the same but with scala's multi-line string

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

@@ -47,17 +47,19 @@ class DellyCaller(val root: Configurable) extends BiopetCommandLineFunction with
   }
 
   def cmdLine = required(executable) +
-    "-t" + required(analysistype) +
-    "-o" + required(outputvcf) +
+    required("-t", analysistype) +
+    required("-o", outputvcf) +
     required(input) +
     createEmptyOutputIfNeeded
 
   // when no variants are found then the tool doesn't generate the output file either, in Biopet it's needed that the empty file would be there
-  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")
+  private def createEmptyOutputIfNeeded =
+    s"""
+       |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""".stripMargin
 
 }