Commit 1db23864 authored by bow's avatar bow
Browse files

Fix bug caused by incorrect type usage

parent 266b9f1a
......@@ -50,19 +50,31 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
override def afterGraph {
this.checkExecutable
val fastqcDir = executable.substring(0, executable.lastIndexOf("/"))
contaminants = contaminants match {
// user-defined contaminants file take precedence
case userDefinedValue @ Some(_) => userDefinedValue
// otherwise, use default contaminants file (depending on FastQC version)
case None =>
val fastqcDir = executable.substring(0, executable.lastIndexOf("/"))
val defaultContams = getVersion match {
case "v0.11.2" => Option(new File(fastqcDir + "/Configuration/contaminant_list.txt"))
case _ => Option(new File(fastqcDir + "/Contaminants/contaminant_list.txt"))
case "v0.11.2" => new File(fastqcDir + "/Configuration/contaminant_list.txt")
case _ => new File(fastqcDir + "/Contaminants/contaminant_list.txt")
}
config("contaminants", default = defaultContams)
}
adapters = adapters match {
// user-defined contaminants file take precedence
case userDefinedValue @ Some(_) => userDefinedValue
// otherwise, check if adapters are already present (depending on FastQC version)
case None =>
val defaultAdapters = getVersion match {
case "v0.11.2" => Option(new File(fastqcDir + "/Configuration/adapter_list.txt"))
case "v0.11.2" => Some(new File(fastqcDir + "/Configuration/adapter_list.txt"))
case _ => None
}
config("contaminants", default = defaultContams)
case wrapped @ Some(_) => wrapped
defaultAdapters.collect { case adp => config("adapters", default = adp) }
}
}
......
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