Support tricycle

Author: bbimber

singlecell/resources/chunks/RunTricycle.R

@@ -0,0 +1,12 @@
+ for (datasetId in names(seuratObjects)) {
+    printName(datasetId)
+    seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
+
+    seuratObj <- CellMembrane::RunTricycle(seuratObj)
+
+    saveData(seuratObj, datasetId)
+
+    # Cleanup
+    rm(seuratObj)
+    gc()
+}

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

@@ -94,6 +94,7 @@
 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.RunTricycle;
 import org.labkey.singlecell.pipeline.singlecell.RunVision;
 import org.labkey.singlecell.pipeline.singlecell.ScoreCellCycle;
 import org.labkey.singlecell.pipeline.singlecell.SeuratPrototype;
@@ -297,6 +298,7 @@ public static void registerPipelineSteps()
         SequencePipelineService.get().registerPipelineStep(new RunDecoupler.Provider());
         SequencePipelineService.get().registerPipelineStep(new PerformDefaultNimbleAppend.Provider());
         SequencePipelineService.get().registerPipelineStep(new PerformMhcDimRedux.Provider());
+        SequencePipelineService.get().registerPipelineStep(new RunTricycle.Provider());
 
         SequenceAnalysisService.get().registerReadsetListener(new SingleCellReadsetListener());
     }

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

@@ -0,0 +1,39 @@
+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 RunTricycle extends AbstractCellMembraneStep
+{
+    public RunTricycle(PipelineContext ctx, RunTricycle.Provider provider)
+    {
+        super(provider, ctx);
+    }
+
+    public static class Provider extends AbstractPipelineStepProvider<SingleCellStep>
+    {
+        public Provider()
+        {
+            super("RunTricycle", "Run Tricycle", "CellMembrane/Tricycle", "This will run tricycle on the input object(s) to score cell cycle, and save the results in metadata.", Arrays.asList(
+
+            ), null, null);
+        }
+
+        @Override
+        public RunTricycle create(PipelineContext ctx)
+        {
+            return new RunTricycle(ctx, this);
+        }
+    }
+
+    @Override
+    public String getFileSuffix()
+    {
+        return "tricycle";
+    }
+}