@@ -84,7 +84,7 @@ class ShivaVariantcalling(val root: Configurable) extends QScript
...
@@ -84,7 +84,7 @@ class ShivaVariantcalling(val root: Configurable) extends QScript
defbiopetScript():Unit={
defbiopetScript():Unit={
if(inputBams.isEmpty){
if(inputBams.isEmpty){
Logging.addError("No input bams found")
Logging.addError("No input bams found")
inputBams=Map("test",newFile("."))
inputBams=Map("test"->newFile("."))
}
}
if(callers.isEmpty)Logging.addError("must select at least 1 variantcaller, choices are: "+ShivaVariantcalling.callersList(this).map(_.name).mkString(", "))
if(callers.isEmpty)Logging.addError("must select at least 1 variantcaller, choices are: "+ShivaVariantcalling.callersList(this).map(_.name).mkString(", "))
if(!callers.exists(_.mergeVcfResults))Logging.addError("must select at least 1 variantcaller where merge_vcf_results is true")
if(!callers.exists(_.mergeVcfResults))Logging.addError("must select at least 1 variantcaller where merge_vcf_results is true")