Add step to repeat cell cycle scoring

singlecell/resources/chunks/ScoreCellCycle.R

@@ -0,0 +1,12 @@
+for (datasetId in names(seuratObjects)) {
+    printName(datasetId)
+    seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
+
+    seuratObj <- CellMembrane::ScoreCellCycle(seuratObj, useAlternateG2M = useAlternateG2M)
+
+    saveData(seuratObj, datasetId)
+
+    # Cleanup
+    rm(seuratObj)
+    gc()
+}

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

@@ -222,6 +222,7 @@ public static void registerPipelineSteps()
         SequencePipelineService.get().registerPipelineStep(new FilterDisallowedClasses.Provider());
         SequencePipelineService.get().registerPipelineStep(new SummarizeTCellActivation.Provider());
         SequencePipelineService.get().registerPipelineStep(new RunScMetabolism.Provider());
+        SequencePipelineService.get().registerPipelineStep(new ScoreCellCycle.Provider());
 
         SequenceAnalysisService.get().registerReadsetListener(new SingleCellReadsetListener());
     }

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

@@ -0,0 +1,42 @@
+package org.labkey.singlecell.pipeline.singlecell;
+
+import org.json.JSONObject;
+import org.labkey.api.sequenceanalysis.pipeline.AbstractPipelineStepProvider;
+import org.labkey.api.sequenceanalysis.pipeline.PipelineContext;
+import org.labkey.api.singlecell.pipeline.SeuratToolParameter;
+import org.labkey.api.singlecell.pipeline.SingleCellStep;
+
+import java.util.Arrays;
+
+public class ScoreCellCycle extends AbstractCellMembraneStep
+{
+    public ScoreCellCycle(PipelineContext ctx, ScoreCellCycle.Provider provider)
+    {
+        super(provider, ctx);
+    }
+
+    public static class Provider extends AbstractPipelineStepProvider<SingleCellStep>
+    {
+        public Provider()
+        {
+            super("ScoreCellCycle", "Score Cell Cycle", "CellMembrane/Seurat", "This will score cells by cell cycle phase.", Arrays.asList(
+                    SeuratToolParameter.create("useAlternateG2M", "Use Alternate G2M Genes", "If checked, this will use a smaller set of G2M genes, defined from: https://raw.githubusercontent.com/hbc/tinyatlas/master/cell_cycle/Homo_sapiens.csv", "checkbox", new JSONObject(){{
+                        put("checked", true);
+                    }}, true)
+            ), null, null);
+        }
+
+        @Override
+        public ScoreCellCycle create(PipelineContext ctx)
+        {
+            return new ScoreCellCycle(ctx, this);
+        }
+    }
+
+    @Override
+    public String getFileSuffix()
+    {
+        return "cc";
+    }
+}
+