Commit 7c8fe6be authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixed unit tests

parent c3ec3cb9
......@@ -66,31 +66,31 @@ class Flash(val root: Configurable) extends BiopetCommandLineFunction with Versi
@Output
private var _combinedFastq: File = _
def combinedFastq = _combinedFastq
def combinedFastq = new File(outputDirectory, s"$outputPrefix.extendedFrags.$suffix")
@Output
private var _notCombinedR1: File = _
def notCombinedR1 = _notCombinedR1
def notCombinedR1 = new File(outputDirectory, s"$outputPrefix.notCombined_1.$suffix")
@Output
private var _notCombinedR2: File = _
def notCombinedR2 = _notCombinedR2
def notCombinedR2 = new File(outputDirectory, s"$outputPrefix.notCombined_2.$suffix")
@Output
private var _outputHistogramTable: File = _
def outputHistogramTable = _outputHistogramTable
def outputHistogramTable = new File(outputDirectory, s"$outputPrefix.hist")
@Output
private var _outputHistogram: File = _
def outputHistogram = _outputHistogram
def outputHistogram = new File(outputDirectory, s"$outputPrefix.histogram")
override def beforeGraph(): Unit = {
super.beforeGraph()
_combinedFastq = new File(outputDirectory, s"$outputPrefix.extendedFrags.$suffix")
_notCombinedR1 = new File(outputDirectory, s"$outputPrefix.notCombined_1.$suffix")
_notCombinedR2 = new File(outputDirectory, s"$outputPrefix.notCombined_2.$suffix")
_outputHistogramTable = new File(outputDirectory, s"$outputPrefix.hist")
_outputHistogram = new File(outputDirectory, s"$outputPrefix.histogram")
_combinedFastq = combinedFastq
_notCombinedR1 = notCombinedR1
_notCombinedR2 = notCombinedR2
_outputHistogramTable = outputHistogramTable
_outputHistogram = outputHistogram
}
def cmdLine = executable +
......
......@@ -54,10 +54,10 @@ class SplitLibrariesFastq(val root: Configurable) extends BiopetCommandLineFunct
var maxBarcodeErrors: Option[Double] = config("max_barcode_errors")
var phredOffset: Option[String] = config("phred_offset")
def outputSeqs = _outputSeqs
def outputSeqs = new File(outputDir, "seqs.fna")
@Output
var _outputSeqs: File = _
private var _outputSeqs: File = _
override def defaultCoreMemory = 4.0
......@@ -65,7 +65,7 @@ class SplitLibrariesFastq(val root: Configurable) extends BiopetCommandLineFunct
super.beforeGraph()
require(input.nonEmpty)
require(outputDir != null)
_outputSeqs = new File(outputDir, "seqs.fna")
_outputSeqs = outputSeqs
}
def cmdLine = executable +
......
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