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Fix Sentieon #1746

Merged
merged 5 commits into from
Dec 10, 2024
Merged

Fix Sentieon #1746

merged 5 commits into from
Dec 10, 2024
+414 −7

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FriederikeHanssen
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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).

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github-actions bot commented Dec 9, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 6ba3416

+| ✅ 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 2024-12-09 17:10:53

maxulysse
maxulysse reviewed Dec 9, 2024
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CHANGELOG.md Outdated Show resolved Hide resolved
@edmundmiller edmundmiller self-requested a review December 9, 2024 15:30
@edmundmiller
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Decided we're going to:

  • Run stubs for Sentieon for right now to make sure the channels work properly.
  • Fix the CI later ™️
  • For now, use Sentieon at your own risk; we'd love feedback if anything gets broken accidentally; Sentieon testing isn't a top priority.

edmundmiller
edmundmiller previously approved these changes Dec 9, 2024
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@edmundmiller edmundmiller left a comment

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Should be good to go now!

@edmundmiller edmundmiller mentioned this pull request Dec 9, 2024
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@FriederikeHanssen @maxulysse
Update CHANGELOG.md
6ba3416 
Co-authored-by: Maxime U Garcia <[email protected]>
@FriederikeHanssen FriederikeHanssen merged commit 427801f into nf-core:dev Dec 10, 2024
38 checks passed
@FriederikeHanssen FriederikeHanssen deleted the fixsentieon branch December 10, 2024 08:59
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@edmundmiller edmundmiller edmundmiller approved these changes

@maxulysse maxulysse Awaiting requested review from maxulysse maxulysse is a code owner

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@FriederikeHanssen FriederikeHanssen

@edmundmiller edmundmiller

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@FriederikeHanssen @edmundmiller @maxulysse