Add option to limit max cells for SDA

Author: bbimber

singlecell/resources/chunks/RunSDA.R

@@ -7,7 +7,10 @@ sdaFiles <- data.frame(DatasetId = character(), FileName = character())
  for (datasetId in names(seuratObjects)) {
     printName(datasetId)
     seuratObj <- readRDS(seuratObjects[[datasetId]])
-    gc()
+
+    if (!is.null(maxAllowableCells) && maxAllowableCells > 0 && ncol(seuratObj) > maxAllowableCells) {
+       stop(paste0('The object has ', ncol(seuratObj), ' which is above the maxAllowableCells: ', maxAllowableCells))
+    }
 
     outputFolder <- paste0('sdaOutput.', datasetId)
     if (dir.exists(outputFolder)) {

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

@@ -35,6 +35,9 @@ public Provider()
                     SeuratToolParameter.create("numComps", "Num Comps", "Passed to SDAtools::run_SDA(). 30 is a good minimum but depends on input data complexity.", "ldk-integerfield", new JSONObject(){{
                         put("minValue", 0);
                     }}, 50),
+                    SeuratToolParameter.create("maxAllowableCells", "Max Allowable Cells", "If the input cells are above this value, an error will be thrown. This is designed to limit the amount of data passed to SDA. Use -1 for no limit.", "ldk-integerfield", new JSONObject(){{
+                        put("minValue", -1);
+                    }}, 150000, null, true),
                     SeuratToolParameter.create("featureInclusionList", "Genes to Include", "These genes, entered comma-separated or one/line, will be added to the default Seurat::VariableFeatures gene set when running PCA", "sequenceanalysis-trimmingtextarea", new JSONObject(){{
                         put("height", 150);
                         put("delimiter", ",");