Code style changes

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/PythonCommandLineFunction.scala

@@ -7,11 +7,11 @@ import java.io.File
 import scala.collection.JavaConversions._
 
 trait PythonCommandLineFunction extends BiopetCommandLineFunction {
-  executeble = config.getAsString("python_exe", "python")
-  
   @Input(doc="Python script", required=false)
   var python_script: File = _
-    
+  
+  executeble = config.getAsString("python_exe", "python")
+  
   protected var python_script_name : String = _
   def setPythonScript(script:String) { setPythonScript(script,"") }
   def setPythonScript(script:String, subpackage:String) {
@@ -23,7 +23,7 @@ trait PythonCommandLineFunction extends BiopetCommandLineFunction {
     org.apache.commons.io.IOUtils.copy(is, os)
     os.close()
   }
-    
+  
   def getPythonCommand() : String = {
     required(executeble) + required(python_script)
   }

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

@@ -10,11 +10,22 @@ class FastqSync(val globalConfig: Config) extends PythonCommandLineFunction {
   setPythonScript("__init__.py", "pyfastqc/")
   setPythonScript("sync_paired_end_reads.py")
   
-  @Input(doc="Start fastq") var input_start_fastq: File = _
-  @Input(doc="R1 input") var input_R1: File = _
-  @Input(doc="R2 input") var input_R2: File = _
-  @Output(doc="R1 output") var output_R1: File = _
-  @Output(doc="R2 output") var output_R2: File = _
+  @Input(doc="Start fastq")
+  var input_start_fastq: File = _
+  
+  @Input(doc="R1 input")
+  var input_R1: File = _
+  
+  @Input(doc="R2 input")
+  var input_R2: File = _
+  
+  @Output(doc="R1 output")
+  var output_R1: File = _
+  
+  @Output(doc="R2 output")
+  var output_R2: File = _
+  
+  //No output Annotation so file 
   var output_stats: File = _
   
   def cmdLine = {

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

@@ -9,9 +9,14 @@ class FastqcToContams(val globalConfig: Config) extends PythonCommandLineFunctio
   setPythonScript("__init__.py", "pyfastqc/")
   setPythonScript("fastqc_contam.py")
   
-  @Input(doc="Fastqc output", shortName="fastqc", required=true) var fastqc_output: File = _
-  @Input(doc="Contams input", shortName="fastqc", required=false) var contams_file: File = _
-  @Output(doc="Output file", shortName="out", required=true) var out: File = _
+  @Input(doc="Fastqc output", shortName="fastqc", required=true)
+  var fastqc_output: File = _
+  
+  @Input(doc="Contams input", shortName="fastqc", required=false)
+  var contams_file: File = _
+  
+  @Output(doc="Output file", shortName="out", required=true)
+  var out: File = _
   
   def cmdLine = {
     getPythonCommand + 

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

@@ -9,8 +9,11 @@ class FastqcToQualtype(val globalConfig: Config) extends PythonCommandLineFuncti
   setPythonScript("__init__.py", "pyfastqc/")
   setPythonScript("qual_type_sickle.py")
   
-  @Input(doc="Fastqc output", shortName="fastqc", required=true) var fastqc_output: File = _
-  @Output(doc="Output file", shortName="out", required=true) var out: File = _
+  @Input(doc="Fastqc output", shortName="fastqc", required=true)
+  var fastqc_output: File = _
+  
+  @Output(doc="Output file", shortName="out", required=true)
+  var out: File = _
   
   def cmdLine = {
     getPythonCommand +

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

@@ -9,8 +9,11 @@ class Seqstat(val globalConfig: Config) extends PythonCommandLineFunction {
   setPythonScript("__init__.py", "pyfastqc/")
   setPythonScript("seq_stat.py")
   
-  @Input(doc="Fastq input", shortName="fastqc", required=true) var input_fastq: File = _
-  @Output(doc="Output file", shortName="out", required=true) var out: File = _
+  @Input(doc="Fastq input", shortName="fastqc", required=true)
+  var input_fastq: File = _
+  
+  @Output(doc="Output file", shortName="out", required=true)
+  var out: File = _
   
   var fmt: String = _
   

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

@@ -9,7 +9,8 @@ class Summarize(val globalConfig: Config) extends PythonCommandLineFunction {
   setPythonScript("__init__.py", "pyfastqc/")
   setPythonScript("summarize_flexiprep.py")
   
-  @Output(doc="Output file", shortName="out", required=true) var out: File = _
+  @Output(doc="Output file", shortName="out", required=true)
+  var out: File = _
   
   var samplea: String = _
   var sampleb: String = _