Commit a8a0e1b0 authored by Peter van 't Hof's avatar Peter van 't Hof

Fix type

parent 091a2657
......@@ -35,11 +35,11 @@ class Cuffquant(val root: Configurable) extends BiopetCommandLineFunction with V
means we have 2 samples, each with 2 replicates
so our input is a list of lists of Files
*/
var input: List[List[File]] = List.empty[List[File]]
var input: List[List[File]] = Nil
/** input GTF file */
@Input(doc = "Input GTF file", required = true)
var transcriptsGtf: File = null
var transcriptsGtf: File = _
/** output file, computed automatically from output directory */
@Output(doc = "Output CXB file")
......
......@@ -38,9 +38,9 @@ class Centrifuge(val root: Configurable) extends BiopetCommandLineFunction with
override def beforeGraph(): Unit = {
super.beforeGraph()
deps :+= index + ".1.cf"
deps :+= index + ".2.cf"
deps :+= index + ".3.cf"
deps :+= new File(index + ".1.cf")
deps :+= new File(index + ".2.cf")
deps :+= new File(index + ".3.cf")
}
/**
......
......@@ -31,9 +31,9 @@ class CentrifugeKreport(val root: Configurable) extends BiopetCommandLineFunctio
override def beforeGraph(): Unit = {
super.beforeGraph()
deps :+= index + ".1.cf"
deps :+= index + ".2.cf"
deps :+= index + ".3.cf"
deps :+= new File(index + ".1.cf")
deps :+= new File(index + ".2.cf")
deps :+= new File(index + ".3.cf")
}
def cmdLine = executable +
......
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