Bugfix to AnnotationStep

bbimber · bbimber · commit 5b95849300ef · 2023-10-03T16:54:32.000-07:00
diff --git a/mGAP/src/org/labkey/mgap/pipeline/AnnotationStep.java b/mGAP/src/org/labkey/mgap/pipeline/AnnotationStep.java
@@ -605,7 +605,7 @@ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGeno
 
     private File getFieldConfigFile()
     {
-        return new File(getPipelineCtx().getSourceDirectory(), "funcotatorFields.txt");
+        return new File(getPipelineCtx().getSourceDirectory(true), "funcotatorFields.txt");
     }
 
     private void addToolFieldNames(String toolName, String argName, List<String> options, File outDir, VariantProcessingStepOutputImpl output, @Nullable List<String> extraFields) throws PipelineJobException

Original file line number	Diff line number	Diff line change
`@@ -605,7 +605,7 @@ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGeno`
`605`	`605`
`606`	`606`	`private File getFieldConfigFile()`
`607`	`607`	`{`
`608`		`- return new File(getPipelineCtx().getSourceDirectory(), "funcotatorFields.txt");`
	`608`	`+ return new File(getPipelineCtx().getSourceDirectory(true), "funcotatorFields.txt");`
`609`	`609`	`}`
`610`	`610`
`611`	`611`	`private void addToolFieldNames(String toolName, String argName, List<String> options, File outDir, VariantProcessingStepOutputImpl output, @Nullable List<String> extraFields) throws PipelineJobException`