Merge remote-tracking branch 'origin/bow' into peter

Conflicts:
	biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala
	flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala

@@ -22,9 +22,12 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction {
   override val versionRegex = """(.*)""".r
 
   var default_clip_mode: String = config("default_clip_mode", default = "3")
-  var opt_adapter: Set[String] = Set() + config("adapter")
-  var opt_anywhere: Set[String] = Set() + config("anywhere")
-  var opt_front: Set[String] = Set() + config("front")
+  var opt_adapter: Set[Any] = Set() 
+  if (configContains("adapter")) opt_adapter ++= config("adapter").getList
+  var opt_anywhere: Set[Any] = Set() 
+  if (configContains("anywhere")) opt_anywhere ++= config("anywhere").getList
+  var opt_front: Set[Any] = Set() 
+  if (configContains("front")) opt_front ++= config("front").getList
 
   var opt_discard: Boolean = config("discard")
   var opt_minimum_length: String = config("minimum_length", 1)
@@ -42,4 +45,4 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction {
     required(fastq_input) +
     required("--output", fastq_output) +
     " > " + required(stats_output)
-}
\ No newline at end of file
+}

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala

@@ -55,10 +55,10 @@ class Ln(val root: Configurable) extends InProcessFunction with Configurable {
       // calculate 'distance' from output directory to input
       // which is the number of directory walks required to get to the inUnique directory from outDir
       val outDir = FilenameUtils.getFullPathNoEndSeparator(outUnique)
-      val dist: Int = scala.math.max(0, outDir.split(File.separator).length - 1)
+      val dist: Int = scala.math.max(0, inUnique.split(File.separator).length - 1)
       val result =
         if (dist > 0)
-          ((".." + File.separator) * dist) + File.separator + inUnique
+          ((".." + File.separator) * dist) + inUnique
         else
           inUnique
       result
@@ -86,4 +86,4 @@ class Ln(val root: Configurable) extends InProcessFunction with Configurable {
      ln.relative = relative
      return ln
    }
- }
\ No newline at end of file
+ }