Add starcat tool

Author: Sebastian Benjamin

singlecell/resources/chunks/RunStarCAT.R

@@ -0,0 +1,12 @@
+for (datasetId in names(seuratObjects)) {
+    printName(datasetId)
+    seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
+
+    seuratObj <- CellMembrane::RunStarCAT(seuratObj, reference = reference, assayName = assayName, outputDirectory = tempfile(pattern = 'starcat_'))
+
+    saveData(seuratObj, datasetId)
+
+    # Cleanup
+    rm(seuratObj)
+    gc()
+}

singlecell/src/org/labkey/singlecell/SingleCellModule.java

@@ -97,6 +97,7 @@
 import org.labkey.singlecell.pipeline.singlecell.RunScGate;
 import org.labkey.singlecell.pipeline.singlecell.RunScGateBuiltin;
 import org.labkey.singlecell.pipeline.singlecell.RunSingleR;
+import org.labkey.singlecell.pipeline.singlecell.RunStarCAT;
 import org.labkey.singlecell.pipeline.singlecell.RunVision;
 import org.labkey.singlecell.pipeline.singlecell.ScoreCellCycle;
 import org.labkey.singlecell.pipeline.singlecell.SeuratPrototype;
@@ -248,6 +249,7 @@ public static void registerPipelineSteps()
         SequencePipelineService.get().registerPipelineStep(new RunPCA.Provider());
         SequencePipelineService.get().registerPipelineStep(new RunPHATE.Provider());
         SequencePipelineService.get().registerPipelineStep(new RunSingleR.Provider());
+        SequencePipelineService.get().registerPipelineStep(new RunStarCAT.Provider());
         SequencePipelineService.get().registerPipelineStep(new ClassifyTNKByExpression.Provider());
         SequencePipelineService.get().registerPipelineStep(new RunConga.Provider());
         SequencePipelineService.get().registerPipelineStep(new FindClustersAndDimRedux.Provider());

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

@@ -0,0 +1,53 @@
+package org.labkey.singlecell.pipeline.singlecell;
+
+import org.json.JSONObject;
+import org.labkey.api.sequenceanalysis.pipeline.AbstractPipelineStepProvider;
+import org.labkey.api.sequenceanalysis.pipeline.PipelineContext;
+import org.labkey.api.singlecell.pipeline.SeuratToolParameter;
+import org.labkey.api.singlecell.pipeline.SingleCellStep;
+
+import java.util.Arrays;
+
+public class RunStarCAT extends AbstractCellMembraneStep
+{
+    public RunStarCAT(PipelineContext ctx, RunStarCAT.Provider provider)
+    {
+        super(provider, ctx);
+    }
+
+    public static class Provider extends AbstractPipelineStepProvider<SingleCellStep>
+    {
+        public Provider()
+        {
+            super("RunStarCAT", "Run StarCAT", "CellMembrane/StarCAT", "This will run StarCAT to project cells onto a reference (e.g. TCAT.V1) and append per-cell scores and program usage to metadata.", Arrays.asList(
+                    SeuratToolParameter.create("reference", "Reference", "Either a built-in StarCAT reference name (e.g. TCAT.V1, MYELOID.GLIOMA.V1, BONEMARROW.CD34POS.HSPC.V1) or a path to a custom reference .tsv/.txt file.", "ldk-simplecombo", new JSONObject()
+                    {{
+                        put("multiSelect", false);
+                        put("allowBlank", false);
+                        put("editable", true);
+                        put("forceSelection", false);
+                        put("storeValues", "TCAT.V1;MYELOID.GLIOMA.V1;BONEMARROW.CD34POS.HSPC.V1");
+                        put("initialValues", "TCAT.V1");
+                        put("delimiter", ";");
+                        put("joinReturnValue", true);
+                    }}, "TCAT.V1"),
+                    SeuratToolParameter.create("assayName", "Assay Name", "The name of the assay containing the counts matrix passed to StarCAT.", "textfield", new JSONObject()
+                    {{
+                        put("allowBlank", false);
+                    }}, "RNA")
+            ), null, null);
+        }
+
+        @Override
+        public RunStarCAT create(PipelineContext ctx)
+        {
+            return new RunStarCAT(ctx, this);
+        }
+    }
+
+    @Override
+    public String getFileSuffix()
+    {
+        return "starcat";
+    }
+}