Added scala docs for bwa

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/Bwa.scala

@@ -3,6 +3,8 @@ package nl.lumc.sasc.biopet.extensions.bwa
 import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 
 /**
+ * General bwa extension
+ *
  * Created by pjvan_thof on 1/16/15.
  */
 abstract class Bwa extends BiopetCommandLineFunction {

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala

@@ -6,6 +6,10 @@ import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
 
 /**
+ * Extension for bwa aln
+ *
+ * Based on version 0.7.12-r1039
+ *
  * Created by pjvan_thof on 1/16/15.
  */
 class BwaAln(val root: Configurable) extends Bwa {
@@ -44,6 +48,7 @@ class BwaAln(val root: Configurable) extends Bwa {
   override val defaultVmem = "5G"
   override val defaultThreads = 8
 
+  /** Returns command to execute */
   def cmdLine = required(executable) +
     required("aln") +
     optional("-n", n) +

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala

@@ -22,6 +22,11 @@ import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.core.summary.Summarizable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
+/**
+ * Extension for bwa mem
+ *
+ * Based on version 0.7.12-r1039
+ */
 class BwaMem(val root: Configurable) extends Bwa {
   @Input(doc = "Fastq file R1", shortName = "R1")
   var R1: File = _

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala

@@ -10,7 +10,6 @@ import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
  *
  * based on executable version 0.7.10-r789
  *
- * @param root Configurable
  */
 class BwaSampe(val root: Configurable) extends Bwa {
   @Input(doc = "Fastq file R1", required = true)

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala

@@ -6,7 +6,10 @@ import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
 
 /**
- * Created by pjvan_thof on 1/16/15.
+ * BWA samse wrapper
+ *
+ * based on executable version 0.7.10-r789
+ *
  */
 class BwaSamse(val root: Configurable) extends Bwa {
   @Input(doc = "Fastq file", required = true)
@@ -24,6 +27,7 @@ class BwaSamse(val root: Configurable) extends Bwa {
   var n: Option[Int] = config("n")
   var r: String = _
 
+  /** Returns command to execute */
   def cmdLine = required(executable) +
     required("samse") +
     optional("-n", n) +