Dantas10,31, Dominique Rocha6, Mazdak Salavati9,32, Alexey Sokolov21, Jose Espinosa-Carrasco1*, Cedric Notredame1,33* and 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 {\'E}vora, Polo da Mitra, 7002-554 {\'E}vora, Portugal 3 Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, 1300-477, Lisbon Portugal 4 Centre for Integrative Genetics (CIGENE), Faculty of Biosciences, Norwegian University of Life Sciences, 1430 {\AA}s, Norway 5 Kungliga Techniska H{\"o}gskolan, School of Engineering Sciences in Chemistry, Biotechnology and Health at the Department of Gene Technology 6 INRAE, AgroParisTech, GABI, Universit{\'e} 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, 18196 Dummerstorf, Germany 9 The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, UK. 10 Seqera, Carrer de Mari{\`a} Aguil{\'o}, 28, Barcelona, 08005, Spain 11 IRSD, Universit{\'e} de Toulouse, INSERM, INRAE, ENVT, Univ Toulouse III - Paul Sabatier (UPS), Toulouse, France 12 GenPhySE, Universit{\'e} de Toulouse, INRAE, ENVT, 31326 Castanet-Tolosan, France 13 Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, Leipzig, Saxony, 4103, Germany 14 Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology Hans Kn{\"o}ll Institute, Adolf-Reichwein-Stra{\ss}e 23, Jena, Thuringia, 07745, Germany (Current Address) 15 Associated Research Group of Archaeogenetics, Leibniz Institute for Natural Product Research and Infection Biology Hans Kn{\"o}ll Institute, Adolf-Reichwein-Stra{\ss}e 23, Jena, Thuringia, 07745, Germany (Current Address) 16 Natural Resources Institute Finland (Luke), Applied Statistical Methods, Myllytie 1, 31600 Jokioinen, Finland 17 Department of Pathology, Yale School of Medicine. New Haven, CT 06511, USA 18 Biomedical Data Science, Department of Computer Science, University of T{\"u}bingen, Germany 19 Quantitative Biology Center (QBiC), University of T{\"u}bingen, Germany 20 M3 Research Center, Faculty of Medicine, University of T{\"u}bingen 21 European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK. 22 Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden 23 SciLifeLab, Uppsala University, Uppsala, Sweden 24 Friedrich-Loeffler-Institut (FLI), 17493 Greifswald-Riems, Germany 25 PEGASE, INRAE, Institut Agro, 35590, Saint Gilles, France 26 Department of Biological Sciences and Center for Systems Biology, The University of Texas at Dallas, Richardson, TX 75205, United States 27 Unit of Animal Genomics, GIGA \& Faculty of Veterinary Medicine, University of Li{\`e}ge, Li{\`e}ge, Belgium 28 Institute for Bioinformatics and Medical Informatics (IBMI), University of T{\"u}bingen 29 Boehringer Ingelheim Pharma GmbH \& Co KG, Birkendorfer Stra{\ss}e 65, 88400 Biberach/Riss, 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, United Kingdom DG1 3NE 33 Universitat Pompeu Fabra (UPF), Barcelona, Spain *To whom correspondence should be addressed. ",

year = "2025",

month = jul,

day = "29",

doi = "10.1186/s13059-025-03673-9",

language = "English",

volume = "26",

pages = "228",

journal = "BMC Genome Biology",

issn = "1474-760X",

publisher = "Springer Nature",

number = "1",

}

Langer, BE, Amaral, A, Baudement, M-O, Bonath, F, Charles, M, Chitneedi, PK, Clark, EL, Tommaso, PD, Djebali, S, Ewels, PA, Eynard, S, Yates, JAF, 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 2025, 'Empowering bioinformatics communities with Nextflow and nf-core', BMC Genome Biology, vol. 26, no. 1, 228, pp. 228. https://doi.org/10.1186/s13059-025-03673-9

TY - JOUR

T1 - Empowering bioinformatics communities with Nextflow and nf-core

AU - Langer, Björn E.

AU - Amaral, Andreia

AU - Baudement, Marie-Odile

AU - Bonath, Franziska

AU - Charles, Mathieu

AU - Chitneedi, Praveen Krishna

AU - Clark, Emily L

AU - Tommaso, Paolo Di

AU - Djebali, Sarah

AU - Ewels, Philip A.

AU - Eynard, Sonia

AU - Yates, James A. Fellows

AU - Fischer, Daniel

AU - Floden, Evan W.

AU - Foissac, Sylvain

AU - Gabernet, Gisela

AU - Garcia, Maxime U.

AU - Gillard, Gareth

AU - Gundappa, Manu Kumar

AU - Guyomar, Cervin

AU - Hakkaart, Christopher

AU - Hanssen, Friederike

AU - Harrison, Peter W.

