From 980b2ebdd98f44d522342444554d7046195b6bfb Mon Sep 17 00:00:00 2001
From: seppinho <sebastian.schoenherr@i-med.ac.at>
Date: Mon, 3 Aug 2020 20:27:53 +0200
Subject: [PATCH] Set scores only for PGS testcase

---
 .../java/genepi/imputationserver/steps/ImputationTest.java     | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/test/java/genepi/imputationserver/steps/ImputationTest.java b/src/test/java/genepi/imputationserver/steps/ImputationTest.java
index 71407149..bdbff7ad 100644
--- 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");