From 3117b2973c44677217c2e128890949eba6c94451 Mon Sep 17 00:00:00 2001
From: SusiJo <susanne.jodoin@gmx.de>
Date: Tue, 31 May 2022 14:35:29 +0200
Subject: [PATCH] added test for metrics

---
 tests/modules/gatk4/markduplicatesspark/nextflow.config | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/tests/modules/gatk4/markduplicatesspark/nextflow.config b/tests/modules/gatk4/markduplicatesspark/nextflow.config
index c66f00e6..495a42f3 100644
--- a/tests/modules/gatk4/markduplicatesspark/nextflow.config
+++ b/tests/modules/gatk4/markduplicatesspark/nextflow.config
@@ -2,7 +2,10 @@ process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
+    withName: GATK4_MARKDUPLICATES_SPARK_METRICS {
+        ext.args = '--metrics-file test.metrics'
+    }
 }
-// necessary to override tests/config/nextflow.config
+// override tests/config/nextflow.config
 docker.userEmulation = false