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Important! Template update for nf-core/tools v2.12 #66

Merged
merged 9 commits into from
Feb 2, 2024
Merged

Important! Template update for nf-core/tools v2.12 #66

merged 9 commits into from
Feb 2, 2024

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nf-core-bot
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Version 2.12 of nf-core/tools has just been released with updates to the nf-core template. This automated pull-request attempts to apply the relevant updates to this pipeline.

Please make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the nf-core-template-merge-2.12 branch (or your own fork, if you prefer). Once complete, make a new minor release of your pipeline.

For instructions on how to merge this PR, please see https://nf-co.re/docs/contributing/sync/.

For more information about this release of nf-core/tools, please see the v2.12 release page.

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github-actions bot commented Jan 30, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 42bb23c

+| ✅ 172 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

  • files_exist - File is ignored: conf/igenomes.config
  • files_unchanged - File ignored due to lint config: .gitattributes
  • files_unchanged - File ignored due to lint config: assets/nf-core-spatialtranscriptomics_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-spatialtranscriptomics_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-spatialtranscriptomics_logo_dark.png
  • actions_ci - actions_ci

✅ Tests passed:

Run details

  • nf-core/tools version 2.12.1
  • Run at 2024-02-02 13:34:32

@fasterius
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Since there was a lot of discussions related to the template update with possible incoming fixes, maybe we should wait with this one until the template is stable?

@fasterius fasterius merged commit 5682922 into dev Feb 2, 2024
6 checks passed
@fasterius fasterius deleted the nf-core-template-merge-2.12 branch February 2, 2024 13:42
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@nf-core-bot @fasterius @apeltzer