JOBIM 2020: nf-core, a community effort for collaborative, peer-reviewed analysis pipelines

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About the conference

JOBIM is the French speaking reference bioinformatics conference. It offer the possibility of the entire french community, and also a part of Belgium, Switzerland, Quebec and Maghreb community to exchange together. JOBIM is an international conference, with a large proportion of presentations in English with prestigious international guests speakers. Therefore JOBIM has a unique place in the scientific landscape.

nf-core, a community effort for collaborative, peer-reviewed analysis pipelines

Maxime Garcia will be giving a 20-minute talk about the nf-core community.

Abstract

Paper Reference: Ewels, P.A., Peltzer, A., Fillinger, S. et al. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol (2020). doi.org/10.1038/s41587-020-0439-x

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. 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 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.

The primary portal to the nf-core community is its website nf-co.re, which lists available analysis pipelines, user- and developer-centric documentation, and tutorials, as well as usage and contributor statistics. All code is hosted on GitHub under the nf-core organization github.com/nf-core/ and released under the MIT license.

We hope to welcome more contributors and pipelines to the nf-core community to build on the solid foundation that has already been established.