借助Nextflow和nf-core助力生物信息学社区。

Empowering bioinformatics communities with Nextflow and nf-core.

作者信息

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

机构信息

Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.

MED. University of Évora, Polo da Mitra, Évora, 7002-554, Portugal.

出版信息

Genome Biol. 2025 Jul 29;26(1):228. doi: 10.1186/s13059-025-03673-9.

DOI:10.1186/s13059-025-03673-9

PMID:40731283

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.

摘要

标准化分析流程有助于使数据生物信息学研究符合可查找、可访问、可互操作和可重用性（FAIR）范式，并促进合作。Nextflow和Snakemake这两种流行的命令行解决方案越来越受到用户的采用，对诸如Galaxy等基于图形用户界面（GUI）的平台起到了补充作用。我们报告了nf-core框架在新的Nextflow领域特定语言（DSL2）方面的最新进展。随着资源和需求的允许，大量的模块和子工作流库使研究社区能够逐步采用通用标准。我们概述了一些围绕nf-core建立的研究社区，并展示了六个欧洲FAANG养殖动物研究联盟对它的采用情况。