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Clean up MultiQC and tests #171

Merged
merged 6 commits into from
Oct 21, 2024
Merged

Clean up MultiQC and tests #171

merged 6 commits into from
Oct 21, 2024

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edmundmiller
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@edmundmiller edmundmiller commented Oct 20, 2024 •
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  • chore: Use assertAll in all tests
  • fix(multiqc): Update groHMM plot fn
  • fix: Remove custom FastQC section
  • chore(multiqc): Copy RNA-seq report order
  • chore: Add test profile as default to nf-test

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/nascent 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 20, 2024
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github-actions bot commented Oct 20, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit a989636

+| ✅ 211 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • 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 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:

  • files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • actions_ci - actions_ci

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-10-20 19:55:47

@edmundmiller edmundmiller marked this pull request as ready for review October 21, 2024 03:47
@edmundmiller edmundmiller merged commit af25b3f into dev Oct 21, 2024
13 checks passed
@edmundmiller edmundmiller deleted the hot-fixes branch October 21, 2024 12:36
@edmundmiller edmundmiller added this to the 2.3.0 milestone Nov 26, 2024
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@maxulysse maxulysse maxulysse approved these changes

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