Merge pull request #26 from biopet/fix-BIOPET-582

Fix biopet 582

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

@@ -42,8 +42,19 @@ class DellyCaller(val root: Configurable) extends BiopetCommandLineFunction with
   var analysistype: String = _
 
   def cmdLine = required(executable) +
-    "-t" + required(analysistype) +
-    "-o" + required(outputvcf) +
-    required(input)
+    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
+  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
 
 }

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CatVariants.scala

@@ -37,6 +37,9 @@ class CatVariants(val root: Configurable) extends BiopetJavaCommandLineFunction
   @Gather(classOf[org.broadinstitute.gatk.queue.function.scattergather.SimpleTextGatherFunction])
   var outputFile: File = _
 
+  /** When Gatk's CatVariants has been called with empty VCF-files, then it also outputs an empty file. When this parameter is set to true, then the empty file gets added a valid VCF-file header.*/
+  var writeHeaderToEmptyOutput: Boolean = false
+
   /** assumeSorted should be true if the input files are already sorted (based on the position of the variants) */
   @Argument(fullName = "assumeSorted", shortName = "assumeSorted", doc = "assumeSorted should be true if the input files are already sorted (based on the position of the variants)", required = false, exclusiveOf = "", validation = "")
   var assumeSorted: Boolean = _
@@ -73,5 +76,14 @@ class CatVariants(val root: Configurable) extends BiopetJavaCommandLineFunction
     optional("--variant_index_type", variant_index_type, spaceSeparated = true, escape = true, format = "%s") +
     optional("--variant_index_parameter", variant_index_parameter, spaceSeparated = true, escape = true, format = "%s") +
     optional("-l", logging_level, spaceSeparated = true, escape = true, format = "%s") +
-    optional("-log", log_to_file, spaceSeparated = true, escape = true, format = "%s")
+    optional("-log", log_to_file, spaceSeparated = true, escape = true, format = "%s") +
+    (if (writeHeaderToEmptyOutput) s"""
+       |c=$$?
+       |if [ $$c -eq 0 ] && [ ! -s $outputFile ]; then
+       |  echo '##fileformat=VCFv4.2' > $outputFile
+       |  echo '#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO' >> $outputFile
+       |fi
+       |exit $$c""".stripMargin
+    else "")
+
 }

shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Delly.scala

@@ -36,6 +36,7 @@ class Delly(val root: Configurable) extends SvCaller {
       val catVariants = new CatVariants(this)
       catVariants.outputFile = new File(dellyDir, sample + ".delly.vcf")
       catVariants.isIntermediate = true
+      catVariants.writeHeaderToEmptyOutput = true
 
       if (del) {
         val delly = new DellyCaller(this)