Add null check

bbimber · bbimber · commit 6b2eea5d4d50 · 2021-02-04T11:56:27.000-08:00
diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/AppendCiteSeq.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/AppendCiteSeq.java
@@ -133,7 +133,7 @@ protected Map<Integer, File> prepareCountData(SingleCellOutput output, SequenceO
                 ctx.getLogger().info("CITE-seq not used, skipping: " + parentReadset.getName());
             }
 
-            dataIdToCalls.put(wrapper.getSequenceOutputFileId(), finalOutput.getParentFile());
+            dataIdToCalls.put(wrapper.getSequenceOutputFileId(), finalOutput == null ? null : finalOutput.getParentFile());
         }
 
         return dataIdToCalls;

Original file line number	Diff line number	Diff line change
`@@ -133,7 +133,7 @@ protected Map<Integer, File> prepareCountData(SingleCellOutput output, SequenceO`
`133`	`133`	`ctx.getLogger().info("CITE-seq not used, skipping: " + parentReadset.getName());`
`134`	`134`	`}`
`135`	`135`
`136`		`- dataIdToCalls.put(wrapper.getSequenceOutputFileId(), finalOutput.getParentFile());`
	`136`	`+ dataIdToCalls.put(wrapper.getSequenceOutputFileId(), finalOutput == null ? null : finalOutput.getParentFile());`
`137`	`137`	`}`
`138`	`138`
`139`	`139`	`return dataIdToCalls;`