diff --git a/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerCellHashingHandler.java b/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerCellHashingHandler.java
index 00be83f8c..79c2bcc53 100644
--- a/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerCellHashingHandler.java
+++ b/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerCellHashingHandler.java
@@ -248,7 +248,7 @@ public static File processBarcodeFile(SequenceOutputHandler.JobContext ctx, File
         //prepare whitelist of cell indexes
         File cellBarcodeWhitelist = utils.getValidCellIndexFile();
         Set<String> uniqueBarcodes = new HashSet<>();
-        ctx.getLogger().debug("writing cell barcodes");
+        ctx.getLogger().debug("writing cell barcodes, using file: " + perCellTsv.getPath());
         try (CSVWriter writer = new CSVWriter(PrintWriters.getPrintWriter(cellBarcodeWhitelist), ',', CSVWriter.NO_QUOTE_CHARACTER);CSVReader reader = new CSVReader(IOUtil.openFileForBufferedUtf8Reading(perCellTsv), '\t'))
         {
             int rowIdx = 0;
diff --git a/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJUtils.java b/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJUtils.java
index a71cf5bac..4c376e533 100644
--- a/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJUtils.java
+++ b/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJUtils.java
@@ -376,7 +376,7 @@ public File runRemoteVdjCellHashingTasks(PipelineStepOutput output, String outpu
         File cellBarcodeWhitelist = getValidCellIndexFile();
         Set<String> uniqueBarcodes = new HashSet<>();
         Set<String> uniqueBarcodesIncludingNoCDR3 = new HashSet<>();
-        _log.debug("writing cell barcodes");
+        _log.debug("writing cell barcodes, using file: " + perCellTsv.getPath());
         try (CSVWriter writer = new CSVWriter(PrintWriters.getPrintWriter(cellBarcodeWhitelist), ',', CSVWriter.NO_QUOTE_CHARACTER); CSVReader reader = new CSVReader(Readers.getReader(perCellTsv), ','))
         {
             int rowIdx = 0;
diff --git a/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJWrapper.java b/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJWrapper.java
index b63bdedf5..19fe214ca 100644
--- a/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJWrapper.java
+++ b/tcrdb/src/org/labkey/tcrdb/pipeline/CellRangerVDJWrapper.java
@@ -68,6 +68,7 @@ public CellRangerVDJWrapper(@Nullable Logger logger)
 
     public static final String TARGET_ASSAY = "targetAssay";
     public static final String DELETE_EXISTING_ASSAY_DATA = "deleteExistingAssayData";
+    public static final String INNER_ENRICHMENT_PRIMERS = "innerEnrichmentPrimers";
 
     public static class VDJProvider extends AbstractAlignmentStepProvider<AlignmentStep>
     {
@@ -82,6 +83,13 @@ public VDJProvider()
                     ToolParameterDescriptor.createCommandLineParam(CommandLineParam.create("--force-cells"), "force-cells", "Force Cells", "Force pipeline to use this number of cells, bypassing the cell detection algorithm. Use this if the number of cells estimated by Cell Ranger is not consistent with the barcode rank plot.", "ldk-integerfield", new JSONObject(){{
                         put("minValue", 0);
                     }}, null),
+                    ToolParameterDescriptor.createCommandLineParam(CommandLineParam.createSwitch("--disable-ui"), "disable-ui", "Disable UI", "If checked, this will run cellranger with the optional web-based UI disabled.", "checkbox", new JSONObject(){{
+                        put("checked", true);
+                    }}, true),
+                    ToolParameterDescriptor.create(INNER_ENRICHMENT_PRIMERS, "Inner Enrichment Primers", "An option comma-separated list of the inner primers used for TCR enrichment. These will be used for trimming.", "textarea", new JSONObject(){{
+                        put("height", 100);
+                        put("width", 400);
+                    }}, null),
                     ToolParameterDescriptor.create(TARGET_ASSAY, "Target Assay", "Results will be loaded into this assay.  If no assay is selected, a table will be created with nothing in the DB.", "tcr-assayselectorfield", new JSONObject(){{
                         put("autoSelectAssay", false);
                     }}, null),
@@ -296,6 +304,32 @@ public AlignmentStep.AlignmentOutput performAlignment(Readset rs, File inputFast
             File indexDir = AlignerIndexUtil.getIndexDir(referenceGenome, getIndexCachedDirName(getPipelineCtx().getJob()));
             args.add("--reference=" + indexDir.getPath());
 
+            String primers = StringUtils.trimToNull(getProvider().getParameterByName(INNER_ENRICHMENT_PRIMERS).extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), String.class, null));
+            if (primers != null)
+            {
+                primers = primers.replaceAll("\\s+", ",");
+                primers = primers.replaceAll(",+", ",");
+
+                File primerFile = new File(outputDirectory, "primers.txt");
+                try (PrintWriter writer = PrintWriters.getPrintWriter(primerFile))
+                {
+                    Arrays.stream(primers.split(",")).forEach(x -> {
+                        x = StringUtils.trimToNull(x);
+                        if (x != null)
+                        {
+                            writer.println(x);
+                        }
+                    });
+                }
+                catch (IOException e)
+                {
+                    throw new PipelineJobException(e);
+                }
+
+                output.addIntermediateFile(primerFile);
+                args.add("--inner-enrichment-primers=" + primerFile.getPath());
+            }
+
             args.addAll(getClientCommandArgs("="));
 
             Integer maxThreads = SequencePipelineService.get().getMaxThreads(getPipelineCtx().getLogger());