diff --git a/singlecell/api-src/org/labkey/api/singlecell/pipeline/AbstractSingleCellPipelineStep.java b/singlecell/api-src/org/labkey/api/singlecell/pipeline/AbstractSingleCellPipelineStep.java
index add9ee2da..b10ba3191 100644
--- a/singlecell/api-src/org/labkey/api/singlecell/pipeline/AbstractSingleCellPipelineStep.java
+++ b/singlecell/api-src/org/labkey/api/singlecell/pipeline/AbstractSingleCellPipelineStep.java
@@ -348,38 +348,52 @@ public static void executeR(SequenceOutputHandler.JobContext ctx, String dockerC
         localBashScript.delete();
     }
 
-    protected String prepareValueForR(SeuratToolParameter pd)
+    protected void addParameterVariables(SeuratToolParameter pd, List<String> body)
     {
         String val = StringUtils.trimToNull(pd.extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx()));
         if (val == null)
         {
-            return "NULL";
+            body.add((pd.getVariableName() + " <- NULL"));
         }
         else if ("false".equals(val))
         {
-            return "FALSE";
+            body.add((pd.getVariableName() + " <- FALSE"));
         }
         else if ("true".equals(val))
         {
-            return "TRUE";
+            body.add((pd.getVariableName() + " <- TRUE"));
         }
         else if (NumberUtils.isCreatable(val))
         {
-            return val;
+            body.add((pd.getVariableName() + " <- " + val));
         }
         else if ("sequenceanalysis-trimmingtextarea".equals(pd.getFieldXtype()))
         {
             val = val.replace("'", "\\\'");
-            String[] vals = val.split(pd.getDelimiter());
-            return "c('" + StringUtils.join(vals, "','") + "')";
+            serializeMultiValueParam(pd, body, val);
         }
         else if (pd.isMultiValue())
         {
-            String[] vals = val.split(pd.getDelimiter());
-            return "c('" + StringUtils.join(vals, "','") + "')";
+            serializeMultiValueParam(pd, body, val);
         }
+        else
+        {
+            body.add((pd.getVariableName() + " <- '" + val + "'"));
+        }
+    }
 
-        return  "'" + val + "'";
+    private void serializeMultiValueParam(SeuratToolParameter pd, List<String> body, String val)
+    {
+        String[] vals = val.split(pd.getDelimiter());
+        final int batchSize = 75;
+        int numBatches = (int)Math.ceil((double)vals.length / batchSize);
+
+        for (int i=0;i<numBatches;i++)
+        {
+            int start = (i * batchSize);
+            int end = Math.min(start + batchSize, vals.length);
+            body.add(pd.getVariableName() + " <- " + "c(" + (i == 0 ? "" : pd.getVariableName() + ", ") + "'" + StringUtils.join(Arrays.copyOfRange(vals, start, end), "','") + "')");
+        }
     }
 
     protected List<String> loadChunkFromFile() throws PipelineJobException
@@ -423,7 +437,7 @@ protected Chunk createParamChunk(SequenceOutputHandler.JobContext ctx, List<Seur
                 SeuratToolParameter stp = (SeuratToolParameter)pd;
                 if (stp.shouldIncludeInMarkdown(getPipelineCtx().getJob(), getProvider(), getStepIdx()))
                 {
-                    body.add(((SeuratToolParameter) pd).getVariableName() + " <- " + prepareValueForR(stp));
+                    addParameterVariables(stp, body);
                 }
             }
         }
diff --git a/singlecell/api-src/org/labkey/api/singlecell/pipeline/SeuratToolParameter.java b/singlecell/api-src/org/labkey/api/singlecell/pipeline/SeuratToolParameter.java
index 968b84ade..86e329d57 100644
--- a/singlecell/api-src/org/labkey/api/singlecell/pipeline/SeuratToolParameter.java
+++ b/singlecell/api-src/org/labkey/api/singlecell/pipeline/SeuratToolParameter.java
@@ -50,7 +50,7 @@ public String getVariableName()
         return _rName == null ? getName() : _rName;
     }
 
-    public boolean shouldIncludeInMarkdown(PipelineJob job, PipelineStepProvider provider, int stepIdx)
+    public boolean shouldIncludeInMarkdown(PipelineJob job, PipelineStepProvider<?> provider, int stepIdx)
     {
         if (!_includeIfEmptyOrNull)
         {
diff --git a/singlecell/resources/chunks/NimbleAppend.R b/singlecell/resources/chunks/AppendNimble.R
similarity index 100%
rename from singlecell/resources/chunks/NimbleAppend.R
rename to singlecell/resources/chunks/AppendNimble.R
diff --git a/singlecell/resources/chunks/TcrFilter.R b/singlecell/resources/chunks/TcrFilter.R
index 7da1c4e08..3a5066254 100644
--- a/singlecell/resources/chunks/TcrFilter.R
+++ b/singlecell/resources/chunks/TcrFilter.R
@@ -18,7 +18,11 @@ for (datasetId in names(seuratObjects)) {
 
     cdr3ForLocus <- gsub(cdr3ForLocus, pattern = paste0(fieldName, ':'), replacement = '')
     matchingCells <- sapply(seuratObj@meta.data[[fieldName]], function(x){
-      values <- unlist(strsplit(x, split = ','))
+      if (is.na(x)) {
+        return(FALSE)
+      }
+
+      values <- unlist(strsplit(as.character(x), split = ','))
       return(length(intersect(values, cdr3ForLocus)) != 0)
     })
 
