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Fix that tests are not executed #359

Merged
merged 7 commits into from
Aug 13, 2024
Merged

Fix that tests are not executed #359

merged 7 commits into from
Aug 13, 2024

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grst
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@grst grst commented Aug 13, 2024

Close #358

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/scrnaseq branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented Aug 13, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b1ef5bb

+| ✅ 203 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 2.7.1
  • 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!

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-08-13 14:20:23

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grst commented Aug 13, 2024

as per https://nfcore.slack.com/archives/C043FMKUNLB/p1723553194038819?thread_ts=1723552236.056539&cid=C043FMKUNLB,
the issue with monochromeLogs is not yet fixed, therefore reverting the corresponding commit in #354

@grst grst marked this pull request as ready for review August 13, 2024 13:41
@grst grst requested a review from adamrtalbot August 13, 2024 14:00
@grst grst enabled auto-merge August 13, 2024 14:12
adamrtalbot
adamrtalbot reviewed Aug 13, 2024
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@grst @adamrtalbot
Update CHANGELOG.md
b1ef5bb 
Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
@grst grst merged commit 4f7a09b into dev Aug 13, 2024
13 checks passed
@grst grst deleted the fix-nf-test branch August 13, 2024 14:32
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