Fixed case class

public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala

@@ -35,7 +35,7 @@ class Bam2Wig(val root: Configurable) extends QScript with BiopetQScript {
   var bamFile: File = null
 
   def init(): Unit = {
-    inputFiles :+= InputFile(bamFile)
+    inputFiles :+= new InputFile(bamFile)
   }
 
   def biopetScript(): Unit = {

public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala

@@ -72,7 +72,7 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
 
   /** executed before script */
   def init(): Unit = {
-    inputFiles :+= InputFile(inputBam)
+    inputFiles :+= new InputFile(inputBam)
   }
 
   /** Script to add jobs */

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

@@ -48,7 +48,7 @@ trait BiopetQScript extends Configurable with GatkLogging {
 
   var outputFiles: Map[String, File] = Map()
 
-  protected case class InputFile(file: File, md5: Option[String] = None)
+  type InputFile = BiopetQScript.InputFile
 
   var inputFiles: List[InputFile] = Nil
 
@@ -112,3 +112,7 @@ trait BiopetQScript extends Configurable with GatkLogging {
     add(function)
   }
 }
+
+object BiopetQScript {
+  protected case class InputFile(file: File, md5: Option[String] = None)
+}
\ No newline at end of file

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

@@ -32,7 +32,7 @@ class CheckChecksum extends InProcessFunction {
 
     if (outputChecksum != checksum.toLowerCase) {
       logger.error(s"Input file: '$inputFile' md5sum is not as expected, aborting pipeline")
-      System.exit(1)
+      Runtime.getRuntime.halt(130)
     }
   }
 }
\ No newline at end of file

public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala

@@ -79,8 +79,8 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with
           mapping.input_R1 = config("R1")
           if (config.contains("R2")) mapping.input_R2 = config("R2")
 
-          inputFiles :+= InputFile(mapping.input_R1, config("R1_md5"))
-          mapping.input_R2.foreach(inputFiles :+= InputFile(_, config("R2_md5")))
+          inputFiles :+= new InputFile(mapping.input_R1, config("R1_md5"))
+          mapping.input_R2.foreach(inputFiles :+= new InputFile(_, config("R2_md5")))
 
           mapping.init()
           mapping.biopetScript()

public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala

@@ -85,8 +85,8 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
 
     paired = input_R2.isDefined
 
-    inputFiles :+= InputFile(input_R1)
-    input_R2.foreach(inputFiles :+= InputFile(_))
+    inputFiles :+= new InputFile(input_R1)
+    input_R2.foreach(inputFiles :+= new InputFile(_))
 
     if (input_R1.endsWith(".gz")) R1_name = input_R1.getName.substring(0, input_R1.getName.lastIndexOf(".gz"))
     else if (input_R1.endsWith(".gzip")) R1_name = input_R1.getName.substring(0, input_R1.getName.lastIndexOf(".gzip"))

public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala

@@ -137,8 +137,8 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
     require(sampleId.isDefined, "Missing sample ID on mapping module")
     require(libId.isDefined, "Missing library ID on mapping module")
 
-    inputFiles :+= InputFile(input_R1)
-    input_R2.foreach(inputFiles :+= InputFile(_))
+    inputFiles :+= new InputFile(input_R1)
+    input_R2.foreach(inputFiles :+= new InputFile(_))
 
     paired = input_R2.isDefined
 

public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala

@@ -88,7 +88,7 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
       mapping.sampleId = Some(sampleId)
 
       protected def addJobs(): Unit = {
-        inputFiles :+= InputFile(inputFastq, config("R1_md5"))
+        inputFiles :+= new InputFile(inputFastq, config("R1_md5"))
 
         flexiprep.outputDir = new File(libDir, "flexiprep/")
         flexiprep.input_R1 = inputFastq

public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala

@@ -136,11 +136,11 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
           case (true, _) => mapping.foreach(mapping => {
             mapping.input_R1 = config("R1")
             mapping.input_R2 = config("R2")
-            inputFiles :+= InputFile(mapping.input_R1, config("R1_md5"))
-            mapping.input_R2.foreach(inputFiles :+= InputFile(_, config("R2_md5")))
+            inputFiles :+= new InputFile(mapping.input_R1, config("R1_md5"))
+            mapping.input_R2.foreach(inputFiles :+= new InputFile(_, config("R2_md5")))
           })
           case (false, true) => {
-            inputFiles :+= InputFile(config("bam"), config("bam_md5"))
+            inputFiles :+= new InputFile(config("bam"), config("bam_md5"))
             config("bam_to_fastq", default = false).asBoolean match {
               case true =>
                 val samToFastq = SamToFastq(qscript, config("bam"),

public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala

@@ -35,7 +35,7 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
   var inputVCF: File = _
 
   def init(): Unit = {
-    inputFiles :+= InputFile(inputVCF)
+    inputFiles :+= new InputFile(inputVCF)
   }
 
   override def defaults = ConfigUtils.mergeMaps(Map(