From 2765ff0cd82804f9e219d4ed1e6a5b8e75aab80a Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 17 Aug 2015 14:16:52 +0200
Subject: [PATCH] Added reference trait for tophat (cherry picked from commit
73990f0)
---
.../main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala
index 82332de29..35d39691d 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala
@@ -17,14 +17,14 @@ package nl.lumc.sasc.biopet.extensions
import java.io.File
-import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.core.{Reference, BiopetCommandLineFunction}
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
/**
* Extension for Tophat
*/
-class Tophat(val root: Configurable) extends BiopetCommandLineFunction {
+class Tophat(val root: Configurable) extends BiopetCommandLineFunction with Reference {
executable = config("exe", default = "tophat", freeVar = false)
--
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