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Empowering bioinformatics communities with Nextflow and nf-core

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

in Animal biology / Animal Genetics and Genomics / animal research / Animals / Bibliometrics / Bioinformatics / Biomedical and Life Sciences / Cell Biology / Community / Computational Biology / Computational Biology - methods / Computer science / Decision making / Ecology, Evolution, Behavior and Systematics / Engineering, computing & technology / Evolutionary Biology / Genetics / genome / Human Genetics / Human health and pathology / Ingénierie, informatique & technologie / Life Sciences / Microbial Genetics and Genomics / Médecine vétérinaire & santé animale / Plant Genetics and Genomics / Quantitative Methods / Reproducibility / Review / Sciences du vivant / Sciences informatiques / Software / Teams / Veterinary medicine & animal health / Veterinary medicine and animal Health / Workflow software

2025

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Empowering bioinformatics communities with Nextflow and nf-core

2025

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2025

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Journal Article

Empowering bioinformatics communities with Nextflow and nf-core

Bonath, Franziska,

Fellows Yates, James A.,

Fischer, Daniel,

Harrison, Peter W.,

Foissac, Sylvain,

Patel, Harshil,

Charles, Mathieu,

Mir-Pedrol, Júlia,

Gabernet, Gisela,

Salavati, Mazdak,

Gundappa, Manu Kumar,

Baudement, Marie-Odile,

Ewels, Philip A.,

Kurylo, Cyril,

Hanssen, Friederike,

Notredame, Cedric,

Djebali, Sarah,

Ribeiro-Dantas, Marcel da Câmara,

community, the nf-core,

Lallias, Delphine,

Chitneedi, Praveen Krishna,

Hakkaart, Christopher,

Lagarrigue, Sandrine,

Pitel, Frederique,

Rocha, Dominique,

Sokolov, Alexey,

Clark, Emily L.,

Floden, Evan W.,

Kühn, Christa,

Moreira, Gabriel Costa Monteiro,

Espinosa-Carrasco, Jose,

Garcia, Maxime U.,

Hörtenhuber, Matthias,

Amaral, Andreia,

Di Tommaso, Paolo,

Macqueen, Daniel J.,

Gillard, Gareth,

Guyomar, Cervin,

Nahnsen, Sven,

Ramayo-Caldas, Yuliaxis,

Peltzer, Alexander,

Miller, Edmund,

Langer, Björn E.,

Eynard, Sonia

2025

Overview

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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Publisher

BioMed Central,Springer Nature B.V,BioMed Central Ltd,BMC

Subject

Animal biology

/ Animal Genetics and Genomics

/ animal research

/ Animals

/ Bibliometrics

/ Bioinformatics

/ Biomedical and Life Sciences