Support SoupX processing

Author: bbimber

singlecell/resources/chunks/PrepareRawCounts.R

@@ -2,7 +2,7 @@ for (datasetId in names(seuratObjects)) {
     rawCountDir <- seuratObjects[[datasetId]]
 
     datasetName <- datasetIdToName[[datasetId]]
-    seuratObj <- CellMembrane::ReadAndFilter10xData(dataDir = rawCountDir, datasetId = datasetId, datasetName = datasetName, emptyDropsLower = emptyDropsLower, emptyDropsFdrThreshold = emptyDropsFdrThreshold, useEmptyDropsCellRanger = useEmptyDropsCellRanger, nExpectedCells = nExpectedCells, useCellBender = useCellBender)
+    seuratObj <- CellMembrane::ReadAndFilter10xData(dataDir = rawCountDir, datasetId = datasetId, datasetName = datasetName, emptyDropsLower = emptyDropsLower, emptyDropsFdrThreshold = emptyDropsFdrThreshold, useEmptyDropsCellRanger = useEmptyDropsCellRanger, nExpectedCells = nExpectedCells, useCellBender = useCellBender, useSoupX = useSoupX)
 
     if (!is.null(maxAllowableCells) && ncol(seuratObj) > maxAllowableCells) {
         addErrorMessage(paste0('The seurat object has ', ncol(seuratObj), ' cells, which is more than the max allowable cells (', maxAllowableCells, '). Please review emptyDrops results as this probably means thresholds were suboptimal.'))

singlecell/src/org/labkey/singlecell/analysis/AbstractSingleCellHandler.java

@@ -607,12 +607,15 @@ private List<SingleCellStep.SeuratObjectWrapper> processRawCounts(JobContext ctx
             List<SingleCellStep.SeuratObjectWrapper> inputMatrices = new ArrayList<>();
             inputFiles.forEach(x -> {
                 String datasetName = ctx.getSequenceSupport().getCachedReadset(x.getReadset()).getName();
-                File source = new File(x.getFile().getParentFile(), "raw_feature_bc_matrix");
-                if (!source.exists())
+                File countsDir = new File(x.getFile().getParentFile(), "raw_feature_bc_matrix");
+                if (!countsDir.exists())
                 {
-                    throw new IllegalArgumentException("Unable to find file: " + source.getPath());
+                    throw new IllegalArgumentException("Unable to find file: " + countsDir.getPath());
                 }
 
+                // The outs directory:
+                File source = x.getFile().getParentFile();
+
                 try
                 {
                     File localCopy = new File(ctx.getOutputDir(), x.getRowid() + "_RawData");

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

@@ -35,7 +35,10 @@ public Provider()
                     SeuratToolParameter.create("maxAllowableCells", "Max Cells Allowed", "If more than this many cells are predicted by EmptyDrops, the job will fail", "ldk-integerfield", null, 20000),
                     SeuratToolParameter.create("useEmptyDropsCellRanger", "Use emptyDropsCellRanger", "If checked, this will run emptyDropsCellRanger instead of emptyDrops", "checkbox", null, false),
                     SeuratToolParameter.create("nExpectedCells", "# Expected Cells", "Only applied if emptyDropsCellRanger is selected. Passed to n.expected.cells argument", "ldk-integerfield", null, false),
-                    SeuratToolParameter.create("runCellBender", "Run CellBender", "If checked, cellbender will be run on the raw count matrix (instead of emptyDrops) to remove background/ambient RNA signal", "checkbox", new JSONObject(){{
+                    SeuratToolParameter.create("useCellBender", "Run CellBender", "If checked, cellbender will be run on the raw count matrix (instead of emptyDrops) to remove background/ambient RNA signal", "checkbox", new JSONObject(){{
+
+                    }}, false),
+                    SeuratToolParameter.create("useSoupX", "Run SoupX", "If checked, SoupX will be run on the raw count matrix (instead of emptyDrops) to remove background/ambient RNA signal", "checkbox", new JSONObject(){{
 
                     }}, false)
             ), null, null);