AlexsLemonade / scpca-nf

scpca-nf is the Nextflow workflow for processing Single-cell Pediatric Cancer Atlas Portal data
BSD 3-Clause "New" or "Revised" License
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Add row level metadata to AnnData objects #368

Closed allyhawkins closed 1 year ago

allyhawkins commented 1 year ago

To make our AnnData output as compliable as possible with CZI, we need to update the existing row/gene metadata present in the AnnData objects to include the necessary entries. The full documentation can be found here: https://github.com/chanzuckerberg/single-cell-curation/blob/main/schema/3.0.0/schema.md#var-and-rawvar-gene-metadata

In brief we will need to add:

Again, we might want to consider if we should include these in the SCE objects prior to converting to AnnData so they are automatically there.

sjspielman commented 1 year ago

Closed by #428