Support nimble append

Author: bbimber

singlecell/resources/chunks/PerformDefaultNimbleAppend.R

@@ -0,0 +1,26 @@
+netRc <- paste0(Sys.getenv('USER_HOME'), '/.netrc')
+if (!file.exists(netRc)) {
+  print(list.files(Sys.getenv('USER_HOME')))
+  stop(paste0('Unable to find file: ', netRc))
+}
+
+invisible(Rlabkey::labkey.setCurlOptions(NETRC_FILE = netRc))
+Rdiscvr::SetLabKeyDefaults(baseUrl = serverBaseUrl, defaultFolder = defaultLabKeyFolder)
+
+# NOTE: this file is created by DownloadAndAppendNimble if there was an error. It might exist if a job failed and then was restarted
+if (file.exists('debug.nimble.txt.gz')) {
+  unlink('debug.nimble.txt.gz')
+}
+
+for (datasetId in names(seuratObjects)) {
+  printName(datasetId)
+  seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
+
+  Rdiscvr::PerformDefaultNimbleAppend(seuratObj)
+
+  saveData(seuratObj, datasetId)
+
+  # Cleanup
+  rm(seuratObj)
+  gc()
+}

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

@@ -71,6 +71,7 @@
 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.PerformDefaultNimbleAppend;
 import org.labkey.singlecell.pipeline.singlecell.PhenotypePlots;
 import org.labkey.singlecell.pipeline.singlecell.PlotAssayFeatures;
 import org.labkey.singlecell.pipeline.singlecell.PlotAverageCiteSeqCounts;
@@ -293,6 +294,7 @@ public static void registerPipelineSteps()
         SequencePipelineService.get().registerPipelineStep(new StudyMetadata.Provider());
         SequencePipelineService.get().registerPipelineStep(new UpdateSeuratPrototype.Provider());
         SequencePipelineService.get().registerPipelineStep(new RunDecoupler.Provider());
+        SequencePipelineService.get().registerPipelineStep(new PerformDefaultNimbleAppend.Provider());
 
         SequenceAnalysisService.get().registerReadsetListener(new SingleCellReadsetListener());
     }

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

@@ -0,0 +1,34 @@
+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;
+
+public class PerformDefaultNimbleAppend extends AbstractRDiscvrStep
+{
+    public PerformDefaultNimbleAppend(PipelineContext ctx, PerformDefaultNimbleAppend.Provider provider)
+    {
+        super(provider, ctx);
+    }
+
+    public static class Provider extends AbstractPipelineStepProvider<SingleCellStep>
+    {
+        public Provider()
+        {
+            super("PerformDefaultNimbleAppend", "Default Nimble Append", "RDiscvr", "This uses Rdiscvr to run the default nimble append, adding MHC, KIR, NKG, Viral and Ig data", null, null, null);
+        }
+
+        @Override
+        public PerformDefaultNimbleAppend create(PipelineContext ctx)
+        {
+            return new PerformDefaultNimbleAppend(ctx, this);
+        }
+    }
+
+    @Override
+    public String getFileSuffix()
+    {
+        return "nbl";
+    }
+}
+