Allow scatter/gather job to not produce a VCF

bbimber · bbimber · commit 834878c68003 · 2023-09-27T09:24:47.000-07:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ProcessVariantsHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ProcessVariantsHandler.java
@@ -209,7 +209,8 @@ public static File getScatterOutputByCategory(JobContext ctx, final String categ
 
         if (scatterOutputs.isEmpty())
         {
-            throw new PipelineJobException("Unable to find final VCF");
+            ctx.getLogger().info("No outputs of category: " + category + " were found");
+            return null;
         }
         else if (scatterOutputs.size() > 1)
         {

Original file line number	Diff line number	Diff line change
`@@ -209,7 +209,8 @@ public static File getScatterOutputByCategory(JobContext ctx, final String categ`
`209`	`209`
`210`	`210`	`if (scatterOutputs.isEmpty())`
`211`	`211`	`{`
`212`		`- throw new PipelineJobException("Unable to find final VCF");`
	`212`	`+ ctx.getLogger().info("No outputs of category: " + category + " were found");`
	`213`	`+ return null;`
`213`	`214`	`}`
`214`	`215`	`else if (scatterOutputs.size() > 1)`
`215`	`216`	`{`