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v2.4 - Cobolt Koala

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@ewels ewels released this 16 May 10:14
2.4
f8de281
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Learn about vigilant mode.

This release started off as a patch release to fix some errors introduced in 2.3 (eg. pipeline email template errors). However, it slowly collected enough new features to warrant a proper minor release of its own.

Many thanks to everyone who contributed!

Full Changelog: 2.3.2...2.4

Template

  • ✨ Add actions workflow to respond to @nf-core-bot fix linting comments on pipeline PRs
  • Fix Prettier formatting bug in completion email HTML template (#1509)
  • Fix bug in pipeline readme logo URL
  • Set the default DAG graphic output to HTML to have a default that does not depend on Graphviz being installed on the host system (#1512).
  • Removed retry strategy for AWS tests CI, as Nextflow now handles spot instance retries itself
  • Add .prettierignore file to stop Prettier linting tests from running over test files
  • Made module template test command match the default used in nf-core modules create-test-yml (#1562)
  • Removed black background from Readme badges now that GitHub has a dark mode, added Tower launch badge.
  • Don't save md5sum for versions.yml when running nf-core modules create-test-yml (#1511)
  • Read entire lines when sniffing the samplesheet format (fix #1561)

General

  • ✨ Add actions workflow to respond to @nf-core-bot fix linting comments on nf-core/tools PRs
  • Use $XDG_CONFIG_HOME or ~/.config/nf-core instead of ~/.nfcore for API cache (the latter can be safely deleted)
  • Consolidate GitHub API calls into a shared function that uses authentication from the gh GitHub cli tool or GITHUB_AUTH_TOKEN to avoid rate limiting (#1499)
  • Add an empty line to modules.json, params.json and nextflow-schema.json when dumping them to avoid prettier errors.
  • Remove empty JSON schema definition groups to avoid usage errors (#1419)
  • Bumped the minimum version of rich from v10 to v10.7.0

Modules

  • ✨ Add a new command nf-core modules mulled which can generate the name for a multi-tool container image.
  • ✨ Add a new command nf-core modules test which runs pytests locally.
  • ✨ Print include statement to terminal when modules install (#1520)
  • Allow follow links when generating test.yml file with nf-core modules create-test-yml (1570)
  • Escaped test run output before logging it, to avoid a rich MarkupError

Linting

  • Don't allow a .nf-core.yaml file, should be .yml (#1515).
  • shell blocks now recognised to avoid error when: condition has too many lines (#1557)
  • Fixed error when using comments after input tuple lines (#1542)
  • Don't lint the shell block when script is used (1558)
  • Check that template is used in script blocks
  • Tweaks to CLI output display of lint results
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