Releases: nextflow-io/training
2.3.0
What's Changed
We have two new side quests out!
New training material:
- Development Environment: An introduction to the development environment with a walkthrough of the Nextflow VS Code extension and language server in #632
- Debugging Guide: Helping you debug and resolve issues in your Nextflow pipeline in #639
Both authored by @pinin4fjords
Other changes
- Advanced training has now been updated to use more modern syntax and not raise as many issues with the current language server @adamrtalbot in #641
- Posthog has been added to the training site by @mavi-sqr for better analytics in #640
Full Changelog: 2.2.1...2.3.0
New Contributors
Contributors
Assets 2
2.2.1
What's Changed
We have a new short course out!
New training material: Nextflow Run
This is an abridged version of Hello Nextflow that is focused on learning to run rather than develop pipelines. So it's mostly the same core material, but pared down, streamlined and in some places, reordered to fit the purpose. It's meant to take a half-day to teach in-person. We'll be testing that hypothesis at ISMB!
- Part 1: Run basic operations (Hello World level)
- Part 2: Run pipelines (channels for multiple inputs, multi-step example, modules, containers)
- Part 3: Configuration
Authored by @vdauwera with assistance from @kenibrewer and @mribeirodantas
Other changes
- Address #491 - Selecting a Nextflow version and Environment variables by @KristinaGagalova in #627
Full Changelog: 2.2...2.2.1
New Contributors
- @KristinaGagalova made their first contribution in #627
Contributors
Assets 2
2.2
What's Changed
We have a fairly big update for you this week! The top three highlights are: updated Nextflow version, new "Hello nf-core" mini-course, and transcripts now available for the Hello Nextflow video.
Updated Nextflow version
We've bumped the version of Nextflow that is loaded by default in the training environment to the latest stable version (25.04.3). This fixes an issue that affected using conda environments. There may be some minor (mostly cosmetic) changes in the outputs of exercises, but we don't expect anything to break. If you notice something broken please open an issue to let us know.
New beginner course: Hello nf-core
There's a big jump between plain Nextflow and how nf-core pipelines are engineered. We're introducing a new Hello nf-core mini-course that picks up from the end of Hello Nextflow and shows 1) how to run nf-core pipelines and 2) how to turn a plain Nextflow pipeline into an nf-core-style one.
We have plans to expand this course further in the coming months.
Transcripts for Hello Nextflow videos
The Hello Nextflow videos already had subtitles for accessibility; now we've added the full transcripts, both as web pages on the portal and as text files in the code repository.
Header numbering validation
We've had issues with incorrect header numbers, so Phil @ewels added a validation script that checks the numbering of headers. If you contribute content changes to the repository and you have errors in the header numbers, this will show up as failing tests on your branch. See the documentation about the new validation to understand how it works; if you have trouble fixing these, don't hesitate to reach out and we will help you.
Other changes
- Update French translation for the home page by @vdauwera in #622
- Small fixes to outputs by @mribeirodantas in #620
- Minor link fixes by @vdauwera in #621
- Fix buildx error when image contains attestation manifest by @mribeirodantas in #623
Full Changelog: 2.1.7...2.1.8
Contributors
Assets 2
2.1.7
What's Changed
We had a breaking issue that caused the wrong version of Java to be installed in the training environment. Fixed by @kenibrewer in #609: Install devcontainer tools natively instead of using conda.
Minor Fixes
- Update Copyright years by @mribeirodantas in #608
- Small corrections to Hello_channels text by @maxulysse in #607
Full Changelog: 2.1.6...2.1.7
Contributors
Assets 2
2.1.6
What's Changed
This release introduces a new Side Quest, a Korean translation for the Home and Setup pages of the training portal, and an update to the training environment container.
New Side Quest: Splitting and grouping
Adam Talbot (@adamrtalbot) from the Seqera Scientific Development team has written a new Side Quest that demonstrates how to split and group data using Nextflow's powerful channel operators. It all starts with a samplesheet containing information about different samples and their associated data, and shows you how to manipulate and combine data streams effectively, making your workflows more efficient and easier to understand.
You can check it out here.
Korean translation of Hello Nextflow
Big thanks to @JaeungJayJang for translating the Home and Environment Setup pages of the training portal into Korean, and their colleague @epark35 for reviewing! You can check it out at https://training.nextflow.io/latest/ko/.
General note: If you're interested in contributing translated material in your own langugage, please see the Translation contribution guidelines.
Local devcontainers (take 2)
Jon Manning (@pinin4fjords) from the Seqera Scientific Development team Local updated the devcontainer configuration to make the training environment usable locally (eg on your laptop). This involved making the host file paths valid within the container to appease docker-outside-docker.
Other changes
- Fix for small inconsequential typos by @FriederikeHanssen in #602
- Add tls client environment variable by @FriederikeHanssen in #603
- Post training tweaks by @pinin4fjords in #604
- Clarifications in hello_nextflow docs by @amasplund in #592
- Consistency with using symlink mode by @FriederikeHanssen in #605
Full Changelog: 2.1.5...2.1.6
New Contributors
- @JaeungJayJang made their first contribution in #578
- @amasplund made their first contribution in #592
Contributors
Assets 2
2.1.5
What's Changed
This week's release introduces a new formatting/layout for how we display exercise code, an Italian translation for Hello Nextflow, plus assorted minor fixes.
Exercise code display
We've adopted new Markdown syntax for rendering code snippets that show a before/after state, using a combination of tabs and line highlights. You can see this in action on point 1.1 of the Hello Channels page, for example. Big thanks to @mribeirodantas for going through all of Hello Nextflow to update the exercises. We may still have instances of the old syntax in other materials; feel free to submit a pull request to update those if you see any.
Italian translation of Hello Nextflow
Huge thanks to Margherita Mutarelli (@daisymut) and her students who produced a complete translation of the Hello Nextflow course during the March 2025 nf-core hackathon! You can check it out at https://training.nextflow.io/latest/it/hello_nextflow/
Students who contributed: @Antonio8910, @YuriMar03, @Sara1-ga, @enrica2206, @antofranza, @elenasottile01, @giadabelof, @SaraPappacena, @annapaolagr, @ianniellomaria, @Amelia2505, @elisa270401, @MaraStanco, @RossellaCozzolino.
General note: If you're interested in contributing translated material in your own langugage, please see the Translation contribution guidelines.
Other changes
- Some small fixes to the nf-core introduction by @tinytyranid in #576
- Fixup numbering in WoW by @adamrtalbot in #594
- Fix/java config by @pinin4fjords in #600
Full Changelog: 2.1.4...2.1.5
New Contributors
- @tinytyranid made their first contribution in #576
- @YuriMar03 made their first contribution in #590
Contributors
Assets 2
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
Contributors
Assets 2
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
Contributors
Assets 2
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
Contributors
Assets 2
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 undernf4_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 underside_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
