From 8c98a78d2a0e12d081184736e17ccde3feee3f44 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Thu, 28 Apr 2022 14:07:55 +0200
Subject: [PATCH] Fixed the issue with the BED file

---
 modules/vardictjava/main.nf        | 1 +
 tests/modules/vardictjava/test.yml | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/modules/vardictjava/main.nf b/modules/vardictjava/main.nf
index 26833436..d6b4f1dd 100644
--- a/modules/vardictjava/main.nf
+++ b/modules/vardictjava/main.nf
@@ -26,6 +26,7 @@ process VARDICTJAVA {
     """
     vardict-java \\
         $args \\
+        -c 1 -S 2 -E 3 \\
         -b $bam \\
         -th $task.cpus \\
         -N $prefix \\
diff --git a/tests/modules/vardictjava/test.yml b/tests/modules/vardictjava/test.yml
index 0bd21f4e..77aa9047 100644
--- a/tests/modules/vardictjava/test.yml
+++ b/tests/modules/vardictjava/test.yml
@@ -4,6 +4,6 @@
     - vardictjava
   files:
     - path: output/vardictjava/test.vcf.gz
-      md5sum: 7029066c27ac6f5ef18d660d5741979a
+      md5sum: 2179dcaee6183495b421293f42db11b5
     - path: output/vardictjava/versions.yml
       md5sum: aac455b8c9c9194c5fed80e4fd495b96