Commit 901b11d9 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added base version of centrifuge-kreport extension

parent 6bd92c80
......@@ -19,7 +19,7 @@ class Centrifuge(val root: Configurable) extends BiopetCommandLineFunction with
var inputR2: Option[File] = None
@Input(doc = "Centrifuge index prefix", required = true)
var index: File = _
var index: File = config("centrifige_index")
@Output(doc = "Output with hits per sequence")
var output: File = _
......@@ -42,7 +42,7 @@ class Centrifuge(val root: Configurable) extends BiopetCommandLineFunction with
*
* @return Command to run
*/
protected[core] def cmdLine: String = executable +
def cmdLine: String = executable +
//TODO: Options
optional("--threads", threads)
required("-x", index) +
......
package nl.lumc.sasc.biopet.extensions.centrifuge
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Input, Output}
/**
* Created by pjvanthof on 19/09/16.
*/
class CentrifugeKreport(val root: Configurable) extends BiopetCommandLineFunction {
@Input(doc = "Output files centrifuge", required = true)
var centrifugeOutputFiles: List[File] = Nil
@Output(doc = "Output report")
var output: File = _
@Input(doc = "Centrifuge index prefix", required = true)
var index: File = config("centrifige_index", namespace = "centrifuge")
executable = config("exe", default = "centrifuge-kreport", freeVar = false)
def cmdLine = executable +
//TODO: Options
required("-x", index) +
repeat(centrifugeOutputFiles)
}
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