diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Cutadapt.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Cutadapt.scala
index 267650200972873b2a2a6d9b3f2efde5a16f84b7..17df80bf4cede5cc5c530a5ba83aa6dbcc668efd 100644
--- a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Cutadapt.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Cutadapt.scala
@@ -1,12 +1,14 @@
 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
+}
diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala
index 7b87bbdc2b848696a7bf790181cd576b5786fffa..413defa02ec12e5aadee30bdf7a8628936d74b95 100644
--- a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala
@@ -1,11 +1,13 @@
 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
+}
diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Sickle.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Sickle.scala
index 40b5b9f310762bacc17dc531fe531a1967a5b372..d31ce0ffbad4d582b1d37b663acc640aad187971 100644
--- a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Sickle.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Sickle.scala
@@ -1,12 +1,14 @@
 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
+}
diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
index 222853ba928bb105d70852013fb819b46c40af9e..38b9809da96dab04285e9c96fe58307fdc40f7af 100644
--- a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
@@ -1,15 +1,17 @@
 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 {
diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqSync.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqSync.scala
index 56795a575533641089b4b0e8a8380a8f1ee2a025..827a92f7c0287b0e5b468624c908e13578c53c35 100644
--- a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqSync.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqSync.scala
@@ -1,9 +1,11 @@
 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
+}
diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToContams.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToContams.scala
index 843e890f236447e1c50e9f0862f0e2f3e1056fa1..d12073e3d11d6b9db697e0c8152f64fbfac1dc02 100644
--- a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToContams.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToContams.scala
@@ -1,9 +1,11 @@
 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
+}
diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToQualtype.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToQualtype.scala
index f76cec1a94f3a7e347af5e1b5cef54850db40322..c9aa8cd8ffdc9c201cba66b10052b109fb0d3956 100644
--- a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToQualtype.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToQualtype.scala
@@ -1,9 +1,11 @@
 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
+}
diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala
index c5e03dbb3619b40160b4c779f3dcdfcc58b96d7e..fee321c7da797934db23a5bb8a83df74513bef7a 100644
--- a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala
@@ -1,9 +1,11 @@
 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/")
diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Summarize.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Summarize.scala
index aa1db27aeca606af19fbce8d4f1ff4b11692a183..63f49191a67369ca22e9eb7d28bf7b5ee6479794 100644
--- a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Summarize.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Summarize.scala
@@ -1,9 +1,11 @@
 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
+}