Commit 4aae09e9 authored by Peter van 't Hof's avatar Peter van 't Hof

Style fixes

parent 2c17add4
......@@ -314,8 +314,7 @@ class MultisampleMapping(val parent: Configurable) extends QScript with Multisam
object MultisampleMapping extends PipelineCommand {
object MergeStrategy extends Enumeration {
val None, MergeSam, MarkDuplicates, PreProcessMergeSam,
PreProcessMarkDuplicates, PreProcessSambambaMarkdup = Value
val None, MergeSam, MarkDuplicates, PreProcessMergeSam, PreProcessMarkDuplicates, PreProcessSambambaMarkdup = Value
}
/** When file is not absolute an error is raise att the end of the script of a pipeline */
......
......@@ -14,20 +14,20 @@
*/
package nl.lumc.sasc.biopet.pipelines.mapping
import java.io.{File, FileOutputStream}
import java.io.{ File, FileOutputStream }
import com.google.common.io.Files
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.extensions.centrifuge.Centrifuge
import nl.lumc.sasc.biopet.extensions.picard.{MarkDuplicates, MergeSamFiles}
import nl.lumc.sasc.biopet.extensions.picard.{ MarkDuplicates, MergeSamFiles }
import nl.lumc.sasc.biopet.extensions.sambamba.SambambaMarkdup
import nl.lumc.sasc.biopet.utils.{ConfigUtils, Logging}
import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
import nl.lumc.sasc.biopet.utils.config.Config
import org.apache.commons.io.FileUtils
import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.{AfterClass, DataProvider, Test}
import org.testng.annotations.{ AfterClass, DataProvider, Test }
/**
* Created by pjvanthof on 15/05/16.
......
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