nf-core: Community curated bioinformatics pipelines

Philip Ewels; Alexander Peltzer; Sven Fillinger; Johannes Alneberg; Harshil Patel; Andreas Wilm; Maxime Ulysse Garcia; Paolo Di Tommaso; Sven Nahnsen

doi:10.1101/610741

bioRxivMay 26, 2019BioinformaticsPreprint

nf-core: Community curated bioinformatics pipelines

Philip Ewels iD, Alexander Peltzer iD, Sven Fillinger iD, Johannes Alneberg iD, Harshil Patel iD, Andreas Wilm iD, Maxime Ulysse Garcia iD, Paolo Di Tommaso iD, Sven Nahnsen iD

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Abstract

The standardization, portability, and reproducibility of analysis pipelines is a renowned problem within the bioinformatics community. Most pipelines are designed for execution on-premise, and the associated software dependencies are tightly coupled with the local compute environment. This leads to poor pipeline portability and reproducibility of the ensuing results - both of which are fundamental requirements for the validation of scientific findings. Here, we introduce nf-core: a framework that provides a community-driven, peer-reviewed platform for the development of best practice analysis pipelines written in Nextflow. Key obstacles in pipeline development such as portability, reproducibility, scalability and unified parallelism are inherently addressed by all nf-core pipelines. We are also continually developing a suite of tools that assist in the creation and development of both new and existing pipelines. Our primary goal is to provide a platform for high-quality, reproducible bioinformatics pipelines that can be utilized across various institutions and research facilities.

Abstract summary

Claude Opus 5.5 · xhigh effort · 18 Oct 2026 · from the abstract · CC BY-NC 4.0

A peer-reviewed, community-run framework for Nextflow analysis pipelines, plus helper tooling, meant to make workflows portable and reproducible across institutions rather than tied to one cluster.

Bioinformatics pipelines are usually written against a particular local compute environment, so their software dependencies travel badly and results are hard to reproduce elsewhere. The authors propose a shared, peer-reviewed set of Nextflow pipelines and development tools so that portability and reproducibility come from the framework instead of from each group's own conventions.

Key results

Claimednf-core is presented as a community-driven, peer-reviewed platform on which best-practice analysis pipelines are written in Nextflow.
Described in the abstract as a framework with community development and peer review; no counts of pipelines, contributors or adopting sites are given. · Abstract
ClaimedThe authors argue that portability, reproducibility, scalability and parallel execution are handled by the framework itself, so every pipeline built on it inherits them.
Stated as a property of all nf-core pipelines; the abstract reports no benchmark, no cross-site execution test and no reproducibility measurement to support it. · Abstract
ClaimedA companion suite of tools is being developed to help authors create new pipelines and bring existing ones into the framework.
Described as under continual development; the individual tools and their functions are not named in the abstract. · Abstract

Methods, data and reproducibility

Description of a framework and community process for writing analysis pipelines in the Nextflow workflow language, together with an accompanying set of development tools for new and existing pipelines.

Methods & tools: nf-core, Nextflow

Limitations (2)

The abstract makes no measurement: there is no evidence that pipelines run identically across sites, no runtime or scaling figures, and no count of pipelines or users. · noted in this summary
No repository, registry or documentation address is given in the available text, so the software cannot be located from this abstract alone. · noted in this summary

Read this if you build or maintain bioinformatics workflows and are weighing a community-curated Nextflow framework against in-house pipelines.