From e5e7978f3665b1de41d6fe0d6eaa8aeab36c9d6d Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 4 Feb 2015 18:52:08 +0100
Subject: [PATCH] Fix bug in gubbins output
---
.../main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
index b87e3cb1e..e732c1023 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
@@ -59,7 +59,7 @@ class RunGubbins(val root: Configurable) extends BiopetCommandLineFunction {
".filtered_polymorphic_sites.fasta",
".filtered_polymorphic_sites.phylip",
".final_tree.tre")
- for (t <- out) outputFiles ::= new File(outputDirectory + File.separator + prefix + t)
+ for (t <- out) outputFiles ::= new File(outputDirectory + File.separator + prefix.getOrElse("gubbins") + t)
}
def cmdLine = required("cd", outputDirectory) + " && " + required(executable) +
--
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