Add option to run DietSeurat prior to merge

Author: bbimber

singlecell/resources/chunks/MergeSeurat.R

@@ -2,6 +2,15 @@ if (length(seuratObjects) == 1) {
     print('There is only one seurat object, no need to merge')
     newSeuratObjects <- seuratObjects
 } else {
+    if (exists('doDiet') && doDiet) {
+        print('Running DietSeurat on inputs')
+        for (datasetId in seuratObjects) {
+            seuratObjects[[datasetId]] <- Seurat::DietSeurat(seuratObjects[[datasetId]])
+        }
+
+        gc()
+    }
+
     newSeuratObjects[[projectName]] <- CellMembrane::MergeSeuratObjs(seuratObjects, projectName = projectName)
 }
 

singlecell/src/org/labkey/singlecell/pipeline/singlecell/MergeSeurat.java

@@ -26,7 +26,8 @@ public Provider()
             super("MergeSeurat", "Merge Seurat Objects", "CellMembrane/Seurat", "This will merge the incoming seurat objects into a single object, merging all assays. Note: this will discard any normalization or DimRedux data, and performs zero validation to ensure this is compatible with downstream steps.", Arrays.asList(
                     SeuratToolParameter.create("projectName", "New Dataset Name", "The updated baseline for this merged object.", "textfield", new JSONObject(){{
                         put("allowBlank", false);
-                    }}, null)
+                    }}, null),
+                    SeuratToolParameter.create("doDiet", "Run DietSeurat", "If selected, this will run DietSeurat and gc() on the incoming seurat objects prior to merge. This is primarily to help with memory.", "checkbox", null, false, "dietSeurat", true, false)
             ), null, null);
         }