Support assayName param for scGate

Author: bbimber

singlecell/resources/chunks/RunScGate.R

@@ -3,9 +3,9 @@ for (datasetId in names(seuratObjects)) {
     seuratObj <- readRDS(seuratObjects[[datasetId]])
 
     if (useRhesusDefaults) {
-        seuratObj <- RIRA::RunScGateWithRhesusModels(seuratObj, dropAmbiguousConsensusValues = dropAmbiguousConsensusValues)
+        seuratObj <- RIRA::RunScGateWithRhesusModels(seuratObj, dropAmbiguousConsensusValues = dropAmbiguousConsensusValues, assayName = assayName)
     } else {
-        seuratObj <- RIRA::RunScGateForModels(seuratObj, modelNames = modelNames, labelRename = list(Tcell = 'T_NK', NK = 'T_NK'), dropAmbiguousConsensusValues = dropAmbiguousConsensusValues, consensusModels = consensusModels)
+        seuratObj <- RIRA::RunScGateForModels(seuratObj, modelNames = modelNames, labelRename = list(Tcell = 'T_NK', NK = 'T_NK'), dropAmbiguousConsensusValues = dropAmbiguousConsensusValues, consensusModels = consensusModels, assayName = assayName)
     }
 
     saveData(seuratObj, datasetId)

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

@@ -41,7 +41,10 @@ public Provider()
                     }}, null, null, true, true),
                     SeuratToolParameter.create("dropAmbiguousConsensusValues", "Drop Ambiguous Consensus Values", "If checked, any consensus calls that are ambiguous will be set to NA", "checkbox", new JSONObject(){{
                         put("checked", true);
-                    }}, true)
+                    }}, true),
+                    SeuratToolParameter.create("assayName", "Assay Name", "Passed directly to UCell::AddModuleScore_UCell.", "checkbox", new JSONObject(){{
+
+                    }}, "RNA")
                 ), null, null);
         }