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

New feature: local module DREAM_DIFFERENTIAL #414

Merged
merged 8 commits into from
Dec 30, 2024
Merged

New feature: local module DREAM_DIFFERENTIAL #414

merged 8 commits into from
Dec 30, 2024
+1,365 −3

Conversation

alanmmobbs93
Copy link

@alanmmobbs93 alanmmobbs93 commented Dec 27, 2024 •
edited
Loading

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).

Reference issues

Main ticket:

Subissues:

New

  • Add local module DREAM_DIFFERENTIAL, which runs in parallel to DESEQ_DIFFERENTIAL (temporary).
  • Groovy function to parse yaml file to create a tuple with required fields that feeds this module.

Perspectives:

  • New set of parameters to customize how to run dream analysis.
  • How to execute the module based on the yml contents.
  • Include outputs to the final markdown report

@nf-core-bot
Copy link
Member

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.0.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

@github-actions GitHub Actions
Copy link

github-actions bot commented Dec 27, 2024 •
edited
Loading

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 2790d2c

+| ✅ 302 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 2024-12-30 20:56:40

@alanmmobbs93 alanmmobbs93 marked this pull request as ready for review December 27, 2024 19:25
nschcolnicov
nschcolnicov requested changes Dec 30, 2024
View reviewed changes
modules/local/dream/differential/main.nf Outdated Show resolved Hide resolved
lib/YMLProcessing.groovy Outdated Show resolved Hide resolved
modules/local/dream/differential/meta.yml Outdated Show resolved Hide resolved
modules/local/dream/differential/tests/main.nf.test.snap Show resolved Hide resolved
modules/local/dream/differential/tests/main.nf.test.snap Show resolved Hide resolved
modules/local/dream/differential/tests/main.nf.test.snap Show resolved Hide resolved
modules/local/dream/differential/tests/main.nf.test.snap Show resolved Hide resolved
modules/local/dream/differential/tests/main.nf.test.snap Show resolved Hide resolved
modules/local/dream/differential/tests/main.nf.test.snap Show resolved Hide resolved
workflows/differentialabundance.nf
}
.set{ ch_contrast_dream }

DREAM_DIFFERENTIAL (
Copy link

Choose a reason for hiding this comment

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

I see that you built it to only trigger with YAML files, since we are looking into replacing csv contrasts files, I think this is OK. Leaving this comment here in case anyone spots this.

nschcolnicov
nschcolnicov approved these changes Dec 30, 2024
View reviewed changes
Copy link

@nschcolnicov nschcolnicov left a comment

Choose a reason for hiding this comment

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

Thanks for addressing the comments! Looks good!

@alanmmobbs93 alanmmobbs93 merged commit 8c1c053 into nf-core:dev_tmp Dec 30, 2024
16 checks passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@nschcolnicov nschcolnicov nschcolnicov approved these changes

@atrigila atrigila Awaiting requested review from atrigila

@apeltzer apeltzer Awaiting requested review from apeltzer

@grst grst Awaiting requested review from grst

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

Successfully merging this pull request may close these issues.
3 participants
@alanmmobbs93 @nf-core-bot @nschcolnicov