Commit d222ab7e authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Adding output files

parent 0a00efdc
......@@ -47,9 +47,18 @@ class Flash(val root: Configurable) extends BiopetCommandLineFunction with Versi
var compressProgArgs: Option[String] = config("compress_prog_args")
var outputSuffix: Option[String] = config("output_suffix")
private def suffix = outputSuffix.getOrElse("fastq") + (if(compress) ".gz" else "")
def combinedFastq = new File(outputDirectory, s"$outputPrefix.extendedFrags.$suffix")
def notCombinedR1 = new File(outputDirectory, s"$outputPrefix.notCombined_1.$suffix")
def notCombinedR2 = new File(outputDirectory, s"$outputPrefix.notCombined_2.$suffix")
def outputHistogramTable = new File(outputDirectory, s"$outputPrefix.hist")
def outputHistogram = new File(outputDirectory, s"$outputPrefix.histogram")
override def beforeGraph(): Unit = {
super.beforeGraph()
//FIXME: output files
outputFiles :::= combinedFastq :: notCombinedR1 ::
notCombinedR2 :: outputHistogramTable :: outputHistogram :: Nil
}
def cmdLine = executable +
......
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