Protected copy content from public

protected/biopet-protected-package/pom.xml

@@ -25,6 +25,11 @@
             <artifactId>BiopetFramework</artifactId>
             <version>0.2.0-DEV</version>
         </dependency>
+        <dependency>
+            <groupId>nl.lumc.sasc</groupId>
+            <artifactId>BiopetPublicPackage</artifactId>
+            <version>0.2.0-DEV</version>
+        </dependency>
         <dependency>
             <groupId>nl.lumc.sasc</groupId>
             <artifactId>BiopetGatkPipelines</artifactId>

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

 package nl.lumc.sasc.biopet.core
 
-object BiopetExecutableProtected extends BiopetExecutable {
-  lazy val pipelines: List[MainCommand] = List(
-    nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep,
-    nl.lumc.sasc.biopet.pipelines.mapping.Mapping,
-    nl.lumc.sasc.biopet.pipelines.gentrap.Gentrap,
-    nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics,
+trait BiopetExecutableProtected extends BiopetExecutablePublic {
+  override def pipelines: List[MainCommand] = super.pipelines ::: List(
     nl.lumc.sasc.biopet.pipelines.gatk.GatkBenchmarkGenotyping,
     nl.lumc.sasc.biopet.pipelines.gatk.GatkGenotyping,
     nl.lumc.sasc.biopet.pipelines.gatk.GatkVariantcalling,
     nl.lumc.sasc.biopet.pipelines.gatk.GatkPipeline,
     nl.lumc.sasc.biopet.pipelines.gatk.GatkVariantRecalibration,
     nl.lumc.sasc.biopet.pipelines.gatk.GatkVcfSampleCompare,
-    nl.lumc.sasc.biopet.pipelines.sage.Sage,
-    nl.lumc.sasc.biopet.pipelines.basty.Basty,
-    nl.lumc.sasc.biopet.pipelines.yamsvp.Yamsvp)
-
-  lazy val tools: List[MainCommand] = List(
-    nl.lumc.sasc.biopet.tools.WipeReads,
-    nl.lumc.sasc.biopet.tools.ExtractAlignedFastq,
-    nl.lumc.sasc.biopet.tools.BiopetFlagstat,
-    nl.lumc.sasc.biopet.tools.CheckAllelesVcfInBam,
-    nl.lumc.sasc.biopet.tools.VcfToTsv,
-    nl.lumc.sasc.biopet.tools.VcfFilter,
-    nl.lumc.sasc.biopet.tools.FindRepeatsPacBio,
-    nl.lumc.sasc.biopet.tools.BedToInterval,
-    nl.lumc.sasc.biopet.tools.MpileupToVcf,
-    nl.lumc.sasc.biopet.tools.FastqSplitter,
-    nl.lumc.sasc.biopet.tools.BedtoolsCoverageToCounts,
-    nl.lumc.sasc.biopet.tools.SageCountFastq,
-    nl.lumc.sasc.biopet.tools.SageCreateLibrary,
-    nl.lumc.sasc.biopet.tools.SageCreateTagCounts,
-    nl.lumc.sasc.biopet.tools.BastyGenerateFasta,
-    nl.lumc.sasc.biopet.tools.MergeAlleles,
-    nl.lumc.sasc.biopet.tools.SamplesTsvToJson)
+    nl.lumc.sasc.biopet.pipelines.basty.Basty)
 }

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala

@@ -5,9 +5,9 @@ import org.apache.log4j.Logger
 
 trait BiopetExecutable extends Logging {
 
-  val pipelines: List[MainCommand]
+  def pipelines: List[MainCommand]
 
-  val tools: List[MainCommand]
+  def tools: List[MainCommand]
 
   val modules: Map[String, List[MainCommand]] = Map(
     "pipeline" -> pipelines,

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

 package nl.lumc.sasc.biopet.core
 
-object BiopetExecutablePublic extends BiopetExecutable {
-  lazy val pipelines: List[MainCommand] = List(
+trait BiopetExecutablePublic extends BiopetExecutable {
+  def pipelines: List[MainCommand] = List(
     nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep,
     nl.lumc.sasc.biopet.pipelines.mapping.Mapping,
     nl.lumc.sasc.biopet.pipelines.gentrap.Gentrap,
@@ -9,7 +9,7 @@ object BiopetExecutablePublic extends BiopetExecutable {
     nl.lumc.sasc.biopet.pipelines.sage.Sage,
     nl.lumc.sasc.biopet.pipelines.yamsvp.Yamsvp)
 
-  lazy val tools: List[MainCommand] = List(
+  def tools: List[MainCommand] = List(
     nl.lumc.sasc.biopet.tools.WipeReads,
     nl.lumc.sasc.biopet.tools.ExtractAlignedFastq,
     nl.lumc.sasc.biopet.tools.BiopetFlagstat,