Tkakar/cat 1015 document containers #142
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tkakar
commented
Jan 3, 2025
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This test folder had slipped into the last PR, so removed it here.
tkakar
commented
Jan 14, 2025
containers/mudata-to-ui/README.md
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| ## Normalization | ||
| All data from the input is scaled to [zero-mean unit-variance] (https://github.com/hubmapconsortium/salmon-rnaseq/blob/master/bin/analysis/scanpy_entry_point.py#L31-L33). |
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@NickAkhmetov I copied it from the anndata-to-ui readme assuming they both follow the same normalization, can you please confirm if this is correct?
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There's some similar code in the multiome pipeline to avoid confusion: https://github.com/hubmapconsortium/multiome-rna-atac-pipeline/blob/a52b6bb37f56dcd78d45ceef1868095d59ef1aac/bin/downstream.py#L30-L37
My understanding is that anything that uses the mudata-to-ui pipeline is passed through the multiome-rna-atac-pipeline beforehand, so it seems logical to link to that pipeline instead.
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This PR expands the readme in each container to explicitly state the inputs, outputs, as well as any normalization done to the inputs.