Empowering bioinformatics communities with Nextflow and nf-core

Standardised analysis pipelines are an important part of FAIR bioinformatics research. Over the last decade, there has been a notable shift from point-and-click pipeline solutions like Galaxy to command-line solutions such as Nextflow and Snakemake. We report on the process that led six European research consortia, under the EuroFAANG umbrella and dedicated to farmed animal genomics, to adopt Nextflow, and nf-core as implementation standard for Nextflow pipelines. This adoption of a common standard has been driven by recent advancements in nf-core and Nextflow, such as DSL2, and the promise of faster development, better interoperability, and collaboration with the nf-core community. Given the general lack of dedicated resources, a key factor in adoption was the progressive nature of the standardization process, enabling effective bottom-up adoption. Authors: 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, Mazdak Salavati, Alexey Sokolov, Jose Espinosa-Carrasco, Cedric Notredame and the nf-core community