From 1b34e7eac325aadb8af7fa07913eee77f1ad7f4d Mon Sep 17 00:00:00 2001 From: akaljuvee Date: Tue, 28 Feb 2017 14:23:08 +0100 Subject: [PATCH] one log line --- .../scala/nl/lumc/sasc/biopet/extensions/delly/DellyCaller.scala | 1 + 1 file changed, 1 insertion(+) 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 3c80f8913..1a5a1b9c1 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, -- GitLab