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Add nf-test sharding CI #1668

Merged
merged 61 commits into from
Oct 28, 2024
Merged

Add nf-test sharding CI #1668

merged 61 commits into from
Oct 28, 2024

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edmundmiller
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  • ci: Copy over from methylseq
  • ci: Move Sarek specific settings to ci
  • ci: tap => xml

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/sarek 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).

@edmundmiller edmundmiller self-assigned this Oct 1, 2024
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github-actions bot commented Oct 1, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit f3b96aa

+| ✅ 215 tests passed       |+
#| ❔  11 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • 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 base.config: Check the defaults for all processes

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-10-28 10:13:18

@edmundmiller edmundmiller marked this pull request as ready for review October 2, 2024 13:53
@edmundmiller edmundmiller reopened this Oct 2, 2024
@maxulysse
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I guess now you'd have a couple of merge conflicts

maxulysse
maxulysse reviewed Oct 4, 2024
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maxulysse
maxulysse reviewed Oct 4, 2024
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maxulysse
maxulysse reviewed Oct 28, 2024
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@maxulysse maxulysse disabled auto-merge October 28, 2024 10:23
@maxulysse maxulysse merged commit b5fe848 into dev Oct 28, 2024
24 of 26 checks passed
@maxulysse maxulysse deleted the fresh-nf-test branch October 28, 2024 10:24
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@edmundmiller @maxulysse @FriederikeHanssen