diff --git a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala index 10036b6bc88bfb9061a2d6e8e78eb5bc821db4da..8bac4aaf68c33a245da877d460bc26abb9ebe564 100644 --- a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala +++ b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala @@ -50,7 +50,7 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr def init() { if (outputName == null && sampleID != null) outputName = sampleID - else if (outputName == null) outputName = "noname" + else if (outputName == null) outputName = config("output_name", default = "noname") if (outputDir == null) throw new IllegalStateException("Missing Output directory on gatk module") else if (!outputDir.endsWith("/")) outputDir += "/"