Port Anndata merge changes from scpca-nf #88
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jashapiro
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jaclyn-taroni
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Aug 13, 2024
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Closes #87
This PR incorporates changes made to the merge workflow in scpca-nf up to scpca-nf:v0.8.4 to improve compatibility with scanpy expectations.
This includes renaming the script that reformats Anndata and updating it to change PCA matrices to ndarrays, as well as changing PCA and UMAP matrices to lower case and adding a
highly_expressedcolumn.Note that the
--output_pca_tsvoption insce_to_anndata.Ris unused in this workflow, but is retained to keep the scripts in sync between workflows as much as possible.