Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Mention missing dots in report volcano #232

Merged
merged 6 commits into from
Feb 27, 2024
Merged

Mention missing dots in report volcano #232

merged 6 commits into from
Feb 27, 2024

Conversation

WackerO
Copy link
Collaborator

@WackerO WackerO commented Feb 8, 2024

Instead of #229

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).

@github-actions GitHub Actions
Copy link

github-actions bot commented Feb 8, 2024 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e393cdd

+| ✅ 273 tests passed       |+
!| ❗   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 passed:

Run details

  • nf-core/tools version 2.13
  • Run at 2024-02-27 07:57:32

pinin4fjords
pinin4fjords reviewed Feb 8, 2024
View reviewed changes
Copy link
Member

@pinin4fjords pinin4fjords left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Assume the GSEA changes here are because we need to merge in master.

Actually. what I was thinking with the warning is to actually check the data for values of 0 in the p values, and conditionally display a prominent warning under the plot:

"x features with p values of 0 are not shown- please refer to the results tables"

@WackerO
Copy link
Collaborator Author

WackerO commented Feb 8, 2024 •
edited
Loading

Assume the GSEA changes here are because we need to merge in master.

Actually. what I was thinking with the warning is to actually check the data for values of 0 in the p values, and conditionally display a prominent warning under the plot:

"x features with p values of 0 are not shown- please refer to the results tables"

Ah, those are in this PR because I created volcano_round from dev after adding the GSEA update.

Can also do that.

@WackerO
Copy link
Collaborator Author

WackerO commented Feb 12, 2024

How about this? @pinin4fjords
SRP254919 2.html.zip

pinin4fjords
pinin4fjords approved these changes Feb 19, 2024
View reviewed changes
Copy link
Member

@pinin4fjords pinin4fjords left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Looks good - thanks Oskar. Tiny question about default behaviour, but I'll leave you to resolve that (or not) before you merge.

nextflow.config Outdated Show resolved Hide resolved
@WackerO WackerO merged commit e5d11f8 into nf-core:dev Feb 27, 2024
12 checks passed
@WackerO WackerO deleted the volcano_round branch February 27, 2024 10:30
This was referenced Feb 27, 2024
Closed
Closed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@pinin4fjords pinin4fjords pinin4fjords approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

None yet
2 participants
@WackerO @pinin4fjords