From f5ffdbb40d8cd3dfffa19d5ba4d3ef773f72b6ef Mon Sep 17 00:00:00 2001
From: Wai Yi Leung <w.y.leung@lumc.nl>
Date: Mon, 4 Apr 2016 13:45:09 +0200
Subject: [PATCH] sequenceDictionary is a File... fixed
---
.../scala/nl/lumc/sasc/biopet/extensions/picard/SortVcf.scala | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortVcf.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortVcf.scala
index b43e9f61b..36f31b399 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortVcf.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortVcf.scala
@@ -31,7 +31,7 @@ class SortVcf(val root: Configurable) extends Picard {
var output: File = _
@Argument(doc = "Sequence dictionary to use", required = false)
- var sequenceDictionary: String = config("sort_order", default = "coordinate")
+ var sequenceDictionary: File = _
/** Returns command to execute */
override def cmdLine = super.cmdLine +
--
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