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.

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

Add lowmem parameter to MOFA #311

Draft
wants to merge 2 commits into
base: main
Choose a base branch
from
Draft

Add lowmem parameter to MOFA #311

wants to merge 2 commits into from

Conversation

wlason
Copy link
Contributor

@wlason wlason commented Aug 20, 2024

This solves #308

  • Added lowmem option to batch_correct_mofa.py, which recalculates ATAC HVFs, keeping just top 25k
  • Added lowmem to the integration YAML
  • Fixed a bug where MOFA would error if filter_by_hvg in YAML is set to anything other than True (filter_by_hvg was erroneously passed to mu.tl.mofa kwargs)

@wlason wlason requested a review from bio-la August 20, 2024 15:59
@wlason
Copy link
Contributor Author

wlason commented Aug 20, 2024

I think as additional improvements it would be worth to print number of features in every mod used by MOFA in the logging info - easier to troubleshoot

@bio-la bio-la marked this pull request as draft September 4, 2024 08:06
@bio-la bio-la self-requested a review September 4, 2024 08:11
@bio-la
Copy link
Collaborator

bio-la commented Sep 4, 2024

@wlason this seems to work fine, i would just like you to add a new CI to test the lowmem parameter for MOFA.
Can you please check the integration actions we are running with the respective pipeline.yml and create a new one? you can simply create a copy the action and the pipeline ymls, giving them a different name, and edit the relevant MOFA sections in the yaml. happy to help!

@bio-la bio-la requested a review from deevdevil88 September 4, 2024 09:36
@bio-la bio-la self-assigned this Oct 29, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

3 participants