diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala
index e9edcc85e01dd89e14c20f51e090e4c501726d00..9dca25f250f980e9852f82ab0a24e5613c5c5f43 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala
@@ -5,39 +5,9 @@ import org.apache.log4j.Logger
 
 trait BiopetExecutable extends Logging {
 
-  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,
-    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)
-
-  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)
+  val pipelines: List[MainCommand]
+
+  val tools: List[MainCommand]
 
   val modules: Map[String, List[MainCommand]] = Map(
     "pipeline" -> pipelines,
diff --git a/public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutablePublic.scala b/public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutablePublic.scala
index 015c254b2d91dfb826ff6d382cd4d1ff57449799..242695bbe1e379d49af8a926f8b85be4e2494974 100644
--- a/public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutablePublic.scala
+++ b/public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutablePublic.scala
@@ -1,3 +1,30 @@
 package nl.lumc.sasc.biopet.core
 
-object BiopetExecutablePublic extends BiopetExecutable
+object BiopetExecutablePublic extends BiopetExecutable {
+  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,
+    nl.lumc.sasc.biopet.pipelines.sage.Sage,
+    nl.lumc.sasc.biopet.pipelines.yamsvp.Yamsvp)
+
+  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)
+}