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

Fix type

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