Allow user to specify chain when running cellranger vdj

Author: bbimber

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

@@ -301,12 +301,6 @@ public AlignmentStep.IndexOutput createIndex(ReferenceGenome referenceGenome, Fi
                 args.add("--seqs=" + getGenomeFasta().getPath());
                 args.add("--genome=" + indexDir.getName());
 
-                String chain = getProvider().getParameterByName(CHAIN).extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), String.class);
-                if (StringUtils.trimToNull(chain) != null)
-                {
-                    args.add("--chain=" + chain);
-                }
-
                 getWrapper().setWorkingDir(indexDir.getParentFile());
                 getWrapper().execute(args);
 
@@ -342,6 +336,12 @@ public AlignmentStep.AlignmentOutput performAlignment(Readset rs, List<File> inp
             File indexDir = AlignerIndexUtil.getIndexDir(referenceGenome, getIndexCachedDirName(getPipelineCtx().getJob()));
             args.add("--reference=" + indexDir.getPath());
 
+            String chainArg = getProvider().getParameterByName(CHAIN).extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), String.class);
+            if (StringUtils.trimToNull(chainArg) != null)
+            {
+                args.add("--chain=" + chainArg);
+            }
+
             String primers = StringUtils.trimToNull(getProvider().getParameterByName(INNER_ENRICHMENT_PRIMERS).extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), String.class, null));
             if (primers != null)
             {