Nf-core
 | |
| Formation | 2018 |
|---|---|
| Founder | Philip Ewels, Alex Peltzer |
| Founded at | Sweden, Germany |
| Purpose | Community curated bioinformatics pipelines |
| Origins | SciLifeLab, Sweden, Quantitative Biology Center (QBiC), Germany |
Key people |
|
| Website | https://nf-co.re/ |
Nf-core is a not-for-profit community effort dedicated to collecting a curated set of bioinformatics pipelines. In bioinformatics, a pipeline refers to a predefined sequence of algorithmic steps normally used to process next-generation sequencing (NGS) data. Nf-core pipelines are written using Nextflow, an open-source language for building and managing pipelines. Pipelines developed by nf-core contributors are freely available under an MIT license.
Nf-core has some similarities to other central pipeline repositories in bioinformatics such as qPortal, Truwl, and the Galaxy Toolshed. A focus of the nf-core project is on ensuring that pipelines are reproducible and portable across different hardware, operating systems, and software versions.[1]
History
The nf-core effort grew out of work led by Phil Ewels, head of development for NGI Stockholm (National Genomics Infrastructure), part of SciLifeLab Sweden.[2] NGI initially developed analysis pipelines for its own purposes using a set of internal guidelines to ensure that pipelines were FAIR (findable, accessible, interoperable, and reusable).[3][4] A community of like-minded researchers joined this effort from other research institutions including the Quantitative Biology Center (QBiC) at the University of Tübingen, the A*STAR Genome Institute of Singapore, the Centre for Genomic Regulation in Barcelona and the Francis Crick Institute in London.[2][4] This group's work was published in Nature Biotechnology in February of 2020.[5] As the number of users and contributors to the effort grew, all relevant pipelines were moved to the new nf-core GitHub organization to facilitate collaboration.[6][7]
Project Supporters
As of June, 2022 there were 440+ active contributors to the nf-core GitHub repositories and 67 available pipelines.[7] According to nf-core organizers, the vast majority of development is done on a volunteer basis.[8] nf-core have also received financial support from third-parties. Among these are:
- The Chan Zuckerberg Initiative through their Essential Open Source Software for Science (EOSS) grants. Nextflow and nf-core have received three separate EOSS grants:[9]
- Amazon Web Services (AWS) who provide usage credits to run full-sized nf-core datasets and support benchmarks with each Nextflow release.[8]
External links
References
- ↑ Ewels, Philip; Peltzer, Alexander; Fillinger, Sven; Alneberg, Johannes; Patel, Harshil; Wilm, Andreas; Garcia, Maxime Ulysse; Di Tommaso, Paolo; Nahnsen, Sven (April 1, 2019). "Nf-core: Community curated bioinformatics pipelines". Research Gate. Retrieved June 30, 2022. Unknown parameter
|url-status=ignored (help) - ↑ 2.0 2.1 Zapata Garin, Claire-Alix. "nf-core: a community-driven initiative to standardise Nextflow-based pipelines". Lifebit.ai. Retrieved June 30, 2022. Unknown parameter
|url-status=ignored (help) - ↑ Sansone, Susanna-Assunta; McQuilton, Peter; Rocca-Serra, Philippe; Gonzalez-Beltran, Alejandra; Izzo, Massimiliano; Lister, Allyson L.; Thurston, Milo (April 2, 2018). "FAIRsharing as a community approach to standards, repositories and policies". Nature Biotechnology. Retrieved June 30, 2022. Unknown parameter
|url-status=ignored (help) - ↑ 4.0 4.1 "The nf-core community provides computational pipelines". SciLifeLab. February 14, 2020. Retrieved June 30, 2022. Unknown parameter
|url-status=ignored (help) - ↑ "The nf-core framework for community-curated bioinformatics pipelines". Nature Biotechnology. February 13, 2020. Retrieved June 30, 2022. Unknown parameter
|url-status=ignored (help) - ↑ "About nf-core Details about the nf-core project and how it was started". nf-core. Retrieved June 20, 2022. Unknown parameter
|url-status=ignored (help) - ↑ 7.0 7.1 "GitHub nf-core project page". GitHub. Retrieved June 30, 2022. Unknown parameter
|url-status=ignored (help) - ↑ 8.0 8.1 "Nf-core - About - Financial Support". nf-core. Retrieved June 30, 2022. Unknown parameter
|url-status=ignored (help) - ↑ "NGI awarded Chan Zuckerberg Initiative grant for nf-core". National Genomics Infrastructure. Retrieved June 30, 2022. Unknown parameter
|url-status=ignored (help)
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