Remove protected executable

protected/biopet-protected-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutableProtected.scala

-/**
- * Due to the license issue with GATK, this part of Biopet can only be used inside the
- * LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
- * on how to use this protected part of biopet or contact us at sasc@lumc.nl
- */
-package nl.lumc.sasc.biopet
-
-import nl.lumc.sasc.biopet.utils.{ BiopetExecutable, MainCommand }
-
-object BiopetExecutableProtected extends BiopetExecutable {
-  def pipelines: List[MainCommand] = BiopetExecutablePublic.publicPipelines ::: List(
-    nl.lumc.sasc.biopet.pipelines.gatk.Shiva)
-
-  def tools = BiopetExecutablePublic.tools
-}
\ No newline at end of file

public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutablePublic.scala

@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet
 import nl.lumc.sasc.biopet.utils.{ BiopetExecutable, MainCommand }
 
 object BiopetExecutablePublic extends BiopetExecutable {
-  def publicPipelines: List[MainCommand] = List(
+  def pipelines: List[MainCommand] = List(
     nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep,
     nl.lumc.sasc.biopet.pipelines.mapping.Mapping,
     nl.lumc.sasc.biopet.pipelines.mapping.MultisampleMapping,
@@ -34,12 +34,9 @@ object BiopetExecutablePublic extends BiopetExecutable {
     nl.lumc.sasc.biopet.pipelines.gears.Gears,
     nl.lumc.sasc.biopet.pipelines.gwastest.GwasTest,
     nl.lumc.sasc.biopet.pipelines.shiva.ShivaVariantcalling,
-    nl.lumc.sasc.biopet.pipelines.basty.Basty
-  )
-
-  def pipelines: List[MainCommand] = List(
+    nl.lumc.sasc.biopet.pipelines.basty.Basty,
     nl.lumc.sasc.biopet.pipelines.shiva.Shiva
-  ) ::: publicPipelines
+  )
 
   def tools: List[MainCommand] = BiopetToolsExecutable.tools
 }