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Updated samshee #240

Merged
merged 11 commits into from
Aug 12, 2024
Merged

Updated samshee #240

merged 11 commits into from
Aug 12, 2024
+50 −125

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nschcolnicov
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Addresses this:
#237

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/demultiplex 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).

@nschcolnicov nschcolnicov requested a review from a team as a code owner August 12, 2024 14:26
@nschcolnicov nschcolnicov requested review from matthdsm and removed request for a team August 12, 2024 14:26
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github-actions bot commented Aug 12, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit ec12969

+| ✅ 192 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   6 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
  • 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
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-08-12 19:55:57

apeltzer
apeltzer reviewed Aug 12, 2024
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apeltzer
apeltzer approved these changes Aug 12, 2024
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Looks good to me - some explanation as a comment for config

edmundmiller
edmundmiller approved these changes Aug 12, 2024
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Awesome, thanks for taking care of that so quickly!

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@apeltzer apeltzer added this to the 1.5.0 milestone Aug 12, 2024
@apeltzer apeltzer merged commit b25ae5f into dev Aug 12, 2024
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@apeltzer apeltzer deleted the samshee_improvements branch August 12, 2024 20:00
@apeltzer apeltzer mentioned this pull request Aug 12, 2024
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@apeltzer apeltzer apeltzer approved these changes

@edmundmiller edmundmiller edmundmiller approved these changes

@matthdsm matthdsm Awaiting requested review from matthdsm matthdsm is a code owner automatically assigned from nf-core/demultiplex

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@nschcolnicov @apeltzer @edmundmiller