Add wrapper for IdentifyAndStoreActiveClonotypes

Author: bbimber

singlecell/resources/chunks/IdentifyAndStoreActiveClonotypes.R

@@ -0,0 +1,13 @@
+for (datasetId in names(seuratObjects)) {
+  printName(datasetId)
+  seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
+
+  Rdiscvr::IdentifyAndStoreActiveClonotypes(seuratObj, chain = 'TRA')
+  Rdiscvr::IdentifyAndStoreActiveClonotypes(seuratObj, chain = 'TRB')
+
+  saveData(seuratObj, datasetId)
+
+  # Cleanup
+  rm(seuratObj)
+  gc()
+}

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

@@ -70,6 +70,7 @@
 import org.labkey.singlecell.pipeline.singlecell.FilterRawCounts;
 import org.labkey.singlecell.pipeline.singlecell.FindClustersAndDimRedux;
 import org.labkey.singlecell.pipeline.singlecell.FindMarkers;
+import org.labkey.singlecell.pipeline.singlecell.IdentifyAndStoreActiveClonotypes;
 import org.labkey.singlecell.pipeline.singlecell.IntegrateData;
 import org.labkey.singlecell.pipeline.singlecell.MergeSeurat;
 import org.labkey.singlecell.pipeline.singlecell.NormalizeAndScale;
@@ -305,6 +306,7 @@ public static void registerPipelineSteps()
         SequencePipelineService.get().registerPipelineStep(new ApplyKnownClonotypicData.Provider());
         SequencePipelineService.get().registerPipelineStep(new CalculateTcrRepertoireStats.Provider());
         SequencePipelineService.get().registerPipelineStep(new PredictTcellActivation.Provider());
+        SequencePipelineService.get().registerPipelineStep(new IdentifyAndStoreActiveClonotypes.Provider());
 
         SequenceAnalysisService.get().registerReadsetListener(new SingleCellReadsetListener());
     }

singlecell/src/org/labkey/singlecell/pipeline/singlecell/IdentifyAndStoreActiveClonotypes.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.List;
+
+public class IdentifyAndStoreActiveClonotypes extends AbstractRDiscvrStep
+{
+    public IdentifyAndStoreActiveClonotypes(PipelineContext ctx, IdentifyAndStoreActiveClonotypes.Provider provider)
+    {
+        super(provider, ctx);
+    }
+
+    public static class Provider extends AbstractPipelineStepProvider<SingleCellStep>
+    {
+        public Provider()
+        {
+            super("IdentifyAndStoreActiveClonotypes", "Identify And Store Active Clonotypes", "Rdiscvr", "This uses RDiscvr::IdentifyAndStoreActiveClonotypes to predict TCR-triggered T cells and save the results to the database", List.of(), null, null);
+        }
+
+
+        @Override
+        public IdentifyAndStoreActiveClonotypes create(PipelineContext ctx)
+        {
+            return new IdentifyAndStoreActiveClonotypes(ctx, this);
+        }
+    }
+
+    @Override
+    public String getFileSuffix()
+    {
+        return "is";
+    }
+}
+