support for conversion of cellranger filtered h5 to h5mu - #1170
Open
dorien-er wants to merge 10 commits into
Open
support for conversion of cellranger filtered h5 to h5mu#1170dorien-er wants to merge 10 commits into
dorien-er wants to merge 10 commits into
Conversation
dorien-er
changed the title
dorien-er
marked this pull request as ready for review
April 22, 2026 13:17
Comment on lines
+452
to
+461
| if input_data.get("filtered_counts"): | ||
| mudata_per_sample = process_counts_filtered( | ||
| input_data["filtered_counts"], | ||
| ) | ||
| else: | ||
| mudata_per_sample = process_counts( | ||
| input_data["count"], | ||
| input_data["multiplexing_analysis"], | ||
| input_data["metrics_summary"], | ||
| ) |
Member
There was a problem hiding this comment.
Hmm, when I put the mudata construction here I already had the feeling that it would not be the best idea...Should we make it separate from from the processing of the auxiliary modalities?
So in the main function construct the mudata's with separate functions and pass those on into the get_modalities function?
And have a different function for detecting the input? Like detect_count_matrices and detect_modality_input? That would also remove some complexity from the input detection?
I'm not sure, what do you think?
Contributor
Author
There was a problem hiding this comment.
Makes sense, there's a proposal in the latest commit :-)
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Changelog
... Describe your changes ...
Issue ticket number and link
Closes #xxxx (Replace xxxx with the GitHub issue number)
Checklist before requesting a review
I have performed a self-review of my code
Conforms to the Contributor's guide
Check the correct box. Does this PR contain:
Proposed changes are described in the CHANGELOG.md
CI tests succeed!