Capture CS-Core output

Author: bbimber

singlecell/resources/chunks/RunCsCore.R

@@ -2,7 +2,9 @@ for (datasetId in names(seuratObjects)) {
     printName(datasetId)
     seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
 
-    seuratObj <- CellMembrane::RunCsCore(seuratObj, saveFile = 'cscoreResults.rds')
+    outFile <- paste0(outputPrefix, '.', makeLegalFileName(datasetId), '.markers.txt')
+    module_list <- CellMembrane::RunCsCore(seuratObj, saveFile = paste0(outFile, '.cscore.rds'))
+    saveRDS(module_list, paste0(outFile, '.cscore.wgcna.rds'))
 
     saveData(seuratObj, datasetId)
 

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

@@ -1,13 +1,14 @@
 package org.labkey.singlecell.pipeline.singlecell;
 
-import org.json.JSONObject;
+import org.labkey.api.pipeline.PipelineJobException;
 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.sequenceanalysis.pipeline.SequenceOutputHandler;
 import org.labkey.api.singlecell.pipeline.SingleCellStep;
 
-import java.util.Arrays;
+import java.io.File;
 import java.util.Collections;
+import java.util.List;
 
 public class RunCsCore extends AbstractCellMembraneStep
 {
@@ -30,9 +31,37 @@ public RunCsCore create(PipelineContext ctx)
         }
     }
 
+    @Override
+    public boolean createsSeuratObjects()
+    {
+        return false;
+    }
+
     @Override
     public String getFileSuffix()
     {
         return "cscore";
     }
+
+    @Override
+    public Output execute(SequenceOutputHandler.JobContext ctx, List<SeuratObjectWrapper> inputObjects, String outputPrefix) throws PipelineJobException
+    {
+        Output output = super.execute(ctx, inputObjects, outputPrefix);
+
+        // Add the RDS files:
+        File[] outputs = ctx.getOutputDir().listFiles(f -> f.isDirectory() && f.getName().endsWith(".cscore.wgcna.rds"));
+        if (outputs == null || outputs.length == 0)
+        {
+            return output;
+        }
+
+        for (File rds : outputs)
+        {
+            String sn = rds.getName().replaceAll(".cscore.wgcna.rds", "");
+
+            output.addSequenceOutput(rds, "CS-CORE: " + sn, "CS-CORE Results", inputObjects.get(0).getReadsetId(), null, ctx.getSequenceSupport().getCachedGenomes().iterator().next().getGenomeId(), null);
+        }
+
+        return output;
+    }
 }