Releases · nextflow-io/training

What's Changed

This release of the Nextflow training portal constitutes a major update to the training content and how it is organized.

Pared down and streamlined the Hello Nextflow course (v2)
Spun out the genomics material into a separate mini-course, Nextflow for Genomics
Added stubs/placeholders for upcoming material (Nextflow Run and Side Quests)
Consolidated experimental and/or unfinished content (related to nf-core and troubleshooting) into other/
Updated and streamlined the training index page to reflect all those changes

Read on for details of what you should care about most.

Hello Nextflow v2

Hello Nextflow is the beginners' training course we introduced in 2024 as a more goal-oriented and digestible alternative to the traditional Fundamentals Training course. After delivering the initial version of the Hello Nextflow training in a variety of settings, we collected key lessons learned and rebuilt the training to be even more accessible and more streamlined.

This new version of the course is now completely domain-agnostic (no more reliance on genomics examples) and fits into a single day's worth of training. It also provides a more step-by-step introduction to the use of channels and operators, which we hope will significantly smooth out the Nextflow learning curve.

The table of contents of Hello Nextflow v2 is as follows:

1. Hello World: Introduction to reading and running Nextflow
2. Hello Channels: Using channels and operators to handle inputs from different sources
3. Hello Workflow: Adding more steps and connecting processes
4. Hello Modules: Modularizing code to reuse processes between pipelines
5. Hello Containers: Using containers to manage software dependencies
6. Hello Config: Using configuration files to manage and adapt execution in different settings

Material that has been removed from Hello Nextflow

We made the decision to move some material elsewhere in order to keep the Hello Nextflow beginners' training tight and on-point. We are repurposing all of that material in some form as detailed below, though some of that work is still pending. All the original material is still accessible on the training portal under the 2.0.1 version tag if you need to use any of it in the meantime.

Hello-Genomics and Hello Operators
We spun these two out into a standalone mini-course called Nextflow for Genomics that aims to show how you'd apply the lessons from Hello Nextflow v2 to a genomics use case (variant calling with GATK). Currently that is a fairly direct port of the original material, but we plan to improve it and extend it in future by adding genomics-specific configuration and testing.
Hello nf-test
We are in the process of adapting this into a domain-agnostic standalone mini-course (which will be part of a collection called Side Quests). The genomics-specific parts will be repurposed for the expanded version of Nextflow for Genomics.
Hello nf-core and Hello Seqera
These two are going to be adapted into a mini-course called Nextflow Run, together with an abridged version of the beginner training for people who only want to run existing pipelines rather than develop their own Nextflow code. The Nextflow Run course will be modular, and there will be pointers for learners to pick up the nf-core and Seqera introductory materials after completing Hello Nextflow v2.

Future plans

In addition to the work in progress mentioned above, we are also developing a domain-specific mini-course similar to Nextflow for Genomics but for RNAseq, and we are considering doing the same for other scientific use cases. They will all be collected under Nextflow for Science.

Here is an overview of how we envision this all fitting together:

Pull requests involved

fix path to logo by @maxulysse in #509
New multi-course structure for training materials by @vdauwera in #486

Full Changelog: 2.0.1...2.1

Highlight

The main change in this release is a switch from GitPod to GitHub Codespaces. This is needed as GitPod Classic is soon to be retired, and GitPod Flex requires a non-zero amount of setup which doesn't always fit well with our training scenarios.

This is likely to be the last release before the major revamp of the training materials.

What's Changed