2.7.0 Nextflow for Bioimaging

What's Changed

• De-emphasize metadata basics and fix errors in splitting_and_grouping by @pinin4fjords in #678
• Add Python 3.13 to devcontainer to support latest nf-core tools by @pinin4fjords in #683
• Add Claude configuration for training materials development by @pinin4fjords in #681
• Add survey and next steps to Nextflow Run by @vdauwera in #684
• Feat/nextflow run for bioimaging by @kenibrewer in #680

Full Changelog: 2.6.0...2.7.0

2.6.0

What's Changed

• refactor(docs): rename ide_features.md to dev_environment.md and simplify heading by @adamrtalbot in #645
• Add Scripting essentials module by @pinin4fjords in #652

Full Changelog: 2.5.0...2.6.0

2.5.0

What's Changed

• Remove duplicate nf-test in sidebar by @ewels in #669
• Fix broken links in homepage to archived material by @pinin4fjords in #670
• Fixes link to point to training_collections/ by @mribeirodantas in #671
• Tighten up the debugging module by @pinin4fjords in #675

Full Changelog: 2.4.0...2.5.0

2.4.0

What's Changed

New and re-organised material

The big thing in this release is a re-organisation and augmentation of our existing materials around splitting/ grouping patterns, as well as file handling. You'll see new side quests for Metadata and File handling (Work by @adamrtalbot @FriederikeHanssen @pinin4fjords in #644, #651, #654, #665).

We've also introduced a new concept of 'training collections', allowing us to arrange our growing bank of side quests into mini-courses pitched at different scenarios/ audiences, and moved some of our older content into a new 'archive' section (work by @pinin4fjords , @vdauwera in #657, #664). To support that more agile use of content we've also started recording approximately how long modules take to deliver as training (#647), which we hope will be useful for Nextflow trainers everywhere.

Other changes

• Use getGroupTarget to upwrap groupKey instead of converting to Map. by @robsyme in #649
• Updating old forms by @mavi-sqr in #656
• Fix typo in nextflow_run/01_basics.md by @mihaitodor in #655
• Minor edit: add tree depth limit to match output in material by @pontushojer in #630

New Contributors

• @mihaitodor made their first contribution in #655
• @pontushojer made their first contribution in #630

Full Changelog: 2.3.0...2.4.0

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

• @mavi-sqr made their first contribution in #640

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

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

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

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

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