8000 Important! Template update for nf-core/tools v2.13.1 by nf-core-bot · Pull Request #75 · nf-core/viralintegration · GitHub
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Important! Template update for nf-core/tools v2.13.1 #75

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Merged
merged 19 commits into from
Apr 26, 2024
Merged

Important! Template update for nf-core/tools v2.13.1 #75

merged 19 commits into from
Apr 26, 2024

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nf-core-bot
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Version 2.13.1 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-2.13.1 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 v2.13.1 release page.

@alyssa-ab alyssa-ab self-assigned this Mar 19, 2024
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github-actions bot commented Mar 21, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 693d359

+| ✅ 169 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗  10 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 main.nf: Remove this line if you don't need a FASTA file
  • pipeline_todos - TODO string in README.md: Add full-sized test dataset and amend the paragraph below if applicable
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • 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

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/nf-core-viralintegration_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-viralintegration_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-viralintegration_logo_dark.png

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-04-25 22:33:52

@edmundmiller
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I think this is related to nf-core/tools#2893

@alyssa-ab alyssa-ab requested a review from edmundmiller April 25, 2024 22:52
edmundmiller
edmundmiller approved these changes Apr 26, 2024
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@edmundmiller edmundmiller left a comment •
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Looks great! Quick merge it before another tools release happens!

@alyssa-ab alyssa-ab merged commit b51643c into dev Apr 26, 2024
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@alyssa-ab alyssa-ab deleted the nf-core-template-merge-2.13.1 branch April 26, 2024 16:01
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