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2.12 - Aluminium Wolf
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@mashehu mashehu released this 29 Jan 14:42
· 804 commits to master since this release
2.12
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v2.12 - Aluminium Wolf - [2024-01-29]

Template

  • Add a Github Action Workflow to the pipeline template that tests a successful download with 'nf-core download' (#2618)
  • Use pre-commit to lint files in GitHub CI (#2635)
  • Use pdiff also on gitpod for nf-test (#2640)
  • switch to new image syntax in readme (#2645)
  • Add conda channel order to nextflow.config (#2094)
  • Fix tyop in pipeline nextflow.config (#2664)
  • Remove nfcore_external_java_deps.jar from lib directory in pipeline template (#2675)
  • Add function to check -profile is well formatted (#2678)
  • Add new pipeline error message pointing to docs when 'requirement exceeds available memory' error message (#2680)
  • add 👀👍🏻🎉😕 reactions to fix-linting-bot action (#2692)

Linting

  • Fix linting of a pipeline with patched custom module (#2669)
  • linting a pipeline also lints the installed subworkflows (#2677)
  • environment.yml name must be lowercase (#2676)
  • allow ignoring specific files when template_strings (#2686)
  • lint nextflow.config default values match the ones specified in nextflow_schema.json (#2684)

Modules

  • Fix empty json output for nf-core list local (#2668)

General

  • Run CI-pytests for nf-core tools on self-hosted runners (#2550)
  • Add Ruff linter and formatter replacing Black, isort and pyupgrade (#2620)
  • Set pdiff as nf-test differ in Docker image for Gitpod (#2642)
  • Fix Renovate Dockerfile updating issues (#2648 and #2651)
  • Add new subcommand nf-core tui, which launches a TUI (terminal user interface) to intuitively explore the command line flags, built using Trogon (#2655)
  • Add new subcommand: nf-core logo-create to output an nf-core logo for a pipeline (instead of going through the website) (#2662)
  • Handle api redirects from the old site (#2672)
  • Remove redundanct v in pipeline version for emails (#2667)
  • add function to check -profile is well formatted (#2678)
  • Update pre-commit hook astral-sh/ruff-pre-commit to v0.1.14 (#2674)
  • Update pre-commit hook pre-commit/mirrors-mypy to v1.8.0 (#2630)
  • Update mshick/add-pr-comment action to v2 (#2632)
  • update python image version in docker file (#2636)
  • Update actions/cache action to v4 (#2666)
  • Update peter-evans/create-or-update-comment action to v4 (#2683) and (#2695)
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