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Add test suite for UMI handling functionality #1467

Merged
merged 7 commits into from
Dec 11, 2024
Merged

Add test suite for UMI handling functionality #1467

merged 7 commits into from
Dec 11, 2024

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pinin4fjords
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@pinin4fjords pinin4fjords commented Dec 10, 2024 •
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We don't currently have tests which exercise the UMI functionality. This does that, thought the test data don't actually have UMIs, so there's no meaning to the results.

I don't want to go further with #1466 until I know it doesn't break things, which means I need a baseline.

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/rnaseq branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines 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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This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @pinin4fjords,

It looks like this pull-request is has been made against the nf-core/rnaseq master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the nf-core/rnaseq dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

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github-actions bot commented Dec 10, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 52ba2d4

+| ✅ 188 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   8 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • 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
  • 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

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-12-11 18:16:07

@pinin4fjords pinin4fjords changed the base branch from master to dev December 11, 2024 18:12
@pinin4fjords pinin4fjords changed the title Test umi Add test suite for UMI handling functionality Dec 11, 2024
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Thanks @maxulysse !

@pinin4fjords pinin4fjords merged commit 631f0e3 into dev Dec 11, 2024
28 checks passed
@pinin4fjords pinin4fjords deleted the test_umi branch December 11, 2024 18:40
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@maxulysse maxulysse maxulysse approved these changes

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