Merge branch 'fix-268' into 'develop'

Fix 268

Fixes #268 

See merge request !318

public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala

@@ -23,9 +23,7 @@ import nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
 import nl.lumc.sasc.biopet.utils.Logging
 import org.broadinstitute.gatk.queue.{ QScript, QSettings }
 import org.broadinstitute.gatk.queue.function.QFunction
-import org.broadinstitute.gatk.queue.function.scattergather.ScatterGatherableFunction
 import org.broadinstitute.gatk.queue.util.{ Logging => GatkLogging }
-import org.broadinstitute.gatk.utils.commandline.Argument
 
 /** Base for biopet pipeline */
 trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
@@ -99,7 +97,8 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
 
     inputFiles.foreach { i =>
       if (!i.file.exists()) Logging.addError(s"Input file does not exist: ${i.file}")
-      else if (!i.file.canRead) Logging.addError(s"Input file can not be read: ${i.file}")
+      if (!i.file.canRead) Logging.addError(s"Input file can not be read: ${i.file}")
+      if (!i.file.isAbsolute) Logging.addError(s"Input file should be an absulute path: ${i.file}")
     }
 
     functions.filter(_.jobOutputFile == null).foreach(f => {

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/VarscanMpileup2cns.scala

@@ -39,7 +39,7 @@ class VarscanMpileup2cns(val root: Configurable) extends Varscan {
   var vcfSampleList: Option[File] = config("vcf_sample_list")
   var variants: Option[Int] = config("variants")
 
-  override def defaultCoreMemory = 6.0
+  override def defaultCoreMemory = 8.0
 
   override def beforeGraph(): Unit = {
     val validValues: Set[Int] = Set(0, 1)