Added sub path instead of submodule

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

@@ -11,13 +11,15 @@ import org.broadinstitute.gatk.queue.extensions.gatk.CommandLineGATK
 trait GatkGeneral extends CommandLineGATK with BiopetJavaCommandLineFunction {
   memoryLimit = Option(3)
 
-  if (config.contains("gatk_jar")) jarFile = config("gatk_jar")
+  override def subPath = "gatk" :: super.subPath
+
+  jarFile = config("gatk_jar", required = true)
 
   override val defaultVmem = "7G"
 
-  if (config.contains("intervals", submodule = "gatk")) intervals = config("intervals", submodule = "gatk").asFileList
-  if (config.contains("exclude_intervals", submodule = "gatk")) excludeIntervals = config("exclude_intervals", submodule = "gatk").asFileList
-  reference_sequence = config("reference", submodule = "gatk")
-  gatk_key = config("gatk_key", submodule = "gatk")
-  if (config.contains("pedigree", submodule = "gatk")) pedigree = config("pedigree", submodule = "gatk").asFileList
+  if (config.contains("intervals")) intervals = config("intervals").asFileList
+  if (config.contains("exclude_intervals")) excludeIntervals = config("exclude_intervals").asFileList
+  reference_sequence = config("reference")
+  gatk_key = config("gatk_key")
+  if (config.contains("pedigree")) pedigree = config("pedigree").asFileList
 }

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/Bedtools.scala

@@ -18,6 +18,7 @@ package nl.lumc.sasc.biopet.extensions.bedtools
 import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 
 abstract class Bedtools extends BiopetCommandLineFunction {
+  override def subPath = "bedtools" :: super.subPath
   executable = config("exe", default = "bedtools", submodule = "bedtools")
   override def versionCommand = executable + " --version"
   override val versionRegex = """bedtools (.*)""".r

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala

@@ -18,27 +18,29 @@ package nl.lumc.sasc.biopet.extensions.picard
 import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
 import org.broadinstitute.gatk.utils.commandline.{ Argument }
 
-trait Picard extends BiopetJavaCommandLineFunction {
+abstract class Picard extends BiopetJavaCommandLineFunction {
+  override def subPath = "picard" :: super.subPath
+
   @Argument(doc = "VERBOSITY", required = false)
-  var verbosity: String = config("verbosity", submodule = "picard")
+  var verbosity: String = config("verbosity")
 
   @Argument(doc = "QUIET", required = false)
-  var quiet: Boolean = config("quiet", default = false, submodule = "picard")
+  var quiet: Boolean = config("quiet", default = false)
 
   @Argument(doc = "VALIDATION_STRINGENCY", required = false)
-  var stringency: String = config("validationstringency", submodule = "picard")
+  var stringency: String = config("validationstringency")
 
   @Argument(doc = "COMPRESSION_LEVEL", required = false)
-  var compression: Option[Int] = config("compressionlevel", submodule = "picard")
+  var compression: Option[Int] = config("compressionlevel")
 
   @Argument(doc = "MAX_RECORDS_IN_RAM", required = false)
-  var maxRecordsInRam: Option[Int] = config("maxrecordsinram", submodule = "picard")
+  var maxRecordsInRam: Option[Int] = config("maxrecordsinram")
 
   @Argument(doc = "CREATE_INDEX", required = false)
-  var createIndex: Boolean = config("createindex", default = true, submodule = "picard")
+  var createIndex: Boolean = config("createindex", default = true)
 
   @Argument(doc = "CREATE_MD5_FILE", required = false)
-  var createMd5: Boolean = config("createmd5", default = false, submodule = "picard")
+  var createMd5: Boolean = config("createmd5", default = false)
 
   //  override def versionCommand = executable + " " + javaOpts + " " + javaExecutable + " -h"
   //  override val versionRegex = """Version: (.*)""".r

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala

@@ -21,7 +21,9 @@ abstract class Sambamba extends BiopetCommandLineFunction {
   override val defaultVmem = "4G"
   override val defaultThreads = 2
 
-  executable = config("exe", default = "sambamba", submodule = "sambamba", freeVar = false)
+  override def subPath = "sambamba" :: super.subPath
+
+  executable = config("exe", default = "sambamba", freeVar = false)
   override def versionCommand = executable
   override val versionRegex = """sambamba v(.*)""".r
   override val versionExitcode = List(0, 1)

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/Samtools.scala

@@ -18,7 +18,8 @@ package nl.lumc.sasc.biopet.extensions.samtools
 import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 
 abstract class Samtools extends BiopetCommandLineFunction {
-  executable = config("exe", default = "samtools", submodule = "samtools", freeVar = false)
+  override def subPath = "samtools" :: super.subPath
+  executable = config("exe", default = "samtools", freeVar = false)
   override def versionCommand = executable
   override val versionRegex = """Version: (.*)""".r
   override val versionExitcode = List(0, 1)

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/Seqtk.scala

@@ -21,7 +21,8 @@ import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
  * Abstract class for all seqtk wrappers.
  */
 abstract class Seqtk extends BiopetCommandLineFunction {
-  executable = config("exe", default = "seqtk", submodule = "seqtk")
+  override def subPath = "seqtk" :: super.subPath
+  executable = config("exe", default = "seqtk", freeVar = true)
   override def versionCommand = executable
   override val versionRegex = """Version: (.*)""".r
   override val versionExitcode = List(0, 1)