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@mirpedrol mirpedrol released this 20 Feb 15:26
2.13
b51c7d8
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v2.13 - Tin Puppy - [2024-02-20]

Highlights 🌟

This new version of nf-core/tools includes a refactoring of the pipelines template.

  • The lib directory is removed: 👋 Groovy code
  • We now use nf-core subworkflows for pipeline initialisation (replacing the code from the lib directory)
  • The nf-validation plugin is now used to create an input channel from a sample sheet file.

Check the nf-core blog post for more information!

Template

  • Add empty line in README.md to fix badges. (#2729)
  • Replace automatic branch detection in nf-core download CI test with hardcoded dev and input. (#2727)
  • Add Github Action to automatically cleanup ubuntu-latest runners to fix runner running out of diskspace errors(#2755)
  • Fix GitHub Actions CI and Linting badges links (#2757)
  • Add hashtags to release announcement on mastodon (#2761)
  • update fastqc and multiqc in template (#2776)
  • template refactoring: remove the lib directory and use nf-core subworkflows (#2736)
  • use nf-validation to create an input channel from a sample sheet (#2736)

Linting

  • Make creat-lint-wf composable (#2733)
  • Add looser comparison when pipeline logos (#2744)
  • Handle multiple aliases in module imports correctly during linting (#2762)
  • Switch to markdown based API and error docs (#2758)

Modules

  • Handle dirty local module repos by force checkout of commits and branches if needed (#2734)
  • Patch: handle file not found when it is an added file to a module (#2771)
  • Handle symlinks when migrating pytest (#2770)
  • Add --profile parameter to nf-test command (#2767)

General

  • fix ignoring changes in partially templated files (e.g. .gitignore) (#2722)
  • update ruff to 0.2.0 and add it to pre-commit step (#2725)
  • Update codecov/codecov-action digest to e0b68c6 (#2728)
  • Update pre-commit hook astral-sh/ruff-pre-commit to v0.2.1 (#2730)
  • Update python:3.11-slim Docker digest to 2a746e2 (#2743)
  • Update actions/setup-python action to v5 (#2739)
  • Update gitpod/workspace-base Docker digest to 45e7617 (#2747)
  • chore(deps): pin jlumbroso/free-disk-space action to 54081f1 (#2756)
  • chore(deps): update actions/github-script action to v7 (#2766)
  • chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.2.2 (#2769)
  • Update gitpod/workspace-base Docker digest to 728e1fa (#2780)
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