nf-core: A community effort to collect curated Nextflow pipelines
Slides from my talk at the CRG Nextflow Hackathon, November 2018. The Swedish National Genomics Infrastructure (NGI) has been a key user and proponent of nextflow since soon after its initial release. We have produced several popular pipelines as well as writing recommendations on best practices. Our oldest pipeline for RNA sequencing analysis is used in production at NGI Stockholm and has been used to process nearly 20,000 samples since April 2017. The open-source NGI pipelines hosted on GitHub have now been forked by hundreds of users for their own development. This collaborative expansion has proceeded rapidly and is now beginning to outgrow the NGI branding of the pipelines. To encourage further growth and greater collaboration, we started a new initiative called nf-core (http://nf-co.re): a community effort to collect, curate and collaborate on high quality nextflow bioinformatics workflows. Shared pipelines will give increased reproducibility between groups and greater collective development power. To help pipeline developers we have written a companion cookiecutter template to generate starter workflows and a command line tool to lint code and check for adherence to nf-core guidelines. Pipelines make the best use of Nextflow features possible, with support for conda, docker and singularity, with reference genomes available from the cloud. Consistency between pipelines means that all work in a similar manner with comparable requirements. There has been fantastic feedback from the user community about nf-core. The first twitter post in February 2018 was seen by nearly four thousand people and the account now has over 140 followers. There are currently seven pipelines available (at the time of writing) with many more on the way.
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nf-core: A community effort to collect curated Nextflow pipelines
- 1. A community effort to collect curated nextflow pipelines Phil Ewels SciLifeLab National Genomics Infrastructure phil.ewels@scilifelab.se
- 2. A long time ago in a institute far, far away....
- 7. Alex Peltzer Andreas Wilm
- 16. A D D I N G A P I P E L I N E
- 17. Nextflow MIT Docker CI Testing Stable releases Documentation Passing tests Bioconda* Responsible person G U I D E L I N E S
- 25. S Y N C H R O N I S AT I O N
- 26. initial commit, tools v1.3 Develop pipeline Some more coding..nf-core tools v1.4 Template v1.4 updates Template v1.5 updates nf-core tools v1.5 Sven Fillinger
- 30. Group review of first release TEMPLATE dev master
- 32. G E T T I N G I N V O LV E D
- 33. https://nf-co.re/ GITTER Hackathons! https://github.com/nf-core/ G E T T I N G I N V O LV E D Email list
- 34. Hackathons! G E T T I N G I N V O LV E D August 6-10 (2018) Stockholm November 22-23 (2018) Barcelona April 8-10 (2019) Tübingen
- 35. ngisweden.scilifelab.se opensource.scilifelab.se NGI Stockholm Maxime Garcia Johannes Alneberg Max Käller Remi-Andre Olsen Chuan Wang Denis Moreno Rickard Hammarén Senthil Panneerselvam QBiC Tübingen Sven Fillinger Alexander Peltzer GIS Singapore Andreas Wilm Chih Chuan CRG Barcelona Paolo Di Tommaso Phil Ewels phil.ewels@scilifelab.se ewels tallphil ngisweden Icons: flaticon.com nf-co.re
- 38. ngisweden.scilifelab.se opensource.scilifelab.se Phil Ewels phil.ewels@scilifelab.se ewels tallphil We're hiring! Systems / devops No biology background required ngisweden Icons: flaticon.com nf-co.re