Support decoupleR

Author: bbimber

singlecell/resources/chunks/RunDecoupler.R

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

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

@@ -82,6 +82,7 @@
 import org.labkey.singlecell.pipeline.singlecell.RunCelltypistCustomModel;
 import org.labkey.singlecell.pipeline.singlecell.RunConga;
 import org.labkey.singlecell.pipeline.singlecell.RunCsCore;
+import org.labkey.singlecell.pipeline.singlecell.RunDecoupler;
 import org.labkey.singlecell.pipeline.singlecell.RunEscape;
 import org.labkey.singlecell.pipeline.singlecell.RunLDA;
 import org.labkey.singlecell.pipeline.singlecell.RunPCA;
@@ -291,6 +292,7 @@ public static void registerPipelineSteps()
         SequencePipelineService.get().registerPipelineStep(new CustomGSEA.Provider());
         SequencePipelineService.get().registerPipelineStep(new StudyMetadata.Provider());
         SequencePipelineService.get().registerPipelineStep(new UpdateSeuratPrototype.Provider());
+        SequencePipelineService.get().registerPipelineStep(new RunDecoupler.Provider());
 
         SequenceAnalysisService.get().registerReadsetListener(new SingleCellReadsetListener());
     }

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

@@ -0,0 +1,37 @@
+package org.labkey.singlecell.pipeline.singlecell;
+
+import org.labkey.api.sequenceanalysis.pipeline.AbstractPipelineStepProvider;
+import org.labkey.api.sequenceanalysis.pipeline.PipelineContext;
+import org.labkey.api.singlecell.pipeline.SingleCellStep;
+
+import java.util.Arrays;
+
+public class RunDecoupler extends AbstractCellMembraneStep
+{
+    public RunDecoupler(PipelineContext ctx, RunDecoupler.Provider provider)
+    {
+        super(provider, ctx);
+    }
+
+    public static class Provider extends AbstractPipelineStepProvider<SingleCellStep>
+    {
+        public Provider()
+        {
+            super("RunDecoupler", "Run decoupleR", "decoupleR", "This will run decoupleR to score transcription factor enrichment.", Arrays.asList(
+
+            ), null, null);
+        }
+
+        @Override
+        public RunDecoupler create(PipelineContext ctx)
+        {
+            return new RunDecoupler(ctx, this);
+        }
+    }
+
+    @Override
+    public String getFileSuffix()
+    {
+        return "decoupler";
+    }
+}