通过Nextflow和nf-core增强生物信息学社区的能力

IF 10.1 1区生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genome Biology Pub Date : 2025-07-29 DOI:10.1186/s13059-025-03673-9

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, the nf-core community

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引用次数: 0

摘要

标准化的分析管道有助于使数据生物信息学研究符合可查找性、可访问性、互操作性和可重用性（FAIR）的范式，并促进协作。Nextflow和Snakemake这两种流行的命令行解决方案越来越多地被用户采用，它们是Galaxy等基于gui的平台的补充。我们报告了使用新的Nextflow领域特定语言（DSL2）的ncore框架的最新发展。广泛的模块和子工作流库使研究社区能够在资源和需求允许的情况下逐步采用通用标准。我们介绍了一些围绕nf-core建立的研究社区的概述，并展示了六个EuroFAANG养殖动物研究联盟对其的采用。

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Empowering bioinformatics communities with Nextflow and nf-core

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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来源期刊

Genome Biology Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

21.00

自引率

3.30%

发文量

241

审稿时长

2 months

期刊介绍： Genome Biology stands as a premier platform for exceptional research across all domains of biology and biomedicine, explored through a genomic and post-genomic lens. With an impressive impact factor of 12.3 (2022),* the journal secures its position as the 3rd-ranked research journal in the Genetics and Heredity category and the 2nd-ranked research journal in the Biotechnology and Applied Microbiology category by Thomson Reuters. Notably, Genome Biology holds the distinction of being the highest-ranked open-access journal in this category. Our dedicated team of highly trained in-house Editors collaborates closely with our esteemed Editorial Board of international experts, ensuring the journal remains on the forefront of scientific advances and community standards. Regular engagement with researchers at conferences and institute visits underscores our commitment to staying abreast of the latest developments in the field.