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Commit e5e7978f authored by Peter van 't Hof's avatar Peter van 't Hof
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Fix bug in gubbins output

parent 5121ff20
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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
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View file @ e5e7978f
...@@ -59,7 +59,7 @@ class RunGubbins(val root: Configurable) extends BiopetCommandLineFunction { ...@@ -59,7 +59,7 @@ class RunGubbins(val root: Configurable) extends BiopetCommandLineFunction {
".filtered_polymorphic_sites.fasta", ".filtered_polymorphic_sites.fasta",
".filtered_polymorphic_sites.phylip", ".filtered_polymorphic_sites.phylip",
".final_tree.tre") ".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) + def cmdLine = required("cd", outputDirectory) + " && " + required(executable) +
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