2.1.4

What's Changed

This week's release is purely technical, no new material.

Streamlined container image

We ran into some issues that were due to the container image being too large. People using the Github Codespace who picked a VM with less than 8 cores (which come with smaller disk too) were getting 'recovery mode' errors about Nextflow not being installed and were unable to do the training.

To address this, @ewels and the Seqera Sci Dev team changed the base image and did some additional pruning to get the container image down to a smaller size. As a bonus, this should also speed up the loading process as well.

Other changes

• Minor fixes to header numbering in Hello Nextflow by @juanesarango
• Tweaks to the default colors to improve readability by @ewels
• A few other deployment-related updates by @ewels:
  • Only rebuild the container image on PRs if the devcontainer config has changed
  • Deploy the master branch as a 'dev' version of the materials (where changes are accumulated pending a release)

Full Changelog: 2.1.3...2.1.4

New Contributors

• @juanesarango made their first contribution in #564

2.1.3

What's Changed

Another week, another new mini-course!

New training material

This week the MVP of the training squad is @FriederikeHanssen with a port of the introduction to nf-core previously featured in Hello Nextflow, now located under Side Quests.

Other changes

• Various small errors issues were patched by @mashehu and @rmzelle.
• Minor updates to navigation, Side Quests index and orientation pages by @vdauwera

Full Changelog: 2.1.2...2.1.3

New Contributors

• @mashehu made their first contribution in #559

2.1.2

What's Changed

Another week, another release, and this one is a beauty.

Walkthrough videos for Hello Nextflow

Phil @ewels put in a huge effort to record videos that walk you through the entire Hello Nextflow course, which are now embedded into each of the pages of the course. The full set of videos is also available as a YouTube playlist.

Graphics credit to Luis Loulé from the Design team at Seqera.

New training material

We also have a few notable updates and additions to the training courses themselves:

• Nextflow for Genomics: Two sections covering modules and testing with nf-test by @pinin4fjords
• Workflow of workflows: New side-quest on composing complex workflows by @pinin4fjords

Note that "Side Quest: nf-test" has been renamed to "Testing with nf-test".

Other changes

• Various small errors and cosmetic issues were patched by @ewels, @pinin4fjords, @kenibrewer, @vdauwera, @rmzelle and others who contributed issue reports.
• On the infrastructure side, @ewels cleaned up the Devcontainers setup to speed up loading Github Codespaces a little and get rid of some legacy stuff from the Gitpod days.

Full Changelog: 2.1.1...2.1.2

New Contributors

• @rmzelle made their first contribution in #548

2.1.1

What's Changed

We're delighted to have two new training mini-courses make their debut in this release:

• Nextflow for RNAseq (aka NF4 RNAseq) by @vdauwera
  Located under nf4_science/rnaseq, this is a brand new domain-specific mini-course that aims to demonstrate how to apply the learnings from Hello Nextflow to an RNAseq processing use case.
• Side Quest: nf-test by @pinin4fjords and @adamrtalbot
  Located under side_quests, this is our very first Side Quest, a deep dive into using nf-test, repurposed and much improved from the Hello nf-test that was originally included in Hello Nextflow v1 (written by @vdauwera and @sateeshperi).

In addition to these brand new materials, this release provides a slew of improvements and fixes to minor errors in Hello Nextflow v2 contributed by @mribeirodantas, @kenibrewer, @ewels, @maxulysse, @axbazin, and @Desk3505, as well as improvements to the devcontainer setup by @pinin4fjords.

Full Changelog: 2.1...2.1.1

New Contributors

• @axbazin made their first contribution in #525
• @Desk3505 made their first contribution in #528

2.1

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

• New multi-course structure for training materials by @vdauwera in #486 with contributions from @robsyme @adamrtalbot @ewels @kenibrewer @mribeirodantas @maxulysse
• fix path to logo by @maxulysse in #509

Full Changelog: 2.0.1...2.1

Nextflow Training: v2.0.1

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

• Add GitHub action to publish new docs on GitHub Release by @ewels in #498
• 💚 ci(pre-commit): replace prettier workflow with pre-commit by @kenibrewer in #501
• Add deprecation warning for when clause by @mribeirodantas in #503
• Fix typos in orientation by @maxulysse in #505
• Point workspaceFolder to /workspaces/training/hello-nextflow/ by @maxulysse in #500
• Goodbye GitPod, hello GitHub Codespaces by @ewels in #507

Full Changelog: 2.0...2.0.1

Nextflow Training: v2.0

Rebooting proper versioning of training materials.

This v2.0 release simply marks the start of the new versioning system. Future releases will contain release notes explaining what has changed.

Final Asciidocs

Last history point of the training material before conversion to markdown.

Nextflow version 22.09.7

An updated nextflow version 22.09.7.
This will become the default version

DSL 1 - final release

The final release of DSL1 training