Walk back create-bam arg in CellRangerVDJWrapper

Author: bbimber

SequenceAnalysis/resources/web/SequenceAnalysis/panel/AnalysisSectionPanel.js

@@ -203,6 +203,8 @@ Ext4.define('SequenceAnalysis.panel.AnalysisSectionPanel', {
             title: 'Add Steps',
             border: false,
             width: 800,
+            autoScroll: true,
+            maxHeight: '90%',
             items: items,
             buttons: [{
                 text: 'Done',

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

@@ -395,9 +395,6 @@ public AlignmentStep.AlignmentOutput performAlignment(Readset rs, List<File> inp
                 lockFile.delete();
             }
 
-            boolean discardBam = getProvider().getParameterByName(AbstractAlignmentStepProvider.DISCARD_BAM).extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), Boolean.class, false);
-            args.add("--create-bam=" + !discardBam);
-
             getWrapper().execute(args);
 
             File outdir = new File(outputDirectory, id);
@@ -490,14 +487,13 @@ private File processOutputsForType(String sampleId, Readset rs, ReferenceGenome
                 }
             }
 
-            boolean discardBam = getProvider().getParameterByName(AbstractAlignmentStepProvider.DISCARD_BAM).extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), Boolean.class, false);
             File bam = new File(sampleDir, "all_contig.bam");
-            if (!discardBam && !bam.exists())
+            if (!bam.exists())
             {
                 throw new PipelineJobException("Unable to find file: " + bam.getPath());
             }
 
-            if (!discardBam && isPrimaryDir)
+            if (isPrimaryDir)
             {
                 output.setBAM(bam);
             }