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Update dev-ratio with changes from dev branch #284

Merged
merged 23 commits into from
Aug 27, 2024
Merged

Update dev-ratio with changes from dev branch #284

merged 23 commits into from
Aug 27, 2024

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bjlang
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@bjlang bjlang commented Aug 27, 2024

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).

pinin4fjords and others added 23 commits May 24, 2024 09:20
@pinin4fjords
Fix pagination on samples tableee
dadf5db
@pinin4fjords
Update CHANGELOG.md
04635ef
@pinin4fjords
Fix CHANGELOG
8353e97
@pinin4fjords
Reset versions after release
2d1f602
@pinin4fjords
Fix linting
349273f
@pinin4fjords
Merge pull request #274 from nf-core/fix_pagination
5ddc8dd 
Fix pagination on samples table
@WackerO
bugfix for gprofiler without gene_sets
925527d
@WackerO
add comment, update changelog
ccb9aa4
@WackerO
simplified gene_sets logic
af2436f
@WackerO
Merge pull request #278 from WackerO/fix_gpro_genesets
2dce45a 
Fix gprofiler2 genesets default object
@pinin4fjords
bump_shinyngs
4c608da
@pinin4fjords
Wire in new shinyngs log options, remove deprecated guessing option
2ab83e7
@pinin4fjords
Fix contrast specification to app creation
57574cf
@pinin4fjords
Can install from master now
b7af68a
@pinin4fjords
Update CHANGELOG
8fb05ca
@pinin4fjords
Merge pull request #280 from nf-core/bump_shinyngs
03b7984 
Bump shinyngs, fix contrasts passed to app creation
Allow caching for -resume
b8221e3
Use recommended format for optional parameters
83b8fdc
Skip copying matrix if not necessary to allow resuming pipeline execu…
b719387 
…tion
Update CHANGELOG.md
0fbdcd6
Keep original matrix file name in the annotation copy to improve resu…
124f21e 
…mability
@bjlang @WackerO
Update CHANGELOG.md
0e6b4fc 
Co-authored-by: WackerO <[email protected]>
@WackerO
Merge pull request #282 from bjlang/dev
c44e6bc 
Dev
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github-actions bot commented Aug 27, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit c44e6bc

+| ✅ 299 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   4 tests had warnings |!
-| ❌   1 tests failed       |-

❌ Test failures:

  • schema_params - Default value for param tools invalid: Not in pipeline parameters. Check nextflow.config.

❗ 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!
  • schema_params - Schema param tools not found from nextflow config

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-08-27 12:26:27

@bjlang bjlang merged commit 5e5c6e4 into dev-ratio Aug 27, 2024
23 of 24 checks passed
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3 participants
@bjlang @pinin4fjords @WackerO