Merge branch 'fix-memory_test_threads' into 'develop'

Fix memory test threads

Java did take a few Gb's for each threads, on a desktop you have not enough memory anymore. Fixed this to give those threads a memory limit.

See merge request !255

public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala

@@ -70,7 +70,7 @@ abstract class GentrapTestAbstract(val expressionMeasure: String) extends TestNG
       .toMap
     )
 
-   val validExpressionMeasures = Set(
+  val validExpressionMeasures = Set(
     "fragments_per_gene", "fragments_per_exon", "bases_per_gene", "bases_per_exon",
     "cufflinks_strict", "cufflinks_guided", "cufflinks_blind")
 

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

@@ -15,7 +15,7 @@
  */
 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.pipelines.flexiprep.Fastqc
@@ -25,7 +25,7 @@ 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 }
 
 /**
  * Test class for [[Mapping]]

public/pom.xml

@@ -80,6 +80,7 @@
                 <version>2.18.1</version>
                 <configuration>
                     <forkCount>1C</forkCount>
+                    <argLine>-Xmx300m</argLine>
                     <workingDirectory>${project.build.directory}</workingDirectory>
                 </configuration>
             </plugin>