Skip to content

Multiome: anndata validation should occur before fragment file validation #1278

Open
@brianraymor

Description

@brianraymor

Context

Reported by @brian-mott on sci-data-eng

It would be very helpful to have anndata checks done first and to return early/exit if these exist, and then move onto fragment file validation. Currently with a real world dataset with ~60k cells, this takes about 30 mins to validate, and I wouldn't know that obs['is_primary_data'] is not all True until the end of that time. With early returns/exits, I could see that's an issue, quickly fix, then make better use of all the compute/space needs for fragment validation

Activity

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

Metadata

Metadata

Assignees

No one assigned

    Labels

    curation softwaretechTech issues that do not require product prioritization. Tech debt, tooling, ops, etc.

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions