Article Dans Une Revue (Article De Synthèse) Genome Biology Année : 2025

Empowering bioinformatics communities with Nextflow and nf-core

Björn E Langer
Andreia Amaral
Marie-Odile Baudement
Franziska Bonath
Praveen Krishna Chitneedi
  • Fonction : Auteur
Emily L Clark
Paolo Di Tommaso
Philip A Ewels
James Fellows Yates
  • Fonction : Auteur
Daniel Fischer
Evan W Floden
Gisela Gabernet
Maxime U Garcia
Gareth Gillard
Manu Kumar Gundappa
  • Fonction : Auteur
Christopher Hakkaart
Friederike Hanssen
Peter W Harrison
Matthias Hörtenhuber
Cyril Kurylo
  • Fonction : Auteur
Christa Kühn
Daniel J Macqueen
Edmund Miller
Júlia Mir-Pedrol
Gabriel Costa Monteiro Moreira
Sven Nahnsen
Harshil Patel
Alexander Peltzer
Yuliaxis Ramayo-Caldas
Dominique Rocha
Mazdak Salavati
Alexey Sokolov
Jose Espinosa-Carrasco
Cedric Notredame
The Nf-Core Community
  • Fonction : Auteur

Résumé

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.

HAL

A comme version hal-04770333 Preprint Björn E Langer, Andreia Amaral, Marie-Odile Baudement, Franziska Bonath, Mathieu Charles, et al.. Empowering bioinformatics communities with Nextflow and nf-core. 2024. ⟨hal-04770333⟩

Dates et versions

hal-05224445 , version 1 (12-03-2026)

Identifiants

Citer

Björn E Langer, Andreia Amaral, Marie-Odile Baudement, Franziska Bonath, Mathieu Charles, et al.. Empowering bioinformatics communities with Nextflow and nf-core. Genome Biology, 2025, 26 (1), pp.228. ⟨10.1186/s13059-025-03673-9⟩. ⟨hal-05224445⟩
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