Turn on automatic DietSeurat when merging many objects

Author: bbimber

singlecell/resources/chunks/MergeSeurat.R

@@ -1,4 +1,9 @@
 doDiet <- exists('doDiet') && doDiet
+disableAutoDietSeurat <- exists('disableAutoDietSeurat') && disableAutoDietSeurat
+if (!doDiet && length(seuratObjects) > 20 && !disableAutoDietSeurat) {
+    logger::log_info('More than 20 objects are being merged, turning on DietSeurat')
+    doDiet <- TRUE
+}
 
 mergeBatch <- function(dat) {
     toMerge <- list()

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

@@ -28,7 +28,8 @@ public Provider()
                         put("allowBlank", false);
                         put("doNotIncludeInTemplates", true);
                     }}, 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),
+                    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, true, "dietSeurat", true, false),
+                    SeuratToolParameter.create("disableAutoDietSeurat", "Disable Auto DietSeurat", "By default, this step will enable DietSeurat if if you try to merge more than 20 objects. This disables that behavior.", "checkbox", null, false),
                     SeuratToolParameter.create("errorOnBarcodeSuffix", "Error On Cell Barcode Suffixes", "In certain cases, software appends a digit (i.e. -1) to the end of cell barcodes; however, no code in DISCVR should do this. These are a problem if different datasets are inconsistent when using them.  If this setting is checked, the code will error if these are encountered.", "checkbox", null, true, "errorOnBarcodeSuffix", true, false),
                     SeuratToolParameter.create("assaysToDrop", "Assays to Drop", "These assays, entered comma-separated or one/line, will be dropped prior to merge.", "sequenceanalysis-trimmingtextarea", new JSONObject(){{
                         put("height", 150);