Dont delete funcotator fields file

bbimber · bbimber · commit 6b7f83e8f596 · 2023-10-04T06:52:41.000-07:00
diff --git a/mGAP/src/org/labkey/mgap/pipeline/AnnotationStep.java b/mGAP/src/org/labkey/mgap/pipeline/AnnotationStep.java
@@ -524,8 +524,6 @@ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGeno
                 }
 
                 File configFile = getFieldConfigFile();
-                output.addIntermediateFile(configFile);
-
                 fr.runFuncotator(funcotatorSourceDir, liftedToGRCh37, funcotatorAnnotated, grch37Genome, configFile, extraArgs);
             }
             else

Original file line number	Diff line number	Diff line change
`@@ -524,8 +524,6 @@ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGeno`
`524`	`524`	`}`
`525`	`525`
`526`	`526`	`File configFile = getFieldConfigFile();`
`527`		`- output.addIntermediateFile(configFile);`
`528`		`-`
`529`	`527`	`fr.runFuncotator(funcotatorSourceDir, liftedToGRCh37, funcotatorAnnotated, grch37Genome, configFile, extraArgs);`
`530`	`528`	`}`
`531`	`529`	`else`