Fixed unit tests

gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleTest.scala

@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.pipelines.gears
 import java.io.File
 
 import com.google.common.io.Files
-import nl.lumc.sasc.biopet.core.BiopetPipe
+import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 import nl.lumc.sasc.biopet.extensions.centrifuge.{ Centrifuge, CentrifugeKreport }
 import nl.lumc.sasc.biopet.extensions.kraken.{ Kraken, KrakenReport }
 import nl.lumc.sasc.biopet.extensions.picard.SamToFastq
@@ -106,7 +106,8 @@ abstract class TestGearsSingle extends TestNGSuite with Matchers {
         gears.outputName shouldBe (if (inputMode == Some("bam")) "bamfile" else "R1")
       }
 
-      val pipesJobs = gears.functions.filter(_.isInstanceOf[BiopetPipe]).flatMap(_.asInstanceOf[BiopetPipe].pipesJobs)
+      val pipesJobs = gears.functions.filter(_.isInstanceOf[BiopetCommandLineFunction])
+        .flatMap(_.asInstanceOf[BiopetCommandLineFunction].pipesJobs)
 
       gears.summarySettings("gears_use_kraken") shouldBe kraken.getOrElse(false)
       gears.summarySettings("gear_use_qiime_rtax") shouldBe qiimeRtax

mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala

@@ -14,10 +14,10 @@
  */
 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.BiopetPipe
+import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 import nl.lumc.sasc.biopet.extensions.centrifuge.Centrifuge
 import nl.lumc.sasc.biopet.pipelines.flexiprep.Fastqc
 import nl.lumc.sasc.biopet.utils.ConfigUtils
@@ -86,7 +86,8 @@ abstract class AbstractTestMapping(val aligner: String) extends TestNGSuite with
     mapping.libId = Some("1")
     mapping.script()
 
-    val pipesJobs = mapping.functions.filter(_.isInstanceOf[BiopetPipe]).flatMap(_.asInstanceOf[BiopetPipe].pipesJobs)
+    val pipesJobs = mapping.functions.filter(_.isInstanceOf[BiopetCommandLineFunction])
+      .flatMap(_.asInstanceOf[BiopetCommandLineFunction].pipesJobs)
 
     //Flexiprep
     mapping.functions.count(_.isInstanceOf[Fastqc]) shouldBe (if (skipFlexiprep) 0 else if (paired) 4 else 2)

mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTest.scala

@@ -14,13 +14,13 @@
  */
 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.BiopetPipe
+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.utils.{ConfigUtils, Logging}
+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
@@ -88,7 +88,8 @@ trait MultisampleMappingTestTrait extends TestNGSuite with Matchers {
       val numberFastqLibs = (if (sample1) 1 else 0) + (if (sample2) 2 else 0) + (if (sample3 && bamToFastq) 1 else 0) + (if (sample4 && bamToFastq) 1 else 0)
       val numberSamples = (if (sample1) 1 else 0) + (if (sample2) 1 else 0)
 
-      val pipesJobs = pipeline.functions.filter(_.isInstanceOf[BiopetPipe]).flatMap(_.asInstanceOf[BiopetPipe].pipesJobs)
+      val pipesJobs = pipeline.functions.filter(_.isInstanceOf[BiopetCommandLineFunction])
+        .flatMap(_.asInstanceOf[BiopetCommandLineFunction].pipesJobs)
 
       import MultisampleMapping.MergeStrategy
       pipeline.functions.count(_.isInstanceOf[MarkDuplicates]) shouldBe (numberFastqLibs +