Copy bbmap index to correct dir

bbimber · bbimber · commit bf6e784c29a2 · 2025-05-18T09:35:08.000-07:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/BBMapWrapper.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/BBMapWrapper.java
@@ -91,7 +91,7 @@ public AlignmentOutput performAlignment(Readset rs, List<File> inputFastqs1, @Nu
                 throw new PipelineJobException("ref dir not found: " + localIdx);
             }
 
-            File refDir = new File(getPipelineCtx().getWorkingDirectory(), "ref");
+            File refDir = new File(outputDirectory, "ref");
             try
             {
                 if (refDir.exists())

Original file line number	Diff line number	Diff line change
`@@ -91,7 +91,7 @@ public AlignmentOutput performAlignment(Readset rs, List<File> inputFastqs1, @Nu`
`91`	`91`	`throw new PipelineJobException("ref dir not found: " + localIdx);`
`92`	`92`	`}`
`93`	`93`
`94`		`- File refDir = new File(getPipelineCtx().getWorkingDirectory(), "ref");`
	`94`	`+ File refDir = new File(outputDirectory, "ref");`
`95`	`95`	`try`
`96`	`96`	`{`
`97`	`97`	`if (refDir.exists())`