3.3 - Update nf-core training to use topics for version channel

Content updates

• Hello nf-core (#896):
  • Updated course and rebuilt all solution files (Parts 2-5) for nf-core tools 3.5.2.
  • Added version capture section with topic channels to Part 4.
  • Removed shebangs from module file code snippets and fixed hl_lines in Part 4.
  • Fixed assorted typos and inconsistencies across Parts 2-4 docs.

Full Changelog: 3.2...3.3

3.2 Standardized 'Nextflow for Science' courses

Content updates

In this release, we mainly reworked the structure, instructions and formatting of the two main Nextflow for Science courses, Genomics and RNAseq, to be more consistent with each other. This will serve as the model for adding more 'For Science' courses going forward. The existing Imaging course will be updated to fit in the near future, and the draft Metagenomics course will be adapted as well.

• RNAseq and Genomics courses (#875):

  • Added workflow outputs and test profiles, improved solution file structure (now per-part with modules)
  • Added Excalidraw workflow/method diagrams
  • Standardized lesson structure across both courses
  • Replaced sample_bams.txt with samplesheet.csv in the Genomics course.
  • Minor fixes for Genomics (#868): Fixed final "what's next" paragraph, format errors, and updated the genomics survey.

• Hello Nextflow

  • Addressed DSL1 parser warning (#867): Added a warning admonition for the first time learners may encounter a v1 syntax parser error.
  • Bug fixes (#877/#880, #887): Fixed a bug reported in issue #877 and here along with additional minor issues.

• NF4Science course template

  • Added a reusable template for creating new NF4Science domain courses (#879).

• Side Quests

  • Typo fix in side quest metadata lesson (#883).

Translations

• Catalan translation (#882): Added a new Catalan (ca) translation of the training materials.
• Fixed truncated translations (#863): Completed 36 truncated translation files across 8 languages, fixed missing YAML
  frontmatter, and removed incorrect page layouts.
• Refactored translation scripts (#870): Reorganized translation scripts into a package with glossary-based post-processing
  for more consistent terminology.
• Translation fix mode (#864): Added a fix mode that scans all translation files for structural/semantic issues and
  re-translates broken ones, with post-translation verification and automatic retry.
• Fixed broken image links in translated files (#873).
• Routine translation updates (#869, #872, #881, #885).

New Contributors

• @dependabot[bot] made their first contribution in #876
• @b-brankovics made their first contribution in #883
• @ctuni made their first contribution in #882

Full Changelog: 3.1...3.2

3.1 Nextflow for Genomics update

Content Updates

This release features some important content updates that didn't quite make it into the 3.0 release, particularly in the Nextflow for Genomics course.

• Nextflow for Genomics: Major updates (#844)
  • Restructured the genomics course with a new methodology overview lesson
  • Streamlined per-sample and joint calling lessons to focus on Nextflow implementation
  • Removed the standalone modules lesson (we now start with modules right away)
  • Removed the testing lesson (superseded by nf-test Side Quest)
• Hello Nextflow
  • Minor content improvements to the Hello Nextflow course (#838).
  • Hello Config: use -output-dir throughout (#842): Refactored the Hello Config lesson to use the -output-dir CLI option exclusively instead of params.batch in outputDir, providing cleaner separation between base output path and subdirectory structure.
  • Updated Hello Nextflow videos (#856): Replaced video embeds with 2026 versions and added caption/language preference parameters to YouTube embeds.
  • Remove module shebangs (#841): Removed #!/usr/bin/env nextflow from module files (not needed in module .nf files, only in entry scripts).
• Assorted minor fixes
  • Fix Hello nf-core getting started link paths (#831)
  • Typo fix (#858): "our" was spelled "out"

Site and infrastructure

• Merged CI workflows (#819): Combined docs-dev and docs-release into a single docs.yml workflow.
• Fix cookie consent (#836): Cookie consent now works correctly across all versions and languages.
• Language dropdown UX (#825): Hover trigger changed from the entire list area to the navbar element only.
• Version picker (#835): Moved the dev version to the bottom of the dropdown.
• Quiz config (#834): Moved mkdocs-quiz CLI config to root-level config file.
• Security fix (#826): Updated tj-actions/changed-files to v47.0.1 (CVE-2025-30066).
• CI fixes (#828, #829, #818): Fixed ANSI codes in GitHub Actions output, clarified docs workflow, and fixed mkdocs build
  output path.

Translation system

Significant improvements to the automated translation pipeline:

• Parallel translation support (#851): Translations can now run concurrently.
• Improved consistency (#860): Set temperature=0 and added diff-aware updates for more deterministic translations.
• Reliability fixes (#821, #827, #832, #850, #862): Added retry logic, fixed race conditions, fixed truncation issues, fixed
  orphaned file deletion, and improved baseline detection.
• Observability (#823, #849, #853): Added verbose JSON logging, prompt change detection, and improved CI output.
• Polish translation examples (#847): Added examples of good writing style for Polish translations.
• Fix typo: "our" was spelled "out" (#858)
• Language translation fixes and updates

New Contributors

• @joshv2 made their first contribution in #858

Full Changelog: 3.0...3.1

3.0 Major refresh of the Nextflow training materials for strict v2 syntax + improved beginners' courses

Overall summary

This work represents a major refactor, modernization, and polish pass across the Nextflow training materials, with a strong focus on strict v2 syntax compatibility, pedagogical clarity, and documentation quality.

