Fix bowtie2 readgroup

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie2.scala

@@ -116,7 +116,7 @@ class Bowtie2(val root: Configurable) extends BiopetCommandLineFunction with Ref
   var no_sq: Boolean = config("no_sq", default = false)
 
   var rg_id: Option[String] = config("rg_id")
-  var rg: Option[String] = config("rg")
+  var rg: List[String] = config("rg")
 
   var omit_sec_seq: Boolean = config("omit_sec_seq", default = false)
 
@@ -202,7 +202,7 @@ class Bowtie2(val root: Configurable) extends BiopetCommandLineFunction with Ref
     conditional(no_head, "--no-head") +
     conditional(no_sq, "--no-sq") +
     optional("--rg-id", rg_id) +
-    optional("--rg", rg) +
+    repeat("--rg", rg)
     conditional(omit_sec_seq, "--omit-sec-seq") +
     /* Performance */
     optional("--threads", threads) +

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

@@ -441,6 +441,11 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
   /** Add bowtie2 jobs **/
   def addBowtie2(R1: File, R2: Option[File], output: File): File = {
     val bowtie2 = new Bowtie2(this)
+    bowtie2.rg_id = Some(readgroupId)
+    bowtie2.rg +:= ("LB:" + libId.get)
+    bowtie2.rg +:= ("PL:" + platform)
+    bowtie2.rg +:= ("PU:" + platformUnit)
+    bowtie2.rg +:= ("SM:" + sampleId.get)
     bowtie2.R1 = R1
     if (paired) bowtie2.R2 = Some(R2.get)
     val sortSam = new SortSam(this)