Welcome

We are excited to have you on the path to writing reproducible and scalable scientific workflows using Nextflow. This guide complements the full Nextflow documentation - if you ever have any doubts, please refer to that.

Objectives

By the end of this course you should:

1. Be proficient in writing Nextflow workflows
2. Know the basic Nextflow concepts of Channels, Processes and Operators
3. Have an understanding of containerized workflows
4. Understand the different execution platforms supported by Nextflow
5. Be introduced to the Nextflow community and ecosystem

Follow the training videos

We run a free online training event for this course approximately every six months. Videos are streamed to YouTube and questions are handled in the nf-core Slack community. You can watch the recording of the most recent training (September, 2023) in the YouTube playlist below:

If English is not your preferred language, you may find it useful to follow the training from the March 2023 event, which we ran in multiple languages. Please note that some parts of the training material may have been updated since this was recorded.

• English recording
• Hindi recording
• Spanish recording
• Portuguese recording
• French recording

Overview

To get you started with Nextflow as quickly as possible, we will walk through the following steps:

1. Set up a development environment to run Nextflow
2. Explore Nextflow concepts using some basic workflows, including a multi-step RNA-Seq analysis
3. Build and use Docker containers to encapsulate all workflow dependencies
4. Dive deeper into the core Nextflow syntax, including Channels, Processes, and Operators
5. Cover cluster and cloud deployment scenarios and explore Nextflow Tower capabilities

This will give you a broad understanding of Nextflow, to start writing your own workflows. We hope you enjoy the course! This is an ever-evolving document - feedback is always welcome.