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Reproducible bioinformatics for everyone: Nextflow & nf-core
The document discusses the nf-core project, which provides a collection of reproducible bioinformatics analysis pipelines built using Nextflow. It includes community-driven guidelines, tools, and support for cloud computing with various platforms like Microsoft Azure and AWS. Key features highlighted are modular design, collaboration, and intuitive interfaces for managing workflows.
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Reproducible bioinformatics for everyone: Nextflow & nf-core
- 1. Phil Ewels phil@seqera.io Reproducible bioinformaticsfor everyone: Nextflow & nf-core
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- 13. A community e ff ortto collect a curated set of analysis pipelines built using Next fl ow. https://nf-co.re
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- 15. https://nf-co.re Develop with the community Usea common template Collaborate, don’t duplicate
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- 20. Documentation Slack workspace Hackathons Twitter updates Startertemplate Code guidelines Helper tools CI code linting and tests Stable pipelines Centralised con fi gs Download for o ffl ine use List and update pipelines
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- 23. Launch wizard nf-core launch--id 1637063024_d92e0f1632c2 nextflow run nf-core/rnaseq -params-file nf-params.json https://nf-co.re/launch
- 24. Running in thecloud Microsoft Azure
- 25. Running in thecloud https://github.com/nf-core/viralrecon
- 26. Running in thecloud https://nf-co.re/viralrecon
- 27. Running in thecloud https://nf-co.re/viralrecon
- 28. Next fl ow DSL2 Modular designgives clearer pipeline code Di ff erent pipelines can reuse tool wrappers and software images Proper unit testing of individual steps in each pipeline Library of tool wrappers makes building a new pipeline fast
- 29. Next fl ow DSL2 Update command fetcheslatest versions CI tests check that module fi les have not been edited Metadata fi le tracks git hash of modules repo Copies module fi les in to pipeline $ nf-core modules install fastqc $ nf-core modules list
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- 33. Intuitive launchpad interface Launch,manage, and monitor Share runs and work in teams Create cloud infrastructure with a click https://tower.nf
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