Bugfix to cellranger VDJ

Author: bbimber

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

@@ -37,11 +37,76 @@
 import org.labkey.singlecell.analysis.ProcessSingleCellHandler;
 import org.labkey.singlecell.analysis.SingleCellReadsetListener;
 import org.labkey.singlecell.button.FeatureBarcodeButton;
-import org.labkey.singlecell.pipeline.singlecell.*;
+import org.labkey.singlecell.pipeline.singlecell.AppendCiteSeq;
+import org.labkey.singlecell.pipeline.singlecell.AppendMetadata;
+import org.labkey.singlecell.pipeline.singlecell.AppendNimble;
+import org.labkey.singlecell.pipeline.singlecell.AppendSaturation;
+import org.labkey.singlecell.pipeline.singlecell.AppendTcr;
+import org.labkey.singlecell.pipeline.singlecell.AvgExpression;
+import org.labkey.singlecell.pipeline.singlecell.CalculateGeneComponentScores;
+import org.labkey.singlecell.pipeline.singlecell.CalculateUCellScores;
+import org.labkey.singlecell.pipeline.singlecell.CellBarcodeFilter;
+import org.labkey.singlecell.pipeline.singlecell.CheckExpectations;
+import org.labkey.singlecell.pipeline.singlecell.CiteSeqDimReduxDist;
+import org.labkey.singlecell.pipeline.singlecell.CiteSeqDimReduxPca;
+import org.labkey.singlecell.pipeline.singlecell.CiteSeqPlots;
+import org.labkey.singlecell.pipeline.singlecell.CiteSeqWnn;
+import org.labkey.singlecell.pipeline.singlecell.ClassifyTNKByExpression;
+import org.labkey.singlecell.pipeline.singlecell.ClearCommands;
+import org.labkey.singlecell.pipeline.singlecell.ClrNormalizeByGroup;
+import org.labkey.singlecell.pipeline.singlecell.CommonFilters;
+import org.labkey.singlecell.pipeline.singlecell.CustomGSEA;
+import org.labkey.singlecell.pipeline.singlecell.CustomUCell;
+import org.labkey.singlecell.pipeline.singlecell.DietSeurat;
+import org.labkey.singlecell.pipeline.singlecell.DimPlots;
+import org.labkey.singlecell.pipeline.singlecell.DoubletFinder;
+import org.labkey.singlecell.pipeline.singlecell.Downsample;
+import org.labkey.singlecell.pipeline.singlecell.DropAssays;
+import org.labkey.singlecell.pipeline.singlecell.DropCiteSeq;
+import org.labkey.singlecell.pipeline.singlecell.FeaturePlots;
+import org.labkey.singlecell.pipeline.singlecell.FilterDisallowedClasses;
+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.IntegrateData;
+import org.labkey.singlecell.pipeline.singlecell.MergeSeurat;
+import org.labkey.singlecell.pipeline.singlecell.NormalizeAndScale;
+import org.labkey.singlecell.pipeline.singlecell.PhenotypePlots;
+import org.labkey.singlecell.pipeline.singlecell.PlotAssayFeatures;
+import org.labkey.singlecell.pipeline.singlecell.PlotAverageCiteSeqCounts;
+import org.labkey.singlecell.pipeline.singlecell.PredictScTour;
+import org.labkey.singlecell.pipeline.singlecell.PrepareRawCounts;
+import org.labkey.singlecell.pipeline.singlecell.RemoveCellCycle;
+import org.labkey.singlecell.pipeline.singlecell.RunCellHashing;
+import org.labkey.singlecell.pipeline.singlecell.RunCelltypist;
+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.RunEscape;
+import org.labkey.singlecell.pipeline.singlecell.RunLDA;
+import org.labkey.singlecell.pipeline.singlecell.RunPCA;
+import org.labkey.singlecell.pipeline.singlecell.RunPHATE;
+import org.labkey.singlecell.pipeline.singlecell.RunRiraClassification;
+import org.labkey.singlecell.pipeline.singlecell.RunSDA;
+import org.labkey.singlecell.pipeline.singlecell.RunScGate;
+import org.labkey.singlecell.pipeline.singlecell.RunScGateBuiltin;
+import org.labkey.singlecell.pipeline.singlecell.RunScMetabolism;
+import org.labkey.singlecell.pipeline.singlecell.RunSingleR;
+import org.labkey.singlecell.pipeline.singlecell.RunVision;
+import org.labkey.singlecell.pipeline.singlecell.ScoreCellCycle;
+import org.labkey.singlecell.pipeline.singlecell.SeuratPrototype;
+import org.labkey.singlecell.pipeline.singlecell.SplitSeurat;
+import org.labkey.singlecell.pipeline.singlecell.StudyMetadata;
+import org.labkey.singlecell.pipeline.singlecell.SubsetSeurat;
+import org.labkey.singlecell.pipeline.singlecell.SummarizeTCellActivation;
+import org.labkey.singlecell.pipeline.singlecell.TcrFilter;
+import org.labkey.singlecell.pipeline.singlecell.TrainCelltypist;
+import org.labkey.singlecell.pipeline.singlecell.TrainScTour;
+import org.labkey.singlecell.pipeline.singlecell.UpdateSeuratPrototype;
+import org.labkey.singlecell.pipeline.singlecell.VireoHandler;
 import org.labkey.singlecell.run.CellRangerFeatureBarcodeHandler;
 import org.labkey.singlecell.run.CellRangerGexCountStep;
 import org.labkey.singlecell.run.CellRangerVDJWrapper;
-import org.labkey.singlecell.run.CellRangerVLoupeRepairHandler;
 import org.labkey.singlecell.run.NimbleAlignmentStep;
 import org.labkey.singlecell.run.NimbleAnalysis;
 import org.labkey.singlecell.run.VelocytoAlignmentStep;
@@ -166,7 +231,6 @@ public static void registerPipelineSteps()
         SequencePipelineService.get().registerPipelineStep(new MergeSeurat.Provider());
         SequencePipelineService.get().registerPipelineStep(new NormalizeAndScale.Provider());
         SequencePipelineService.get().registerPipelineStep(new ClrNormalizeByGroup.Provider());
-        SequenceAnalysisService.get().registerFileHandler(new CellRangerVLoupeRepairHandler());
         SequencePipelineService.get().registerPipelineStep(new PrepareRawCounts.Provider());
         SequenceAnalysisService.get().registerFileHandler(new VireoHandler());