Add steps for CITE-seq DimRedux

Author: bbimber

singlecell/resources/chunks/CiteSeqDimRedux.R

@@ -0,0 +1,11 @@
+for (datasetId in names(seuratObjects)) {
+    seuratObj <- seuratObjects[[datasetId]]
+
+    seuratObj <- CellMembrane::CiteSeqDimRedux(seuratObj)
+
+    newSeuratObjects[[datasetId]] <- seuratObj
+
+    # Cleanup
+    seuratObjects[[datasetId]] <- NULL
+    gc()
+}

singlecell/resources/chunks/CiteSeqWnn.R

@@ -0,0 +1,11 @@
+for (datasetId in names(seuratObjects)) {
+    seuratObj <- seuratObjects[[datasetId]]
+
+    seuratObj <- CellMembrane::RunSeuratWnn(seuratObj)
+
+    newSeuratObjects[[datasetId]] <- seuratObj
+
+    # Cleanup
+    seuratObjects[[datasetId]] <- NULL
+    gc()
+}

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

@@ -41,6 +41,8 @@
 import org.labkey.singlecell.button.CellHashingButton;
 import org.labkey.singlecell.button.CiteSeqButton;
 import org.labkey.singlecell.pipeline.singlecell.AppendCiteSeq;
+import org.labkey.singlecell.pipeline.singlecell.CiteSeqDimRedux;
+import org.labkey.singlecell.pipeline.singlecell.CiteSeqWnn;
 import org.labkey.singlecell.pipeline.singlecell.DoubletFinder;
 import org.labkey.singlecell.pipeline.singlecell.Downsample;
 import org.labkey.singlecell.pipeline.singlecell.FilterRawCounts;
@@ -172,6 +174,8 @@ public static void registerPipelineSteps()
         SequencePipelineService.get().registerPipelineStep(new FindClustersAndDimRedux.Provider());
         SequencePipelineService.get().registerPipelineStep(new SplitSeurat.Provider());
         SequencePipelineService.get().registerPipelineStep(new SubsetSeurat.Provider());
+        SequencePipelineService.get().registerPipelineStep(new CiteSeqDimRedux.Provider());
+        SequencePipelineService.get().registerPipelineStep(new CiteSeqWnn.Provider());
     }
 
     @Override

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

@@ -0,0 +1,31 @@
+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 CiteSeqDimRedux extends AbstractCellMembraneStep
+{
+    public CiteSeqDimRedux(PipelineContext ctx, CiteSeqDimRedux.Provider provider)
+    {
+        super(provider, ctx);
+    }
+
+    public static class Provider extends AbstractPipelineStepProvider<SingleCellStep>
+    {
+        public Provider()
+        {
+            super("CiteSeqDimRedux", "CiteSeq DimRedux", "Seurat", "This will run DimRedux steps on the ADT data.", Arrays.asList(
+
+            ), null, null);
+        }
+
+        @Override
+        public CiteSeqDimRedux create(PipelineContext ctx)
+        {
+            return new CiteSeqDimRedux(ctx, this);
+        }
+    }
+}

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

@@ -0,0 +1,31 @@
+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 CiteSeqWnn extends AbstractCellMembraneStep
+{
+    public CiteSeqWnn(PipelineContext ctx, CiteSeqWnn.Provider provider)
+    {
+        super(provider, ctx);
+    }
+
+    public static class Provider extends AbstractPipelineStepProvider<SingleCellStep>
+    {
+        public Provider()
+        {
+            super("CiteSeqWnn", "Seurat WNN", "Seurat", "This will run DimRedux steps on the ADT data.", Arrays.asList(
+
+            ), null, null);
+        }
+
+        @Override
+        public CiteSeqWnn create(PipelineContext ctx)
+        {
+            return new CiteSeqWnn(ctx, this);
+        }
+    }
+}