Merge remote-tracking branch 'remotes/origin/develop' into fix-shiva_fails

public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala

@@ -39,7 +39,7 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
   }
 
   override def defaults = Map(
-    "varianteffectpredictor" -> Map("everything" -> true)
+    "varianteffectpredictor" -> Map("everything" -> true, "failed" -> true)
   )
 
   //defaults ++= Map("varianteffectpredictor" -> Map("everything" -> true))
@@ -80,7 +80,7 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
         vcfWithVcf.input = outputFile
         vcfWithVcf.secondaryVcf = exacFile
         vcfWithVcf.output = swapExt(outputDir, outputFile, ".vcf.gz", ".exac.vcf.gz")
-        vcfWithVcf.fields ::= ("MAF", "MAF_exac", None)
+        vcfWithVcf.fields ::= ("AF", "AF_exac", None)
         add(vcfWithVcf)
         outputFile = vcfWithVcf.output
       case _ =>