diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Sickle.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Sickle.scala index d31ce0ffbad4d582b1d37b663acc640aad187971..e29f8a5997cfe333f7bb9691613837ccf86aa564 100644 --- a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Sickle.scala +++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Sickle.scala @@ -11,25 +11,25 @@ import nl.lumc.sasc.biopet.core.config._ class Sickle(val root: Configurable) extends BiopetCommandLineFunction { @Input(doc = "R1 input") - var input_R1: File = null + var input_R1: File = _ @Input(doc = "R2 input", required = false) - var input_R2: File = null + var input_R2: File = _ @Input(doc = "qualityType file", required = false) var qualityTypeFile: File = _ @Output(doc = "R1 output") - var output_R1: File = null + var output_R1: File = _ @Output(doc = "R2 output", required = false) - var output_R2: File = null + var output_R2: File = _ @Output(doc = "singles output", required = false) - var output_singles: File = null + var output_singles: File = _ @Output(doc = "stats output") - var output_stats: File = null + var output_stats: File = _ executable = config("exe", default = "sickle") var qualityType: String = config("qualitytype")