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Important! Template update for nf-core/tools v2.12 #563

Merged
merged 8 commits into from
Feb 1, 2024
Merged

Important! Template update for nf-core/tools v2.12 #563

merged 8 commits into from
Feb 1, 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 Feb 1, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 428a0d3

+| ✅ 211 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file [TODO: try and test using for --host_fasta and --host_genome]
  • 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 WorkflowMag.groovy: Optionally add in-text citation tools to this list.
  • schema_lint - Input mimetype is missing or empty

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.12.1
  • Run at 2024-02-01 20:00:17

@CarsonJM
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CarsonJM commented Feb 1, 2024

@nf-core-bot fix linting

@CarsonJM CarsonJM self-assigned this Feb 1, 2024
@jfy133
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jfy133 commented Feb 1, 2024

@CarsonJM the last linting error can be solved if you do the same as just did with eager :):

https://github.com/nf-core/eager/blob/2336c5b2dbce9fb45c7d5ba8d1c9bc4da6569457/.nf-core.yml#L3-L6

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jfy133 commented Feb 1, 2024

Sorry, did it myself as I want to get everything in before tomorrow afternoon's dev session so we can do the release together 😬

@jfy133 jfy133 merged commit 5a614d9 into dev Feb 1, 2024
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@jfy133 jfy133 deleted the nf-core-template-merge-2.12 branch February 5, 2024 14:52
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