Nextflow Training¶
Welcome to the Nextflow community training portal!
We have several distinct training courses available on this website. Scroll down to find the one that's right for you!
The training courses listed below are designed to be useable as a self-service resource; you can work through them on your own at any time (see Environment Setup for practical details). However, you may get even more out of them by joining a group training event.
- Free online events are run regularly by the nf-core community, see the nf-core events page for more.
- Seqera (the company that develops Nextflow) runs a variety of training events, see the Seqera Events page and look for 'Seqera Sessions' and 'Nextflow Summit'.
- Our Community team also regularly teaches trainings hosted by third party organizations; announcements and signups for those are typically managed by the third-party hosts.
When you're ready to get down to work, click on the 'Open in Gitpod' button, either on this page or on the index page of the course you chose, to open a web-based training environment (requires a free GitHub account).
Training Environment Setup¶
Environment Setup
Essential for setting up your environment for the first time.
Instructions for setting up your environment to work through training materials (all courses). Provides an orientation to Gitpod as well as alternate installation instructions for working on your own local machine.
Nextflow for Newcomers¶
Hello Nextflow
A modular training series for getting started with Nextflow.
This is a foundational course for those who are completely new to Nextflow. It consists of a series of training modules that are designed to help learners build up their skills progressively. The series covers the core components of the Nextflow language as well as essential pipeline design and development practices, and effective use of third-party resources.
In-depth Nextflow Training¶
Fundamentals Training
Comprehensive training material for exploring the full scope of Nextflow's capabilities.
The fundamentals training material covers all things Nextflow. Excellent reference material for anyone looking to build complex workflows with Nextflow.
Advanced Training
Advanced training material for mastering Nextflow.
Advanced material exploring the more advanced features of the Nextflow language and runtime, and how to use them to write efficient and scalable data-intensive workflows.
Other/Experimental¶
Configure the execution of an nf-core pipeline
This course will help you to understand how to customize the execution of an nf-core pipeline.
A "learn by doing" tutorial focusing on the configuration of nf-core pipelines.
Develop a pipeline with the nf-core template
This course will help you to understand the structure of the nf-core pipeline template.
A "learn by doing" pipeline development tutorial focusing on developing a pipeline with the nf-core template.
Troubleshooting exercises
This course will help you troubleshooting common pipeline errors.
A "learn by doing" troubleshooting tutorial for pipeline developers and users.
Deprecated¶
Simple RNA-seq variant calling
A short hands-on tutorial focused on a concrete analysis pipeline example.
This course was developed as a "learn by doing" tutorial intended as a fast, hands-on way to get to grips with Nextflow using a very concrete analysis pipeline example. You can still find the materials in the GitHub repository, but it is no longer being maintained and can no longer be launched in Gitpod or in the training portal.
Resources¶
Quick reference to some handy links:
| Reference | Community |
|---|---|
| Nextflow Docs | Nextflow Slack |
| Nextflow Homepage | nf-core |
| Seqera | Seqera Community Forum |
Not sure where to go? Check out the Getting help page.
Credits and contributions¶
This training material is developed and maintained by Seqera and released under an open-source license (CC BY-NC-ND) for the benefit of the community. You are welcome to reuse these materials according to the terms of the license. If you are an instructor running your own trainings, we'd love to hear about how it goes and what we could do to make it easier.
We welcome fixes and improvements from the community. Every page has a icon in the top right of the page, which will take you to GitHub where you can propose changes to the training source material via a pull request.
