Added contructor

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

@@ -32,11 +32,7 @@ class Cutadapt(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Cutada
       super.cmdLine
     } else {
       analysisName = getClass.getSimpleName + "-ln"
-      val lnOut = new Ln(this)
-      lnOut.in = new java.io.File(required(fastq_input))
-      lnOut.out = new java.io.File(required(fastq_output))
-      lnOut.relative = true
-      lnOut.cmd
+      Ln(this, fastq_input, fastq_output, relative = true).cmd
     }
   }
   
@@ -64,6 +60,14 @@ class Cutadapt(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Cutada
 }
 
 object Cutadapt {
+  def apply(root: Configurable, input:File, output:File): Cutadapt = {
+    val cutadapt = new Cutadapt(root)
+    cutadapt.fastq_input = input
+    cutadapt.fastq_output = output
+    cutadapt.stats_output = new File(output.getAbsolutePath.substring(0, output.getName.lastIndexOf(".")) + ".stats")
+    return cutadapt
+  }
+  
   def mergeSummarys(jsons: List[Json]): Json = {
     return jNull
   }

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

@@ -12,7 +12,6 @@ import scala.io.Source
 
 import org.broadinstitute.gatk.utils.commandline.{ Input }
 
-
 import argonaut._, Argonaut._
 import scalaz._, Scalaz._
 

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

@@ -31,7 +31,8 @@ class FastqSync(val root: Configurable) extends PythonCommandLineFunction {
   //No output Annotation so file 
   var output_stats: File = _
 
-  def cmdLine = getPythonCommand +
+  def cmdLine = {
+    getPythonCommand +
     required(input_start_fastq) +
     required(input_R1) +
     required(input_R2) +
@@ -39,6 +40,7 @@ class FastqSync(val root: Configurable) extends PythonCommandLineFunction {
     required(output_R2) +
     " > " +
     required(output_stats)
+  }
 
   def getSummary: Json = {
     return jNull
@@ -46,6 +48,18 @@ class FastqSync(val root: Configurable) extends PythonCommandLineFunction {
 }
 
 object FastqSync {
+  def apply(root: Configurable, input_start_fastq:File, input_R1:File, input_R2:File, 
+            output_R1:File, output_R2:File, output_stats:File): FastqSync = {
+    val fastqSync = new FastqSync(root)
+    fastqSync.input_start_fastq = input_start_fastq
+    fastqSync.input_R1 = input_R1
+    fastqSync.input_R2 = input_R2
+    fastqSync.output_R1 = output_R1
+    fastqSync.output_R2 = output_R2
+    fastqSync.output_stats = output_stats
+    return fastqSync
+  }
+  
   def mergeSummarys(jsons: List[Json]): Json = {
     return jNull
   }