@@ -37,8 +41,9 @@ for (datasetId in names(seuratObjects)) {
   if (all(is.null(cellsToKeep))) {
     print('There were no matching cells')
   } else {
+    print(paste0('Total passing cells: ', length(cellsToKeep)))
     seuratObj <- subset(seuratObj, cells = cellsToKeep)
-    #saveData(seuratObj, datasetId)
+    saveData(seuratObj, datasetId)
     totalPassed <- totalPassed + 1
   }
 
diff --git a/singlecell/src/org/labkey/singlecell/SingleCellModule.java b/singlecell/src/org/labkey/singlecell/SingleCellModule.java
index 6c2b35a02..821328730 100644
--- a/singlecell/src/org/labkey/singlecell/SingleCellModule.java
+++ b/singlecell/src/org/labkey/singlecell/SingleCellModule.java
@@ -188,7 +188,7 @@ public static void registerPipelineSteps()
         SequencePipelineService.get().registerPipelineStep(new CheckExpectations.Provider());
         SequencePipelineService.get().registerPipelineStep(new CommonFilters.Provider());
         SequencePipelineService.get().registerPipelineStep(new RunVision.Provider());
-        SequencePipelineService.get().registerPipelineStep(new NimbleAppend.Provider());
+        SequencePipelineService.get().registerPipelineStep(new AppendNimble.Provider());
         SequencePipelineService.get().registerPipelineStep(new AppendTcr.Provider());
         SequencePipelineService.get().registerPipelineStep(new TcrFilter.Provider());
 
diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/NimbleAppend.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/AppendNimble.java
similarity index 88%
rename from singlecell/src/org/labkey/singlecell/pipeline/singlecell/NimbleAppend.java
rename to singlecell/src/org/labkey/singlecell/pipeline/singlecell/AppendNimble.java
index bcf8822f6..7088332c1 100644
--- a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/NimbleAppend.java
+++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/AppendNimble.java
@@ -15,9 +15,9 @@
 import java.util.List;
 import java.util.Set;
 
-public class NimbleAppend extends AbstractRDiscvrStep
+public class AppendNimble extends AbstractRDiscvrStep
 {
-    public NimbleAppend(PipelineContext ctx, NimbleAppend.Provider provider)
+    public AppendNimble(PipelineContext ctx, AppendNimble.Provider provider)
     {
         super(provider, ctx);
     }
@@ -35,9 +35,9 @@ public Provider()
 
 
         @Override
-        public NimbleAppend create(PipelineContext ctx)
+        public AppendNimble create(PipelineContext ctx)
         {
-            return new NimbleAppend(ctx, this);
+            return new AppendNimble(ctx, this);
         }
     }
 
@@ -62,6 +62,7 @@ protected Chunk createParamChunk(SequenceOutputHandler.JobContext ctx, List<Seur
         ret.bodyLines.add("nimbleGenomes <- list(");
         String genomeStr = getProvider().getParameterByName("nimbleGenomes").extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), String.class);
         JSONArray json = new JSONArray(genomeStr);
+        String delim = "";
         for (int i = 0; i < json.length(); i++)
         {
             JSONArray arr = json.getJSONArray(i);
@@ -72,7 +73,8 @@ protected Chunk createParamChunk(SequenceOutputHandler.JobContext ctx, List<Seur
 
             int genomeId = arr.getInt(0);
             String targetAssay = arr.getString(1);
-            ret.bodyLines.add("\t" + genomeId + " = " + targetAssay);
+            ret.bodyLines.add("\t" + delim + "'" + genomeId + "' = '" + targetAssay + "'");
+            delim = ",";
         }
         ret.bodyLines.add(")");
 
diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/CheckExpectations.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/CheckExpectations.java
index c98270562..dd9a5b15c 100644
--- a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/CheckExpectations.java
+++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/CheckExpectations.java
@@ -72,10 +72,15 @@ protected Chunk createParamChunk(SequenceOutputHandler.JobContext ctx, List<Seur
 
         for (SeuratObjectWrapper so : inputObjects)
         {
+            if (so.getSequenceOutputFile().getReadset() == null)
+            {
+                throw new PipelineJobException("Unable to find readset for outputfile: " + so.getSequenceOutputFileId() + ". This set requires single-dataset inputs. Removing this step may be a solution.");
+            }
+
             Readset parentReadset = ctx.getSequenceSupport().getCachedReadset(so.getSequenceOutputFile().getReadset());
             if (parentReadset == null)
             {
-                throw new PipelineJobException("Unable to find readset for outputfile: " + so.getSequenceOutputFileId());
+                throw new PipelineJobException("Unable to find readset for outputfile: " + so.getSequenceOutputFileId() + ". This set requires single-dataset inputs. Removing this step may be a solution.");
             }
 
             Set<String> htosPerReadset = CellHashingServiceImpl.get().getHtosForParentReadset(parentReadset.getReadsetId(), ctx.getSourceDirectory(), ctx.getSequenceSupport(), false);