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GSEA- pngs and htmls in same place #265

Merged
merged 5 commits into from
Apr 30, 2024
Merged

GSEA- pngs and htmls in same place #265

merged 5 commits into from
Apr 30, 2024

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pinin4fjords
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Placing HTMLs and PNGs for HTML in different directories is tidy, but breaks links to images used by the HTML. Publish to the same directory instead.

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).

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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 9f3ddd4

+| ✅ 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 2024-04-30 10:33:45

WackerO
WackerO previously approved these changes Apr 30, 2024
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LGTM

@WackerO
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WackerO commented Apr 30, 2024

Actually, I find that the tables don't work either. I think it might be necessary to save all the relevant files into the HTML folder to make it work...

@WackerO WackerO dismissed their stale review April 30, 2024 09:33

See comment about tables

@pinin4fjords pinin4fjords merged commit 47306db into dev Apr 30, 2024
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@pinin4fjords pinin4fjords deleted the gsea_html_fix branch April 30, 2024 10:57
@pinin4fjords pinin4fjords mentioned this pull request Apr 30, 2024
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