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Fix logging by specifying assays to log #266

Merged
merged 11 commits into from
May 7, 2024
Merged

Fix logging by specifying assays to log #266

merged 11 commits into from
May 7, 2024

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pinin4fjords
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@pinin4fjords pinin4fjords commented Apr 30, 2024 •
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In this PR:

  • Move features_log2_assays to exploratory_log2_assays (it's not a setting relevant to feature annotation)

  • Specify assays to log where sensible, rather than guessing. For RNA-seq the raw and normalised matrices are unlogged when input to exploratory analysis, so should be sent for logging.

  • update shinyngs module to allow readable text specification of matrices to log.

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/differentialabundance 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>).
  • 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).

@pinin4fjords pinin4fjords marked this pull request as draft April 30, 2024 10:00
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github-actions bot commented Apr 30, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 9c1a6cf

+| ✅ 268 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 1.5.0
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • 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!

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-05-07 10:09:29

@pinin4fjords pinin4fjords marked this pull request as ready for review May 7, 2024 08:28
@pinin4fjords pinin4fjords changed the title [WIP] Fix logging Fix logging by specifying assays to log May 7, 2024
@pinin4fjords pinin4fjords requested a review from WackerO May 7, 2024 08:29
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Thanks @WackerO !

@pinin4fjords pinin4fjords merged commit 361fb75 into dev May 7, 2024
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@pinin4fjords pinin4fjords deleted the fix_logging branch May 7, 2024 15:14
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@WackerO WackerO WackerO approved these changes

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