AU - Hörtenhuber, Matthias

AU - Kurylo, Cyril

AU - Kühn, Christa

AU - Lagarrigue, Sandrine

AU - Lallias, Delphine

AU - Macqueen, Daniel J.

AU - Miller, Edmund

AU - Mir-Pedrol, Júlia

AU - Moreira, Gabriel Costa Monteiro

AU - Nahnsen, Sven

AU - Patel, Harshil

AU - Peltzer, Alexander

AU - Pitel, Frederique

AU - Ramayo-Caldas, Yuliaxis

AU - Ribeiro-Dantas, Marcel da Câmara

AU - Rocha, Dominique

AU - Salavati, M

AU - Sokolov, Alexey

AU - Espinosa-Carrasco, Jose

AU - Notredame, Cedric

N1 - Empowering bioinformatics communities with Nextflow and nf-core Authors: Björn E. Langer1, Andreia Amaral2,3, Marie-Odile Baudement4, Franziska Bonath5, Mathieu Charles6,7, Praveen Krishna Chitneedi8, Emily L. Clark9, Paolo Di Tommaso10, Sarah Djebali11, Philip A. Ewels10, Sonia Eynard12, James A. Fellows Yates13,14,15, Daniel Fischer16, Evan W. Floden10, Sylvain Foissac12, Gisela Gabernet17, Maxime U. Garcia10, Gareth Gillard4, Manu Kumar Gundappa9, Cervin Guyomar12, Christopher Hakkaart10, Friederike Hanssen18,19,20, Peter W. Harrison21, Matthias Hörtenhuber22,23, Cyril Kurylo12, Christa Kühn8,24, Sandrine Lagarrigue25, Delphine Lallias6, Daniel J. Macqueen9, Edmund Miller26, Júlia Mir-Pedrol19, Gabriel Costa Monteiro Moreira27, Sven Nahnsen18,19,20,28, Harshil Patel10, Alexander Peltzer29, Frederique Pitel12, Yuliaxis Ramayo-Caldas30, Marcel da Câmara Ribeiro-Dantas10,31, Dominique Rocha6, Mazdak Salavati9,32, Alexey Sokolov21, Jose Espinosa-Carrasco1*, Cedric Notredame1,33* and 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, 7002-554 Évora, Portugal 3 Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, 1300-477, Lisbon Portugal 4 Centre for Integrative Genetics (CIGENE), Faculty of Biosciences, Norwegian University of Life Sciences, 1430 Ås, Norway 5 Kungliga Techniska Högskolan, School of Engineering Sciences in Chemistry, Biotechnology and Health at the Department of Gene Technology 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, 18196 Dummerstorf, Germany 9 The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, 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, 31326 Castanet-Tolosan, France 13 Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, Leipzig, Saxony, 4103, Germany 14 Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Adolf-Reichwein-Straße 23, Jena, Thuringia, 07745, Germany (Current Address) 15 Associated Research Group of Archaeogenetics, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Adolf-Reichwein-Straße 23, Jena, Thuringia, 07745, Germany (Current Address) 16 Natural Resources Institute Finland (Luke), Applied Statistical Methods, Myllytie 1, 31600 Jokioinen, 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, Germany 19 Quantitative Biology Center (QBiC), University of Tübingen, Germany 20 M3 Research Center, Faculty of Medicine, University of Tübingen 21 European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK. 22 Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden 23 SciLifeLab, Uppsala University, Uppsala, Sweden 24 Friedrich-Loeffler-Institut (FLI), 17493 Greifswald-Riems, Germany 25 PEGASE, INRAE, Institut Agro, 35590, Saint Gilles, France 26 Department of Biological Sciences and Center for Systems Biology, The University of Texas at Dallas, Richardson, TX 75205, United States 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 29 Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorfer Straße 65, 88400 Biberach/Riss, 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, United Kingdom DG1 3NE 33 Universitat Pompeu Fabra (UPF), Barcelona, Spain *To whom correspondence should be addressed.

PY - 2025/7/29

Y1 - 2025/7/29

N2 - 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.

AB - 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.

KW - Animals

KW - Computational Biology/methods

KW - Software

U2 - 10.1186/s13059-025-03673-9

DO - 10.1186/s13059-025-03673-9

M3 - Review article

C2 - 40731283

SN - 1474-760X

VL - 26

SP - 228

JO - BMC Genome Biology

JF - BMC Genome Biology

IS - 1

M1 - 228

ER -

Empowering bioinformatics communities with Nextflow and nf-core

Abstract

Bibliographical note

Keywords

Access to Document

Embargoed Document

Embargoed Document

Embargoed Document

Fingerprint

Cite this