Update cellranger arguments

Author: bbimber

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

@@ -252,6 +252,8 @@ private void processType(List<Pair<File, File>> inputFastqs, AlignmentOutputImpl
             File indexDir = makeDummyIndex(ctx);
             args.add("--transcriptome=" + indexDir.getPath());
 
+            args.add("--create-bam=false");
+
             wrapper.setWorkingDir(ctx.getOutputDir());
 
             //Note: we can safely assume only this server is working on these files, so if the _lock file exists, it was from a previous failed job.
@@ -284,12 +286,10 @@ private void processType(List<Pair<File, File>> inputFastqs, AlignmentOutputImpl
             File outsdir = new File(crDir, "outs");
 
             File bam = new File(outsdir, "possorted_genome_bam.bam");
-            if (!bam.exists())
+            if (bam.exists())
             {
-                throw new PipelineJobException("Unable to find file: " + bam.getPath());
+                throw new PipelineJobException("Did not expect to find BAM: " + bam.getPath());
             }
-            bam.delete();
-            SequenceAnalysisService.get().getExpectedBamOrCramIndex(bam).delete();
 
             wrapper.deleteSymlinks(wrapper.getLocalFastqDir(ctx.getOutputDir()));
 

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

@@ -352,6 +352,8 @@ public AlignmentOutput performAlignment(Readset rs, List<File> inputFastqs1, @Nu
         File indexDir = AlignerIndexUtil.getIndexDir(referenceGenome, getIndexCachedDirName(getPipelineCtx().getJob()));
         args.add("--transcriptome=" + indexDir.getPath());
 
+        args.add("--create-bam=true");
+
         getWrapper().setWorkingDir(outputDirectory);
 
         //Note: we can safely assume only this server is working on these files, so if the _lock file exists, it was from a previous failed job.