Added base version of centrifuge extension

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/centrifuge/Centrifuge.scala

+package nl.lumc.sasc.biopet.extensions.centrifuge
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Version }
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{Input, Output}
+
+import scala.util.matching.Regex
+
+/**
+  * Created by pjvanthof on 19/09/16.
+  */
+class Centrifuge(val root: Configurable) extends BiopetCommandLineFunction with Version {
+  @Input(doc = "Input: FastQ or FastA", required = true)
+  var inputR1: File = _
+
+  @Input(doc = "Input: FastQ or FastA", required = false)
+  var inputR2: Option[File] = None
+
+  @Input(doc = "Centrifuge index prefix", required = true)
+  var index: File = _
+
+  @Output(doc = "Output with hits per sequence")
+  var output: File = _
+
+  @Output(doc = "Output with hits per sequence")
+  var report: Option[File] = None
+
+  override def defaultThreads = 8
+
+  executable = config("exe", default = "centrifuge", freeVar = false)
+
+  /** Command to get version of executable */
+  def versionCommand: String = s"$executable --version"
+
+  /** Regex to get version from version command output */
+  def versionRegex: Regex = ".* version (.*)".r
+
+  /**
+    * This function needs to be implemented to define the command that is executed
+    *
+    * @return Command to run
+    */
+  protected[core] def cmdLine: String = executable +
+    //TODO: Options
+    optional("--threads", threads)
+    required("-x", index) +
+    (inputR2 match {
+      case Some(r2) => required("-1", inputR1) + required("-2", r2)
+      case _        => required("-U", inputR1)
+    }) +
+    (if (outputAsStsout) "" else required("-S", output)) +
+    optional("--report-file", report)
+}