Commit 431621b2 authored by Peter van 't Hof's avatar Peter van 't Hof

Style fixes

parent 0f03cdf4
......@@ -14,20 +14,20 @@
package nl.lumc.sasc.biopet.pipelines.gentrap
import{File, FileOutputStream}
import{ File, FileOutputStream }
import nl.lumc.sasc.biopet.core.{BiopetFifoPipe, BiopetPipe}
import nl.lumc.sasc.biopet.core.{ BiopetFifoPipe, BiopetPipe }
import nl.lumc.sasc.biopet.extensions._
import nl.lumc.sasc.biopet.extensions.gmap.Gsnap
import nl.lumc.sasc.biopet.extensions.hisat.Hisat2
import{BaseCounter, WipeReads}
import nl.lumc.sasc.biopet.utils.{ConfigUtils, Logging}
import{ BaseCounter, WipeReads }
import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
import nl.lumc.sasc.biopet.utils.config.Config
import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.{DataProvider, Test}
import org.testng.annotations.{ DataProvider, Test }
abstract class GentrapTestAbstract(val expressionMeasures: List[String]) extends TestNGSuite with Matchers {
......@@ -68,7 +68,7 @@ abstract class GentrapTestAbstract(val expressionMeasures: List[String]) extends"aligner" -> _) ++"remove_ribosomal_reads" -> _)
val configs: List[Option[Map[String, Any]]] = List(Some(settings), (if (sample1) Some(GentrapTest.sample1) else None), (if (sample2) Some(GentrapTest.sample2) else None))
val config = configs.flatten.foldLeft(GentrapTest.executables)( (a,b) => ConfigUtils.mergeMaps(a, b))
val config = configs.flatten.foldLeft(GentrapTest.executables)((a, b) => ConfigUtils.mergeMaps(a, b))
val gentrap: Gentrap = initPipeline(config)
val numSamples = (sample1, sample2) match {
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