Add ApplyKnownClonotypicData step

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FastqcRunner.java

@@ -17,16 +17,16 @@
 
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
-import org.apache.logging.log4j.Logger;
 import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.Nullable;
 import org.junit.Assert;
 import org.junit.Test;
 import org.labkey.api.module.Module;
 import org.labkey.api.module.ModuleLoader;
 import org.labkey.api.pipeline.PipelineJobService;
-import org.labkey.api.resource.FileResource;
 import org.labkey.api.resource.DirectoryResource;
+import org.labkey.api.resource.FileResource;
 import org.labkey.api.resource.Resource;
 import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService;
 import org.labkey.api.settings.AppProps;
@@ -52,7 +52,6 @@
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
-import java.util.stream.Collectors;
 import java.util.zip.GZIPInputStream;
 
 /**

singlecell/resources/chunks/ApplyKnownClontypicData.R

@@ -0,0 +1,20 @@
+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, connect-timeout = 10))
+Rdiscvr::SetLabKeyDefaults(baseUrl = serverBaseUrl, defaultFolder = defaultLabKeyFolder)
+
+for (datasetId in names(seuratObjects)) {
+    printName(datasetId)
+    seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
+
+    seuratObj <- ApplyKnownClontypicData(seuratObj, groupFields = groupFields, addMetadata = addMetadata)
+    saveData(seuratObj, datasetId)
+
+    # Cleanup
+    rm(seuratObj)
+    gc()
+}

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

@@ -42,6 +42,7 @@
 import org.labkey.singlecell.pipeline.singlecell.AppendNimble;
 import org.labkey.singlecell.pipeline.singlecell.AppendSaturation;
 import org.labkey.singlecell.pipeline.singlecell.AppendTcr;
+import org.labkey.singlecell.pipeline.singlecell.ApplyKnownClonotypicData;
 import org.labkey.singlecell.pipeline.singlecell.AvgExpression;
 import org.labkey.singlecell.pipeline.singlecell.CalculateGeneComponentScores;
 import org.labkey.singlecell.pipeline.singlecell.CalculateUCellScores;
@@ -299,6 +300,7 @@ public static void registerPipelineSteps()
         SequencePipelineService.get().registerPipelineStep(new PerformDefaultNimbleAppend.Provider());
         SequencePipelineService.get().registerPipelineStep(new PerformMhcDimRedux.Provider());
         SequencePipelineService.get().registerPipelineStep(new RunTricycle.Provider());
+        SequencePipelineService.get().registerPipelineStep(new ApplyKnownClonotypicData.Provider());
 
         SequenceAnalysisService.get().registerReadsetListener(new SingleCellReadsetListener());
     }

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

@@ -0,0 +1,39 @@
+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.List;
+
+public class ApplyKnownClonotypicData extends AbstractRDiscvrStep
+{
+    public ApplyKnownClonotypicData(PipelineContext ctx, ApplyKnownClonotypicData.Provider provider)
+    {
+        super(provider, ctx);
+    }
+
+    public static class Provider extends AbstractPipelineStepProvider<SingleCellStep>
+    {
+        public Provider()
+        {
+            super("ApplyKnownClonotypicData", "Append Known Clonotype/Antigen Data", "RDiscvr", "This will query the clone_responses table and append a column tagging each cell for matching antigens (based on clonotype)", List.of(
+
+            ), null, null);
+        }
+
+
+        @Override
+        public ApplyKnownClonotypicData create(PipelineContext ctx)
+        {
+            return new ApplyKnownClonotypicData(ctx, this);
+        }
+    }
+
+    @Override
+    public String getFileSuffix()
+    {
+        return "ctd";
+    }
+}
+