---

1. Migration to strict v2 syntax

• Enforced strict v2 syntax across all tutorials and solutions.
• Replaced legacy patterns (e.g. publishDir, implicit closures, function references in operators).
• Introduced workflow-level outputs (main: / output: blocks) in Hello Nextflow and Nextflow Run.
• Updated all examples, error messages, and console outputs to match NXF_SYNTAX_PARSER=v2 behavior.
• Bumped Nextflow versions and made v2 the default assumption in tutorials.

2. Major refresh of Hello Nextflow & Nextflow Run courses

• Significant refresh of Hello Nextflow:
  • Restructured Hello World and Hello Config
  • Earlier introduction of some key concepts (e.g. view()).
• Ensured all solution pipelines are stand-alone and consistent with lesson endpoints.
• Fixed many subtle issues uncovered during full walkthroughs (paths, params, syntax, outputs).

3. Documentation overhaul & UX improvements

• Streamlined homepage, help pages, course indexes, and navigation.
• Clarified learning objectives and assignments.
• Rehomed environment setup material under Help
• Improved blurbs, wording, and conceptual explanations throughout.
• Add many diagrams to aid in comprehension.
• Extensive formatting cleanup:
  • Admonitions, tabs, grid cards, columns, headings, code blocks.
  • Consistent styling and prettier compliance.
• Replaced placeholder outputs with real, tested command output where that was not yet the case.

4. Translations

• Added tooling for LLM-generated translations for multiple languages.
• Generated updated translations aided by existing materials where available.
• Documented process for future updates.

5. Tooling improvements

• Added scripts and checks to ensure compatibility and reproducibility.
• Improved Claude skills

6. Interactive learning enhancements

• Added interactive quizzes:
  • Hello Nextflow: 48 questions across 6 lessons.
  • Nextflow Run: 30 questions across 3 lessons.
• Integrated mkdocs-quiz into builds, CLI, and Codespaces.
• Added “Learn more” links to quiz feedback.

7. Cleanup, fixes, and polish

• Fixed broken links, malformed front matter, and formatting edge cases.
• Removed TODOs and deprecated content
• Improved consistency across courses (orientation, versioning, naming).

---

List of PRs

• Add Nextflow lint GitHub Actions workflow by @ewels in #739
• Improve the layout of the intro and outro materials for Side Quests by @vdauwera in #727
• Fix bug with linting results comments. by @ewels in #745
• Nextflow lint GHA workflow: check for formatting changes too by @ewels in #746
• Improvements to Side Quest: Working with Files by @vdauwera in #744
• Improvements to Side Quest: Metadata by @vdauwera in #748
• Fixes to Hello nf-core v. 1.1 by @vdauwera in #749
• Fix Docker API version mismatch in devcontainers by @pinin4fjords in #755
• Minor formatting fixes & consistency to side quests by @vdauwera in #754
• Add Claude guidance for correct hl_lines usage in code blocks by @pinin4fjords in #762
• Add run-tutorial and docker-setup Claude skills by @pinin4fjords in #768
• Add missing resource directives to essential scripting patterns solution by @pinin4fjords in #770
• Fix issues in debugging side quest by @pinin4fjords in #771
• Fix formatting issues in nf-test side quest by @pinin4fjords in #769
• Add writing style guidance to Claude configuration by @pinin4fjords in #774
• Refactor Claude skills for better delegation and reduced verbosity by @pinin4fjords in #783
• Feature branch for 3.0 update by @vdauwera in #757
• Standardize license on CC BY-NC-SA 4.0 by @ewels in #789
• Remove archived Fundamentals and Advanced training materials by @ewels in #790
• Update links to documentation in Hello and Run by @vdauwera in #806
• Multi-language AI translation support by @ewels in #793
• Fix mkdocs build output path in CI workflow by @ewels in #811
• Fix uv run command to use inline script dependencies by @ewels in #812
• Consolidate translation workflows and fix docs-dev checkout by @ewels in #813
• Adding a few new diagrams to explain channels better by @vdauwera in #810
• Fix snippets base_path to resolve SVG includes by @ewels in #817
• Rewrite translation scripts with cleaner architecture by @ewels in #816

Full Changelog: 2.8.1...3.0

2.8.1 Pin nf-core tooling

This patch release pins the nf-core tooling for stable content in 'hello nf-core'.

What's Changed

• Pin nf-core to 3.4.1 for training stability by @pinin4fjords in #726

Full Changelog: 2.8.0...2.8.1

2.8.0 Complete Hello nf-core v1 course

What's Changed

New and improved material

We're thrilled to release the completed version of the Hello nf-core course, which improves existing material and adds three new sections covering using an nf-core module(Part 3), making your own nf-core module (Part 4), and validating inputs and parameters (Part 5). This was a big effort by @pinin4fjords, assisted by @vdauwera, @FriederikeHanssen and @mribeirodantas in #672, #691 and #704.

We're also rolling out the first wave of some syntax updates to align with latest Nextflow guidance. This one is fairly trivial and consists of lowercasing Channel to channel everywhere. This was done by @robsyme and @mribeirodantas n #688, #686 and #702. If you see any remaining instances of Channel, please let us know by raising an issue or opening a pull request. FYI, the next wave of syntax updates will introduce workflow-level outputs, which will require more substantial changes.

Other changes

• Assorted fixes for issues reported by external folks by @vdauwera in #690
• Make it clearer where files will be generated by @mribeirodantas in #698
• Fixes map_demo.nf location according to training instructions by @mribeirodantas in #699
• Bump MQC container by @matthdsm in #687
• New survey for v1 of Hello nf-core by @vdauwera #707

Full Changelog: 2.7.0...2.8.0

New Contributors

• @matthdsm made their first contribution in #687

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

Full Changelog: 2.3.0...2.4.0

New Contributors

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