diff --git a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/DellyCaller.scala b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/DellyCaller.scala index 3c80f89137c2d8267e0bedb1e0b32d347da1a735..1a5a1b9c1b6235192cbc434d8e901e82a973de2a 100644 --- a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/DellyCaller.scala +++ b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/DellyCaller.scala @@ -52,6 +52,7 @@ class DellyCaller(val root: Configurable) extends BiopetCommandLineFunction with 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,