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openpipelines-bio / openpipeline

https://openpipelines.bio
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The number of genes in a cell has to be pushed to the obs layer #454

Closed ddemaeyer closed 10 months ago

ddemaeyer commented 11 months ago

https://github.com/openpipelines-bio/openpipeline/blob/50d0394499fb7317854251b491f8f735626cf075/src/filter/filter_with_counts/script.py#L52

The number of genes is required in the obs layer for downstream usage.

DriesSchaumont commented 10 months ago

@ddemaeyer, this metric is added as the column num_nonzero_vars, see https://github.com/openpipelines-bio/openpipeline/blob/ad21c2fb504372872b2fe182ab2a0d1329eddd11/src/qc/calculate_qc_metrics/config.vsh.yaml#L17

DriesSchaumont commented 10 months ago

Closing this issue, please reopen if needed.