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

POC contrasts csv -> yaml #382

Draft
wants to merge 1 commit into
base: dev
Choose a base branch
from
Draft

POC contrasts csv -> yaml #382

wants to merge 1 commit into from
+224 −10

Conversation

nschcolnicov
Copy link

Addresses #370

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).

@nschcolnicov nschcolnicov mentioned this pull request Dec 9, 2024
Open
@github-actions GitHub Actions
Copy link

github-actions bot commented Dec 9, 2024 •
edited
Loading

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 5f25fb3

+| ✅ 300 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   4 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!
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-12-09 14:10:24

nschcolnicov
nschcolnicov commented Dec 9, 2024
View reviewed changes
bin/validate_fom_components_yaml.R
@@ -0,0 +1,208 @@
#!/usr/bin/env Rscript
Copy link
Author

Choose a reason for hiding this comment

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

Not a new file, created from https://github.com/pinin4fjords/shinyngs/blob/develop/exec/validate_fom_components.R

@grst grst mentioned this pull request Dec 10, 2024
Open
@nschcolnicov nschcolnicov marked this pull request as draft December 11, 2024 12:36
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
1 participant
@nschcolnicov