Reproducible bioinformatics for everyone: Nextflow & nf-core
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Slides from my talk at the Karolinska Institute in Huddinge (Stockholm, Sweden). June 2022. General introduction to Nextflow and nf-core, covering what they are and why you should use them!
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Reproducible bioinformatics for everyone: Nextflow & nf-core
- 1. Phil Ewels phil@seqera.io Reproducible bioinformatics for everyone: Nextflow & nf-core
- 3. Language
- 13. A community e ff ort to collect a curated set of analysis pipelines built using Next fl ow. https://nf-co.re
- 15. https://nf-co.re Develop with the community Use a common template Collaborate, don’t duplicate
- 20. Documentation Slack workspace Hackathons Twitter updates Starter template 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
- 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 the cloud Microsoft Azure
- 25. Running in the cloud https://github.com/nf-core/viralrecon
- 26. Running in the cloud https://nf-co.re/viralrecon
- 27. Running in the cloud https://nf-co.re/viralrecon
- 28. Next fl ow DSL2 Modular design gives 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 fetches latest 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
- 30. Next fl ow DSL2
- 31. Next fl ow DSL2
- 33. Intuitive launchpad interface Launch, manage, and monitor Share runs and work in teams Create cloud infrastructure with a click https://tower.nf