Added version tag for vep

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/annotations/Annotations.scala

@@ -14,7 +14,7 @@
  */
 package nl.lumc.sasc.biopet.core.annotations
 
-import nl.lumc.sasc.biopet.core.{BiopetQScript, Reference}
+import nl.lumc.sasc.biopet.core.{ BiopetQScript, Reference }
 import nl.lumc.sasc.biopet.core.BiopetQScript.InputFile
 import nl.lumc.sasc.biopet.utils.LazyCheck
 import org.broadinstitute.gatk.queue.QScript

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

@@ -39,6 +39,8 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
   @Output(doc = "output file", required = true)
   var output: File = null
 
+  override def subPath = super.subPath ++ vepConfig
+
   def versionRegex = """version (\d*)""".r
   def versionCommand = executable + " " + vepScript + " --help"
 
@@ -106,7 +108,7 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
   var skibDbCheck: Boolean = config("skip_db_check", default = false)
 
   // Textual args
-  var vepConfig: Option[String] = config("config", freeVar = false)
+  var vepConfigArg: 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")
@@ -229,7 +231,7 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
       conditional(lrg, "--lrg") +
       conditional(noWholeGenome, "--no_whole_genome") +
       conditional(skibDbCheck, "--skip_db_check") +
-      optional("--config", vepConfig) +
+      optional("--config", vepConfigArg) +
       optional("--species", species) +
       optional("--assembly", assembly) +
       optional("--format", format) +

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/BaseRecalibrator.scala

@@ -149,7 +149,7 @@ class BaseRecalibrator(val root: Configurable) extends CommandLineGATK with Scat
   @Argument(fullName = "filter_bases_not_stored", shortName = "filterNoBases", doc = "Filter out reads with no stored bases (i.e. '*' where the sequence should be), instead of failing with an error", required = false, exclusiveOf = "", validation = "")
   var filter_bases_not_stored: Boolean = config("filter_bases_not_stored", default = false)
 
-  knownSites ::= dbsnpVcfFile
+  dbsnpVcfFile.foreach(knownSites :+= _)
 
   override def beforeGraph() {
     super.beforeGraph()

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/RealignerTargetCreator.scala

@@ -68,7 +68,7 @@ class RealignerTargetCreator(val root: Configurable) extends CommandLineGATK wit
   @Argument(fullName = "filter_bases_not_stored", shortName = "filterNoBases", doc = "Filter out reads with no stored bases (i.e. '*' where the sequence should be), instead of failing with an error", required = false, exclusiveOf = "", validation = "")
   var filter_bases_not_stored: Boolean = config("", default = false)
 
-  known ::= dbsnpVcfFile
+  dbsnpVcfFile.foreach(known :+= _)
 
   override def beforeGraph() {
     super.beforeGraph()