Add steps to annotate seurat objects using scGate or celltypist

Author: bbimber

singlecell/resources/chunks/DropCiteSeq.R

@@ -0,0 +1,11 @@
+for (datasetId in names(seuratObjects)) {
+    seuratObj <- readRDS(seuratObjects[[datasetId]])
+
+    if ('ADT' %in% names(seuratObj@assays)) {
+        seuratObj@assays$ADT <- NULL
+    } else {
+        print('ADT assay not found, skipping')
+    }
+
+    saveData(seuratObj, datasetId)
+}

singlecell/resources/chunks/RunCelltypist.R

@@ -0,0 +1,7 @@
+for (datasetId in names(seuratObjects)) {
+    seuratObj <- readRDS(seuratObjects[[datasetId]])
+
+    seuratObj <- RIRA::RunCellTypist(seuratObj)
+
+    saveData(seuratObj, datasetId)
+}

singlecell/resources/chunks/RunScGate.R

@@ -0,0 +1,7 @@
+for (datasetId in names(seuratObjects)) {
+    seuratObj <- readRDS(seuratObjects[[datasetId]])
+
+    seuratObj <- RIRA::RunScGateForModels(seuratObj, modelNames = c('Bcell', 'Tcell', 'NK', 'Myeloid'), labelRename = list(Tcell = 'T_NK', NK = 'T_NK'))
+
+    saveData(seuratObj, datasetId)
+}

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

@@ -170,6 +170,9 @@ public static void registerPipelineSteps()
         SequencePipelineService.get().registerPipelineStep(new DietSeurat.Provider());
         SequencePipelineService.get().registerPipelineStep(new ClearCommands.Provider());
         SequencePipelineService.get().registerPipelineStep(new PlotAverageCiteSeqCounts.Provider());
+        SequencePipelineService.get().registerPipelineStep(new DropCiteSeq.Provider());
+        SequencePipelineService.get().registerPipelineStep(new RunScGate.Provider());
+        SequencePipelineService.get().registerPipelineStep(new RunCelltypist.Provider());
 
         SequenceAnalysisService.get().registerFileHandler(new NimbleAlignmentStep());
     }

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

@@ -0,0 +1,30 @@
+package org.labkey.singlecell.pipeline.singlecell;
+
+import org.labkey.api.sequenceanalysis.pipeline.PipelineContext;
+import org.labkey.api.sequenceanalysis.pipeline.PipelineStepProvider;
+import org.labkey.api.singlecell.pipeline.AbstractSingleCellPipelineStep;
+import org.labkey.api.util.PageFlowUtil;
+
+import java.util.Collection;
+
+abstract public class AbstractRiraStep extends AbstractSingleCellPipelineStep
+{
+    public static String CONTAINER_NAME = "ghcr.io/bimberlabinternal/rira:latest";
+
+    public AbstractRiraStep(PipelineStepProvider<?> provider, PipelineContext ctx)
+    {
+        super(provider, ctx);
+    }
+
+    @Override
+    public Collection<String> getRLibraries()
+    {
+        return PageFlowUtil.set("RIRA");
+    }
+
+    @Override
+    public String getDockerContainerName()
+    {
+        return CONTAINER_NAME;
+    }
+}

singlecell/src/org/labkey/singlecell/pipeline/singlecell/DropCiteSeq.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 DropCiteSeq extends AbstractCellMembraneStep
+{
+    public DropCiteSeq(PipelineContext ctx, DropCiteSeq.Provider provider)
+    {
+        super(provider, ctx);
+    }
+
+    public static class Provider extends AbstractPipelineStepProvider<SingleCellStep>
+    {
+        public Provider()
+        {
+            super("DropCiteSeq", "Drop CiteSeq", "CellMembrane", "This will remove the CITE-seq (ADT) assay, if it exists.", Arrays.asList(
+
+            ), null, null);
+        }
+
+        @Override
+        public DropCiteSeq create(PipelineContext ctx)
+        {
+            return new DropCiteSeq(ctx, this);
+        }
+    }
+}

singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunCelltypist.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 RunCelltypist extends AbstractRiraStep
+{
+    public RunCelltypist(PipelineContext ctx, RunCelltypist.Provider provider)
+    {
+        super(provider, ctx);
+    }
+
+    public static class Provider extends AbstractPipelineStepProvider<SingleCellStep>
+    {
+        public Provider()
+        {
+            super("RunCelltypist", "Run Celltypist", "Celltypist", "This will run Celltypist with the Immune_All_Low.pkl model.", Arrays.asList(
+
+            ), null, null);
+        }
+
+        @Override
+        public RunCelltypist create(PipelineContext ctx)
+        {
+            return new RunCelltypist(ctx, this);
+        }
+    }
+}

singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunScGate.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 RunScGate extends AbstractRiraStep
+{
+    public RunScGate(PipelineContext ctx, RunScGate.Provider provider)
+    {
+        super(provider, ctx);
+    }
+
+    public static class Provider extends AbstractPipelineStepProvider<SingleCellStep>
+    {
+        public Provider()
+        {
+            super("RunScGate", "Run scGate", "scGate", "This will run scGate with the default built-in models and create a consensus call.", Arrays.asList(
+
+            ), null, null);
+        }
+
+        @Override
+        public RunScGate create(PipelineContext ctx)
+        {
+            return new RunScGate(ctx, this);
+        }
+    }
+}