when Delly doesn't find variants from data then it doesn't generate an output...

when Delly doesn't find variants from data then it doesn't generate an output file either, in Biopet it's needed that there would be at least an empty VCF-file after running the tool, so added script that does that, generates an empty VCF file when Delly hasn't found anything

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/DellyCaller.scala

@@ -49,6 +49,14 @@ class DellyCaller(val root: Configurable) extends BiopetCommandLineFunction with
   def cmdLine = required(executable) +
     "-t" + required(analysistype) +
     "-o" + required(outputvcf) +
-    required(input)
+    required(input) +
+    createEmptyOutputIfNeeded
+
+  def createEmptyOutputIfNeeded = Array("c=$?",
+    "if [ $c -eq 0 ] && [ ! -f " + outputvcf + " ]; then",
+    "echo '##fileformat=VCFv4.2' > " + outputvcf,
+    "echo '#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO' >> " + outputvcf,
+    "fi",
+    "exit $c").mkString("\n", "\n", "\n")
 
 }