Update defaults for CellRangerGexCountStep

Author: bbimber

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

@@ -359,7 +359,8 @@ 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");
+        boolean discardBam = getProvider().getParameterByName(AbstractAlignmentStepProvider.DISCARD_BAM).extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), Boolean.class, false);
+        args.add("--create-bam=" + !discardBam);
 
         getWrapper().setWorkingDir(outputDirectory);