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

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@vdauwera vdauwera released this 03 Feb 11:21
· 30 commits to master since this release
3.0
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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

Contributors

ewels, vdauwera, and pinin4fjords
Assets 2
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