The nf-core framework for community-curated bioinformatics pipelines

Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S

Nat Biotechnol 38 (3) 276-278 [2020-03-00; online 2020-02-13]

The standardization, portability and reproducibility of analysis pipelines are key issues within the bioinformatics community. Most bioinformatics pipelines are designed for use on-premises; as a result, the associated software dependencies and execution logic are likely to be tightly coupled with proprietary computing environments. This can make it difficult or even impossible for others to reproduce the ensuing results, which is a fundamental requirement for the validation of scientific findings. Here, we introduce the nf-core framework as a means for the development of collaborative, peer-reviewed, best-practice analysis pipelines (Fig. 1). All nf-core pipelines are written in Nextflow and so inherit the ability to be executed on most computational infrastructures, as well as having native support for container technologies such as Docker and Singularity. The nf-core community (Supplementary Fig. 1) has developed a suite of tools that automate pipeline creation, testing, deployment and synchronization. Our goal is to provide a framework for high-quality bioinformatics pipelines that can be used across all institutions and research facilities.

NGI Stockholm (Genomics Applications) [Technology development]

NGI Stockholm (Genomics Production) [Technology development]

National Genomics Infrastructure [Technology development]

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PubMed 32055031

DOI 10.1038/s41587-020-0439-x

Crossref 10.1038/s41587-020-0439-x