reduce anndata size

porting AlexsLemonade/scpca-nf#759
AlexsLemonade · May 9, 2024 · f942846 · f942846
1 parent 11ccf64
commit f942846
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diff --git a/modules/merge-sce/resources/usr/bin/move_counts_anndata.py b/modules/merge-sce/resources/usr/bin/move_counts_anndata.py
@@ -49,6 +49,7 @@
     # move logcounts to X and rename
     object.X = object.layers["logcounts"]
     object.uns["X_name"] = "logcounts"
+    del object.layers["logcounts"]
 
     # export object
     object.write_h5ad(args.anndata_file, compression="gzip" if args.compress else None)
diff --git a/modules/merge-sce/resources/usr/bin/sce_to_anndata.R b/modules/merge-sce/resources/usr/bin/sce_to_anndata.R
@@ -183,7 +183,6 @@ if (opt$feature_name == "cellhash") {
   warning("Conversion of altExp data from multiplexed data is not supported.
              The altExp will not be converted.")
   quit(save = "no")
-  # convert altExp
 }
 
 # check for output file