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Include lofreq and indexcov in AWS tests + update figure #1752

Merged
merged 4 commits into from
Dec 11, 2024
Merged

Include lofreq and indexcov in AWS tests + update figure #1752

merged 4 commits into from
Dec 11, 2024

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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).

FriederikeHanssen
FriederikeHanssen commented Dec 11, 2024
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github-actions bot commented Dec 11, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit c2fbec1

+| ✅ 214 tests passed       |+
#| ❔  11 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 3.5.0
  • 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 2024-12-11 08:28:13

@maxulysse maxulysse merged commit cd59770 into nf-core:dev Dec 11, 2024
37 checks passed
@FriederikeHanssen FriederikeHanssen deleted the fullsize branch December 11, 2024 09:20
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@maxulysse maxulysse maxulysse approved these changes

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@FriederikeHanssen @maxulysse