Allow cellranger VDJ to finish when there are no a/b hits

Author: bbimber

singlecell/api-src/org/labkey/api/singlecell/CellHashingService.java

@@ -93,6 +93,7 @@ public static class CellHashingParameters
         public @Nullable Integer genomeId;
         public Integer editDistance = 2;
         public boolean scanEditDistances = false;
+        public boolean skipNormalizationQc = false;
         public Integer minCountPerCell = 5;
         public List<CALLING_METHOD> methods = CALLING_METHOD.getDefaultMethods();
         public String basename = null;
@@ -108,6 +109,7 @@ public static CellHashingService.CellHashingParameters createFromStep(SequenceOu
             CellHashingService.CellHashingParameters ret = new CellHashingService.CellHashingParameters();
             ret.type = type;
             ret.scanEditDistances = step.getProvider().getParameterByName("scanEditDistances").extractValue(ctx.getJob(), step.getProvider(), step.getStepIdx(), Boolean.class, false);
+            ret.skipNormalizationQc = step.getProvider().getParameterByName("skipNormalizationQc").extractValue(ctx.getJob(), step.getProvider(), step.getStepIdx(), Boolean.class, false);
             ret.editDistance = step.getProvider().getParameterByName("editDistance").extractValue(ctx.getJob(), step.getProvider(), step.getStepIdx(), Integer.class, 2);
             ret.minCountPerCell = step.getProvider().getParameterByName("minCountPerCell").extractValue(ctx.getJob(), step.getProvider(), step.getStepIdx(), Integer.class, 3);
             ret.htoOrCiteseqReadset = htoOrCiteseqReadset;
@@ -136,6 +138,7 @@ public static CellHashingParameters createFromJson(BARCODE_TYPE type, File webse
             CellHashingParameters ret = new CellHashingParameters();
             ret.type = type;
             ret.scanEditDistances = params.optBoolean("scanEditDistances", false);
+            ret.skipNormalizationQc = params.optBoolean("skipNormalizationQc", false);
             ret.editDistance = params.optInt("editDistance", 2);
             ret.minCountPerCell = params.optInt("minCountPerCell", 3);
             ret.htoOrCiteseqReadset = htoOrCiteseqReadset;

singlecell/src/org/labkey/singlecell/CellHashingServiceImpl.java

@@ -830,7 +830,8 @@ public List<ToolParameterDescriptor> getDefaultHashingParams(boolean includeExcl
                     put("checked", false);
                 }}, false),
                 ToolParameterDescriptor.create("editDistance", "Edit Distance", null, "ldk-integerfield", null, 2),
-                ToolParameterDescriptor.create("minCountPerCell", "Min Reads/Cell", null, "ldk-integerfield", null, 5)
+                ToolParameterDescriptor.create("minCountPerCell", "Min Reads/Cell", null, "ldk-integerfield", null, 5),
+                ToolParameterDescriptor.create("skipNormalizationQc", "Skip Normalization QC", null, "checkbox", null, true)
         ));
 
         if (type == BARCODE_TYPE.hashing)
@@ -1238,7 +1239,8 @@ private File generateCellHashingCalls(File citeSeqCountOutDir, File outputDir, S
             Set<String> allowableBarcodes = parameters.getAllowableBarcodeNames();
             String allowableBarcodeParam = allowableBarcodes != null ? "c('" + StringUtils.join(allowableBarcodes, "','") + "')" : "NULL";
 
-            writer.println("f <- cellhashR::CallAndGenerateReport(rawCountData = '/work/" + citeSeqCountOutDir.getName() + "', reportFile = '/work/" + htmlFile.getName() + "', callFile = '/work/" + callsFile.getName() + "', metricsFile = '/work/" + metricsFile.getName() + "', cellbarcodeWhitelist  = " + cellbarcodeWhitelist + ", barcodeWhitelist = " + allowableBarcodeParam + ", title = '" + parameters.getReportTitle() + "', methods = c('" + StringUtils.join(methodNames, "','") + "'))");
+            String skipNormalizationQcString = parameters.skipNormalizationQc ? "TRUE" : "FALSE";
+            writer.println("f <- cellhashR::CallAndGenerateReport(rawCountData = '/work/" + citeSeqCountOutDir.getName() + "', reportFile = '/work/" + htmlFile.getName() + "', callFile = '/work/" + callsFile.getName() + "', metricsFile = '/work/" + metricsFile.getName() + "', cellbarcodeWhitelist  = " + cellbarcodeWhitelist + ", barcodeWhitelist = " + allowableBarcodeParam + ", title = '" + parameters.getReportTitle() + "', skipNormalizationQc = " + skipNormalizationQcString + ", methods = c('" + StringUtils.join(methodNames, "','") + "'))");
             writer.println("print('Rmarkdown complete')");
 
         }

singlecell/src/org/labkey/singlecell/run/CellRangerVDJWrapper.java

@@ -374,16 +374,23 @@ public AlignmentStep.AlignmentOutput performAlignment(Readset rs, File inputFast
                 File outputVloupe = new File(outdir, "vloupe.vloupe");
                 if (!outputVloupe.exists())
                 {
-                    throw new PipelineJobException("Unable to find file: " + outputVloupe.getPath());
+                    //NOTE: if there were no A/B hits, the vLoupe isnt created, but all other outputs exist
+                    File csv = new File(outdir, "all_contig_annotations.csv");
+                    if (!csv.exists())
+                    {
+                        throw new PipelineJobException("Unable to find file: " + outputVloupe.getPath());
+                    }
                 }
-
-                File outputVloupeRename = new File(outdir, prefix + outputVloupe.getName());
-                if (outputVloupeRename.exists())
+                else
                 {
-                    outputVloupeRename.delete();
+                    File outputVloupeRename = new File(outdir, prefix + outputVloupe.getName());
+                    if (outputVloupeRename.exists())
+                    {
+                        outputVloupeRename.delete();
+                    }
+                    FileUtils.moveFile(outputVloupe, outputVloupeRename);
+                    output.addSequenceOutput(outputVloupeRename, rs.getName() + " 10x VLoupe", "10x VLoupe", rs.getRowId(), null, referenceGenome.getGenomeId(), null);
                 }
-                FileUtils.moveFile(outputVloupe, outputVloupeRename);
-                output.addSequenceOutput(outputVloupeRename, rs.getName() + " 10x VLoupe", "10x VLoupe", rs.getRowId(), null, referenceGenome.getGenomeId(), null);
             }
             catch (IOException e)
             {