Commit dd80f227 authored by Peter van 't Hof's avatar Peter van 't Hof

Fix compile error

parent d609b6cb
......@@ -14,12 +14,12 @@
*/
package nl.lumc.sasc.biopet.core
import java.io.{File, PrintWriter}
import java.io.{ File, PrintWriter }
import nl.lumc.sasc.biopet.core.summary.WriteSummary
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.utils.{ConfigUtils, Logging}
import org.broadinstitute.gatk.queue.function.{CommandLineFunction, QFunction}
import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
import org.broadinstitute.gatk.queue.function.{ CommandLineFunction, QFunction }
import scala.collection.mutable
import scala.collection.mutable.ListBuffer
......@@ -127,8 +127,9 @@ object WriteDependencies extends Logging with Configurable {
}.toIterator.toMap
mainJobsFile.foreach { file =>
val mainJobs = jobs.filter(_._2("main_job") == true).map { case (name, job) =>
name -> (job + ("depends_on_jobs" -> getMainDependencies(name, jobs)))
val mainJobs = jobs.filter(_._2("main_job") == true).map {
case (name, job) =>
name -> (job + ("depends_on_jobs" -> getMainDependencies(name, jobs)))
}
val writer = new PrintWriter(file)
......@@ -150,7 +151,7 @@ object WriteDependencies extends Logging with Configurable {
def getMainDependencies(jobName: String, jobsMap: Map[String, Map[String, Any]]): List[String] = {
val job = jobsMap(jobName)
val dependencies = job("depends_on_jobs") match {
case l:List[_] => l.map(_.toString)
case l: List[_] => l.map(_.toString)
}
dependencies.flatMap { dep =>
jobsMap(dep)("main_job") match {
......
......@@ -52,7 +52,7 @@ class GearsCentrifuge(val root: Configurable) extends QScript with SummaryQScrip
centrifugeKreport.centrifugeOutputFiles :+= fifo
centrifugeKreport.output = new File(outputDir, s"$outputName.$name.kreport")
centrifugeKreport.onlyUnique = unique
val pipe = new BiopetFifoPipe(this, List(centrifugeKreport, Zcat(this, centrifugeOutput, fifo))))
val pipe = new BiopetFifoPipe(this, List(centrifugeKreport, Zcat(this, centrifugeOutput, fifo)))
pipe.mainFunction = true
add(pipe)
......
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