Moved scripts to general package

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala

 package nl.lumc.sasc.biopet.pipelines.bammetrics
 
-import nl.lumc.sasc.biopet.pipelines.bammetrics.scripts.CoverageStats
+import nl.lumc.sasc.biopet.scripts.CoverageStats
 import org.broadinstitute.gatk.queue.QScript
 import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
 import java.io.File

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala

@@ -6,7 +6,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Argument }
 import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
 import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.extensions.{ Gzip, Pbzip2, Md5sum, Zcat }
-import nl.lumc.sasc.biopet.pipelines.flexiprep.scripts._
+import nl.lumc.sasc.biopet.scripts._
 
 class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
   def this() = this(null)

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepSummary.scala

@@ -3,8 +3,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep
 import java.io.PrintWriter
 import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.extensions.Md5sum
-import nl.lumc.sasc.biopet.pipelines.flexiprep.scripts.{ FastqSync, Seqstat }
-import nl.lumc.sasc.biopet.pipelines.flexiprep.scripts.Seqstat
+import nl.lumc.sasc.biopet.scripts.{ FastqSync, Seqstat }
 import org.broadinstitute.gatk.queue.function.InProcessFunction
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import java.io.File

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/scripts/CoverageStats.scala → biopet-framework/src/main/scala/nl/lumc/sasc/biopet/scripts/CoverageStats.scala

-package nl.lumc.sasc.biopet.pipelines.bammetrics.scripts
+package nl.lumc.sasc.biopet.scripts
 
 import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.extensions.PythonCommandLineFunction

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqSync.scala → biopet-framework/src/main/scala/nl/lumc/sasc/biopet/scripts/FastqSync.scala

-package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
+package nl.lumc.sasc.biopet.scripts
 
 import java.io.File
 

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToContams.scala → biopet-framework/src/main/scala/nl/lumc/sasc/biopet/scripts/FastqcToContams.scala

-package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
+package nl.lumc.sasc.biopet.scripts
 
 import java.io.File
 

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala → biopet-framework/src/main/scala/nl/lumc/sasc/biopet/scripts/Seqstat.scala

-package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
+package nl.lumc.sasc.biopet.scripts
 
 import java.io.File