Convert SCTAssay -> Assay

workflow/scripts/prepare_h5ad.R

@@ -17,11 +17,8 @@ if (class(obj) == "Seurat") {
     assay_name <- DefaultAssay(obj)
 
     # If object contains a V5 assay, convert to V3
-    if (class(obj[[assay_name]]) == "Assay5") {
-        new_assay_name <- paste0(assay_name, "_3")
-        obj[[new_assay_name]] <- as(obj[[assay_name]], Class = "Assay")
-        DefaultAssay(obj) <- new_assay_name
-        obj[[assay_name]] <- NULL
+    if (class(obj[[assay_name]]) %in% c("Assay5", "SCTAssay")) {
+        obj[[assay_name]] <- as(obj[[assay_name]], Class = "Assay")
     }
 
     # Convert object to h5ad