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Bump nf-core from 2.1 to 2.14.1 #89

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@dependabot dependabot bot commented on behalf of github Jun 3, 2024

Bumps nf-core from 2.1 to 2.14.1.

Release notes

Sourced from nf-core's releases.

v2.14.1 - Tantalum Toad - Patch

This is a patch release to fix a broken CI action.

Template

  • Don't cache pip in linting.yml (#2961)

General

  • Fix update github action for components in pipeline template (#2968)
  • Run sync after release on self hosted runners (#2970)

v2.14.0 - Tantalum Toad

This release contains some template changes and nf-core/tools updates.

🌟 Highlights 🌟

nf-core/tools functionalities

  • We included a new linting test to ensure that nf-test snapshots contain the versions.yml file.
  • Components (modules and subworkflows) can now handle more possible git URLs (ssh:// and ftp://).
  • The nf-core download command has a new argument --tag, which allows adding additional tags to select particular revisions in the Seqera Platform interface. For example, --tag "3.10=validated"{:bash} would allow you to quickly select the validated version of the pipeline.

Pipeline template

  • We updated the GitHub Action which tests that the pipeline can be downloaded correctly (download_pipeline.yml)
  • We removed pyproject.toml from the template.
  • Pipeline-specific institutional configs support is now activated for all pipelines by default.
  • The .nf-core.yml file contains now the version of the pipeline template.

Changelog

Template

  • Remove fasta default from nextflow.config (#2828)
  • Update templates to use nf-core/setup-nextflow v2 (#2818)
  • Link to troubleshooting docs when pipeline fails (#2845)
  • Add fallback to download_pipeline.yml in case the pipeline does not support stub runs (#2846)
  • Set topic variable correctly in the mastodon announcement (#2848)
  • Add a cleanup action to download_pipeline.yml to fix failures caused by inadequate storage space on the runner (#2849)
  • Update python to 3.12 (#2805)
  • Remove pyproject.toml from template root
  • Shorten lines in pipeline template (#2908)
  • Add a new hidden --pipelines_testdata_base_path parameter to more easily switch locations of test data in test configs (#2931)[https://redirect.github.com/Adds test data base path to classic test configs for more easily switching between test data location nf-core/tools#2931]
  • Permanently activated pipeline-specific institutional configs support for all pipelines without need for manual intervention (#2936)
  • Template config: conda.channels, not channels (#2950)
  • Handles multiple DOIs + doi.org resolver from manifest.doi (#2946)
  • Update included components (#2949)
  • Update .editorconfig (#2953)

... (truncated)

Changelog

Sourced from nf-core's changelog.

Commits
  • 930ece5 Merge pull request #2971 from nf-core/dev
  • 1b7612c Update CHANGELOG.md
  • 2d8aa3b Merge pull request #2970 from mashehu/run-release-on-self-hosted
  • 1d147cc check first for release trigger
  • 1fecdc4 Generate new screengrabs with rich-codex
  • 39ce3e7 update changelog
  • c2ae96e run sync on self-hosted runners on release
  • 53c77dd Generate new screengrabs with rich-codex
  • c33f80e Merge pull request #2968 from mashehu/fix-modules-update-action
  • c76aa80 Merge branch 'dev' into fix-modules-update-action
  • Additional commits viewable in compare view

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Note
Automatic rebases have been disabled on this pull request as it has been open for over 30 days.

Bumps [nf-core](https://github.com/nf-core/tools) from 2.1 to 2.14.1.
- [Release notes](https://github.com/nf-core/tools/releases)
- [Changelog](https://github.com/nf-core/tools/blob/master/CHANGELOG.md)
- [Commits](nf-core/tools@2.1...2.14.1)

---
updated-dependencies:
- dependency-name: nf-core
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>
@dependabot dependabot bot added dependencies Pull requests that update a dependency file python Pull requests that update Python code labels Jun 3, 2024
@dependabot dependabot bot mentioned this pull request Jun 3, 2024
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