Bugfix feature barcoding

Author: bbimber

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

@@ -143,7 +143,7 @@ public void processFilesRemote(List<Readset> readsets, JobContext ctx) throws Un
             else if (rs.getApplication().equals("CITE-Seq"))
             {
                 category = CITESEQ_CATEGORY;
-                featureFile = createFeatureRefForCiteSeq(ctx.getOutputDir(), CellHashingServiceImpl.get().getValidCiteSeqBarcodeFile(ctx.getSourceDirectory(), rs.getReadsetId()));
+                featureFile = createFeatureRefForCiteSeq(ctx.getOutputDir(), CellHashingServiceImpl.get().getValidCiteSeqBarcodeMetadataFile(ctx.getSourceDirectory(), rs.getReadsetId()));
             }
             else
             {
@@ -163,7 +163,7 @@ else if (rs.getApplication().equals("CITE-Seq"))
                 inputFastqs.add(Pair.of(rd.getFile1(), rd.getFile2()));
             });
 
-            List<String> args = wrapper.prepareCountArgs(output, id, ctx.getOutputDir(), rs, inputFastqs, extraArgs);
+            List<String> args = wrapper.prepareCountArgs(output, id, ctx.getOutputDir(), rs, inputFastqs, extraArgs, false);
 
             //https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis
             File libraryCsv = new File(ctx.getOutputDir(), "libraries.csv");

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

@@ -312,7 +312,7 @@ public AlignmentOutput performAlignment(Readset rs, File inputFastq1, @Nullable
             });
         }
 
-        List<String> args = new ArrayList<>(getWrapper().prepareCountArgs(output, id, outputDirectory, rs, inputFastqs, getClientCommandArgs("=")));
+        List<String> args = new ArrayList<>(getWrapper().prepareCountArgs(output, id, outputDirectory, rs, inputFastqs, getClientCommandArgs("="), true));
 
         Integer gtfId = getProvider().getParameterByName("gtfFile").extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), Integer.class);
         File gtfFile = getPipelineCtx().getSequenceSupport().getCachedData(gtfId);

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

@@ -67,7 +67,7 @@ public File getLocalFastqDir(File outputDirectory)
         return new File(outputDirectory, "localFq");
     }
 
-    public List<String> prepareCountArgs(AlignmentOutputImpl output, String id, File outputDirectory, Readset rs, List<Pair<File, File>> inputFastqPairs, List<String> extraArgs) throws PipelineJobException
+    public List<String> prepareCountArgs(AlignmentOutputImpl output, String id, File outputDirectory, Readset rs, List<Pair<File, File>> inputFastqPairs, List<String> extraArgs, boolean writeFastqArgs) throws PipelineJobException
     {
         List<String> args = new ArrayList<>();
         args.add(getExe(false).getPath());
@@ -96,7 +96,10 @@ public List<String> prepareCountArgs(AlignmentOutputImpl output, String id, File
         output.addIntermediateFile(localFqDir);
 
         Set<String> sampleNames = prepareFastqSymlinks(rs, localFqDir, inputFastqPairs);
-        args.add("--fastqs=" + localFqDir.getPath());
+        if (writeFastqArgs)
+        {
+            args.add("--fastqs=" + localFqDir.getPath());
+        }
 
         getLogger().debug("Sample names: [" + StringUtils.join(sampleNames, ",") + "]");
         if (sampleNames.size() > 1)