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

move pathway related logic out of differential and correlation subworkflows #318

Open
wants to merge 7 commits into
base: dev-ratio
Choose a base branch
from
Open

move pathway related logic out of differential and correlation subworkflows #318

wants to merge 7 commits into from

Conversation

bjlang
Copy link

@bjlang bjlang commented Oct 23, 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).

@github-actions GitHub Actions
Copy link

github-actions bot commented Oct 23, 2024 •
edited
Loading

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 953eb51

+| ✅ 317 tests passed       |+
#| ❔   7 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 2024-10-30 11:17:31

suzannejin
suzannejin reviewed Oct 24, 2024
View reviewed changes
subworkflows/local/experimental/main.nf Outdated
// 2) clean up meta data by removing tool arguments and adding pathway name
return ch_results
.combine(ch_tools_args)
.filter{ meta, data, pathway, arg_map -> meta.subMap(arg_map.keySet()) == arg_map }
Copy link

@suzannejin suzannejin Oct 24, 2024 •
edited
Loading

Choose a reason for hiding this comment

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

if meta has some more elements than 'diff_method' and 'args_diff' (eg. data id, etc), would this matching work?

Copy link
Author

@bjlang bjlang Oct 24, 2024 •
edited
Loading

Choose a reason for hiding this comment

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

Yes, the additional elements are ignored, because the match is only done on the submap that contains 'diff_method' and 'args_diff' (or 'enr_method' and 'args_enr', etc)

@bjlang bjlang marked this pull request as ready for review October 24, 2024 09:50
suzannejin
suzannejin reviewed Oct 30, 2024
View reviewed changes
subworkflows/local/enrichment/main.nf
// TODO: add ch_gm when provided by user, etc.

main:

// initialize empty results channels
ch_enriched = Channel.empty()
ch_gmt = Channel.empty()

ch_adjacency
Copy link

@suzannejin suzannejin Oct 30, 2024 •
edited
Loading

Choose a reason for hiding this comment

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

ch_adjacency can only used for GREA, no need to branch for GREA

suzannejin
suzannejin reviewed Oct 30, 2024
View reviewed changes
subworkflows/local/enrichment/main.nf Outdated

// ----------------------------------------------------
// Construct gene set database
// ----------------------------------------------------

// TODO this should be optional, only run when there is no gene set data provided by user

// empty counts channel of ch_adjacency is empty to skip unnecessary MYGENE computations
Copy link

@suzannejin suzannejin Oct 30, 2024 •
edited
Loading

Choose a reason for hiding this comment

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

MYGENE is always needed as far as the user does not provide a gmt file, and that a enrichment module is called

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@suzannejin suzannejin suzannejin left review comments

@WackerO WackerO Awaiting requested review from WackerO

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

Successfully merging this pull request may close these issues.
2 participants
@bjlang @suzannejin