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Bump shinyngs, fix contrasts passed to app creation #280

Merged
merged 5 commits into from
Jun 25, 2024
Merged

Bump shinyngs, fix contrasts passed to app creation #280

merged 5 commits into from
Jun 25, 2024

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pinin4fjords
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This PR fixes two problems:

  • Earlier work to tie in the log2_assays parameter impacted on the exploratory plotting script, but not the app building. This led to incorrect logging of matrices in the app. The PR passes the parameter to shinyngs, which had to be updated to pass the argument correctly internally. This replaces previous 'guessing' functionality related to log status, in line with previous work on the exploratory script.
  • 'Higher in' messages underneath differential plots were broken in the app, because contrasts were being passed to app creation incorrectly. We just needed to remove the first id part of the contrast passes around internal to differentialabundance.

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 (nf-test test main.nf.test -profile test,docker).
  • 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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github-actions bot commented Jun 25, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 8fb05ca

+| ✅ 294 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

  • 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 2.14.1
  • Run at 2024-06-25 14:39:34

@pinin4fjords pinin4fjords changed the title Bump shinyngs Bump shinyngs, fix contrasts passed to app creation Jun 25, 2024
WackerO
WackerO approved these changes Jun 25, 2024
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LGTM

@pinin4fjords
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Thanks @WackerO !

@pinin4fjords pinin4fjords merged commit 03b7984 into dev Jun 25, 2024
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@pinin4fjords pinin4fjords deleted the bump_shinyngs branch June 25, 2024 14:47
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@WackerO WackerO WackerO approved these changes

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@pinin4fjords @WackerO