Update imports style order

flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Cutadapt.scala

 package nl.lumc.sasc.biopet.function.fastq
 
-import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
-import nl.lumc.sasc.biopet.core.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import java.io.File
 import scala.io.Source._
 import scala.sys.process._
 
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
+import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.core.config.Configurable
+
 class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction {
   @Input(doc = "Input fastq file")
   var fastq_input: File = _
@@ -73,4 +75,4 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction {
       } else logger.warn("File : " + contams_file + " does not exist")
     }
   }
-}
\ No newline at end of file
+}

flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala

 package nl.lumc.sasc.biopet.function.fastq
 
-import nl.lumc.sasc.biopet.core._
-import nl.lumc.sasc.biopet.core.config._
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import java.io.File
 import scala.sys.process._
 
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
+import nl.lumc.sasc.biopet.core._
+import nl.lumc.sasc.biopet.core.config._
+
 class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
 
   @Input(doc = "Contaminants", required = false)
@@ -48,4 +50,4 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
       required(fastqfile) +
       required(" > ", output, escape = false)
   }
-}
\ No newline at end of file
+}

flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Sickle.scala

 package nl.lumc.sasc.biopet.function.fastq
 
-import nl.lumc.sasc.biopet.core._
-import nl.lumc.sasc.biopet.core.config._
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
 import java.io.File
 import scala.io.Source._
 import scala.sys.process._
 
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
+
+import nl.lumc.sasc.biopet.core._
+import nl.lumc.sasc.biopet.core.config._
+
 class Sickle(val root: Configurable) extends BiopetCommandLineFunction {
   @Input(doc = "R1 input")
   var input_R1: File = null
@@ -73,4 +75,4 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction {
     }
     return null
   }
-}
\ No newline at end of file
+}

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

 package nl.lumc.sasc.biopet.pipelines.flexiprep
 
-import nl.lumc.sasc.biopet.core._
-import nl.lumc.sasc.biopet.core.config._
-import nl.lumc.sasc.biopet.function._
-import nl.lumc.sasc.biopet.function.fastq._
+import scala.util.parsing.json._
+
 import org.broadinstitute.gatk.queue.QScript
 import org.broadinstitute.gatk.queue.extensions.gatk._
 import org.broadinstitute.gatk.queue.extensions.picard._
 import org.broadinstitute.gatk.queue.function._
-import scala.util.parsing.json._
 import org.broadinstitute.gatk.utils.commandline.{ Input, Argument }
+
+import nl.lumc.sasc.biopet.core._
+import nl.lumc.sasc.biopet.core.config._
+import nl.lumc.sasc.biopet.function._
+import nl.lumc.sasc.biopet.function.fastq._
 import nl.lumc.sasc.biopet.pipelines.flexiprep.scripts._
 
 class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {

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

 package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
 
+import java.io.File
+
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
 import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.function.PythonCommandLineFunction
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
-import java.io.File
 
 class FastqSync(val root: Configurable) extends PythonCommandLineFunction {
   setPythonScript("sync_paired_end_reads.py")
@@ -34,4 +36,4 @@ class FastqSync(val root: Configurable) extends PythonCommandLineFunction {
     required(output_R2) +
     " > " +
     required(output_stats)
-}
\ No newline at end of file
+}

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

 package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
 
+import java.io.File
+
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
 import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.function.PythonCommandLineFunction
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
-import java.io.File
 
 class FastqcToContams(val root: Configurable) extends PythonCommandLineFunction {
   setPythonScript("__init__.py", "pyfastqc/")
@@ -25,4 +27,4 @@ class FastqcToContams(val root: Configurable) extends PythonCommandLineFunction
       " > " +
       required(out)
   }
-}
\ No newline at end of file
+}

flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToQualtype.scala

 package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
 
+import java.io.File
+
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import nl.lumc.sasc.biopet.core.config.Configurable
+
 import nl.lumc.sasc.biopet.function.PythonCommandLineFunction
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
-import java.io.File
 
 class FastqcToQualtype(val root: Configurable) extends PythonCommandLineFunction {
   setPythonScript("__init__.py", "pyfastqc/")
@@ -21,4 +23,4 @@ class FastqcToQualtype(val root: Configurable) extends PythonCommandLineFunction
       " > " +
       required(out)
   }
-}
\ No newline at end of file
+}

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

 package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
 
+import java.io.File
+
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
 import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.function.PythonCommandLineFunction
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
-import java.io.File
 
 class Seqstat(val root: Configurable) extends PythonCommandLineFunction {
   setPythonScript("__init__.py", "pyfastqc/")

flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Summarize.scala

 package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
 
+import java.io.File
+
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
 import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.function.PythonCommandLineFunction
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
-import java.io.File
 
 class Summarize(val root: Configurable) extends PythonCommandLineFunction {
   setPythonScript("__init__.py", "pyfastqc/")
@@ -33,4 +35,4 @@ class Summarize(val root: Configurable) extends PythonCommandLineFunction {
       required(samplea) +
       required(out)
   }
-}
\ No newline at end of file
+}