Remove chunked files from summary

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Seqstat.scala

@@ -51,9 +51,7 @@ class Seqstat(val root: Configurable) extends BiopetCommandLineFunction with Sum
     ConfigUtils.any2map(map.getOrElse("stats", Map()))
   }
 
-  def summaryFiles: Map[String, File] = {
-    Map("fastq" -> input)
-  }
+  def summaryFiles: Map[String, File] = Map()
 
   override def resolveSummaryConflict(v1: Any, v2: Any, key: String): Any = {
     (v1, v2) match {

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala

@@ -65,14 +65,7 @@ class FastqSync(val root: Configurable) extends BiopetJavaCommandLineFunction wi
       required("-p", outputFastq2) + " > " +
       required(outputStats)
 
-  def summaryFiles: Map[String, File] = {
-    Map("refFastq" -> refFastq,
-      "inputFastq1" -> inputFastq1,
-      "inputFastq2" -> inputFastq2,
-      "outputFastq1" -> outputFastq1,
-      "outputFastq2" -> outputFastq2
-    )
-  }
+  def summaryFiles: Map[String, File] = Map()
 
   def summaryData: Map[String, Any] = {
     val regex = new Regex("""Filtered (\d*) reads from first read file.

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

@@ -85,7 +85,7 @@ class Cutadapt(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Cutada
     }
   }
 
-  def summaryFiles: Map[String, File] = Map("input" -> fastq_input, "output" -> fastq_output)
+  def summaryFiles: Map[String, File] = Map()
 }
 
 object Cutadapt {

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

@@ -62,8 +62,5 @@ class Sickle(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Sickle(r
     }
   }
 
-  def summaryFiles: Map[String, File] = {
-    Map("input_R1" -> input_R1, "output_R1" -> output_R1) ++
-      (if (input_R2 != null) Map("input_R2" -> input_R2, "output_R2" -> output_R2) else Map())
-  }
+  def summaryFiles: Map[String, File] = Map()
 }