Commit 091a2657 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixed input files

parent 4245609f
......@@ -18,7 +18,6 @@ class Centrifuge(val root: Configurable) extends BiopetCommandLineFunction with
@Input(doc = "Input: FastQ or FastA", required = false)
var inputR2: Option[File] = None
@Input(doc = "Centrifuge index prefix", required = true)
var index: File = config("centrifuge_index")
@Output(doc = "Output with hits per sequence")
......@@ -37,6 +36,13 @@ class Centrifuge(val root: Configurable) extends BiopetCommandLineFunction with
/** Regex to get version from version command output */
def versionRegex: Regex = ".* version (.*)".r
override def beforeGraph(): Unit = {
super.beforeGraph()
deps :+= index + ".1.cf"
deps :+= index + ".2.cf"
deps :+= index + ".3.cf"
}
/**
* This function needs to be implemented to define the command that is executed
*
......
......@@ -16,7 +16,6 @@ class CentrifugeKreport(val root: Configurable) extends BiopetCommandLineFunctio
@Output(doc = "Output report")
var output: File = _
@Input(doc = "Centrifuge index prefix", required = true)
var index: File = config("centrifuge_index", namespace = "centrifuge")
var onlyUnique: Boolean = config("only_unique", default = false)
......@@ -30,6 +29,13 @@ class CentrifugeKreport(val root: Configurable) extends BiopetCommandLineFunctio
executable = config("exe", default = "centrifuge-kreport", freeVar = false)
override def beforeGraph(): Unit = {
super.beforeGraph()
deps :+= index + ".1.cf"
deps :+= index + ".2.cf"
deps :+= index + ".3.cf"
}
def cmdLine = executable +
conditional(onlyUnique, "--only-unique") +
conditional(showZeros, "--show-zeros") +
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment