Reproducible research with Nextflow & building pipelines with nf-core
I was invited to give a one-day training event at the University of Oslo, as part of the Oslo Bioinformatics Week 2023. I led the workshop, with support from Maxime Garcia.
Abstract
As bioinformatics data grows ever larger, workflow managers are needed to handle automated workflows. They are able to dynamically launch and manage the chaining of numerous bioinformatics tools for hundreds of samples. Of these, Nextflow (https://nextflow.io) has gained a large community and has become the industry standard for research groups and facilities. The nf-core community (https://nf-co.re) has grown around Nextflow and provides a meeting point for people to collaborate on pipelines and components. In the morning of this workshop, we will introduce Nextflow - the concepts and language it uses and an overview of how pipelines are constructed. In the afternoon we will introduce nf-core, showing how to use community pipelines and how to develop new pipelines using nf-core shared components.
Learning outcomes
- Understand the basics of how Nextflow works
- Be able to write simple workflows from scratch
- Find and launch nf-core pipelines
- Create simple pipelines using nf-core tooling
