Merge branch 'fix-toucan' into 'develop'

Fix toucan



See merge request !279

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala

@@ -17,6 +17,7 @@ package nl.lumc.sasc.biopet.extensions
 
 import java.io.File
 
+import nl.lumc.sasc.biopet.utils.Logging
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.core.{ Version, BiopetCommandLineFunction, Reference }
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
@@ -40,8 +41,8 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
   def versionCommand = executable + " " + vepScript + " --help"
 
   //Boolean vars
-  var v: Boolean = config("v", default = true)
-  var q: Boolean = config("q", default = false)
+  var v: Boolean = config("v", default = true, freeVar = false)
+  var q: Boolean = config("q", default = false, freeVar = false)
   var offline: Boolean = config("offline", default = false)
   var no_progress: Boolean = config("no_progress", default = false)
   var everything: Boolean = config("everything", default = false)
@@ -76,8 +77,8 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
   var old_map: Boolean = config("old_maf", default = false)
   var pubmed: Boolean = config("pubmed", default = false)
 
-  var vcf: Boolean = config("vcf", default = true)
-  var json: Boolean = config("json", default = false)
+  var vcf: Boolean = config("vcf", default = true, freeVar = false)
+  var json: Boolean = config("json", default = false, freeVar = false)
   var gvf: Boolean = config("gvf", default = false)
   var check_ref: Boolean = config("check_ref", default = false)
   var coding_only: Boolean = config("coding_only", default = false)
@@ -103,8 +104,8 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
   var skip_db_check: Boolean = config("skip_db_check", default = false)
 
   // Textual args
-  var vep_config: Option[String] = config("config")
-  var species: Option[String] = config("species")
+  var vep_config: Option[String] = config("config", freeVar = false)
+  var species: Option[String] = config("species", freeVar = false)
   var assembly: Option[String] = config("assembly")
   var format: Option[String] = config("format")
   var dir: Option[String] = config("dir")
@@ -146,9 +147,9 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
   override def beforeGraph(): Unit = {
     super.beforeGraph()
     if (!cache && !database) {
-      throw new IllegalArgumentException("Must supply either cache or database for VariantEffectPredictor")
+      Logging.addError("Must supply either cache or database for VariantEffectPredictor")
     } else if (cache && dir.isEmpty) {
-      throw new IllegalArgumentException("Must supply dir to cache for VariantEffectPredictor")
+      Logging.addError("Must supply dir to cache for VariantEffectPredictor")
     }
   }