Set scores only for PGS testcase

genepi · Aug 3, 2020 · 980b2eb · 980b2eb
1 parent d854b31
commit 980b2eb
Showing 1 changed file with 1 addition and 2 deletions.
diff --git a/src/test/java/genepi/imputationserver/steps/ImputationTest.java b/src/test/java/genepi/imputationserver/steps/ImputationTest.java
@@ -401,7 +401,6 @@ public void testPipelineWithEagle() throws IOException, ZipException {
 
 		// create workflow context
 		WorkflowTestContext context = buildContext(inputFolder, "hapmap2");
-		context.setOutput("outputScores", null);
 
 		// run qc to create chunkfile
 		QcStatisticsMock qcStats = new QcStatisticsMock(configFolder);
@@ -460,6 +459,7 @@ public void testPipelineWithEagleAndScores() throws IOException, ZipException {
 
 		// create workflow context and set scores
 		WorkflowTestContext context = buildContext(inputFolder, "hapmap2");
+		context.setOutput("outputScores", "cloudgene2-hdfs");
 
 		Map<String, Object> pgsPanel = new HashMap<String, Object>();
 		List<String> scores = new Vector<String>();
@@ -1197,7 +1197,6 @@ protected WorkflowTestContext buildContext(String folder, String refpanel) {
 		HdfsUtil.createDirectory(context.getHdfsTemp());
 
 		context.setOutput("outputimputation", "cloudgene-hdfs");
-		context.setOutput("outputScores", "cloudgene2-hdfs");
 
 		context.setOutput("hadooplogs", file.getAbsolutePath() + "/hadooplogs");
 		FileUtil.deleteDirectory(file.getAbsolutePath() + "/hadooplogs");