Added implicit List[File]

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala

@@ -21,5 +21,5 @@ trait GatkGeneral extends CommandLineGATK with BiopetJavaCommandLineFunction {
   if (config.contains("exclude_intervals")) excludeIntervals = config("exclude_intervals").asFileList
   reference_sequence = config("reference")
   if (config.contains("gatk_key")) gatk_key = config("gatk_key")
-  if (config.contains("pedigree")) pedigree = config("pedigree").asFileList
+  if (config.contains("pedigree")) pedigree = config("pedigree")
 }

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala

@@ -313,6 +313,16 @@ object ConfigUtils extends Logging {
     any2list(any).map(_.toString)
   }
 
+  /**
+   * Convert Any to List[File]
+   * @param any Input Any value
+   * @return
+   */
+  def any2fileList(any: Any): List[File] = {
+    if (any == null) return null
+    any2list(any).map(x => new File(x.toString))
+  }
+
   /**
    * Convert Any to Map[String, Any]
    * @param any Input Any value
@@ -505,6 +515,16 @@ object ConfigUtils extends Logging {
       else Nil
     }
 
+    /**
+     * Convert ConfigValue to List[File]
+     * @param value Input ConfigValue
+     * @return
+     */
+    implicit def configValue2fileList(value: ConfigValue): List[File] = {
+      if (requiredValue(value)) any2fileList(value.value)
+      else Nil
+    }
+
     /**
      * Convert ConfigValue to Set[String]
      * @param value Input ConfigValue