Commit 47e33420 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Make dict required for all gatk tools

parent 5b09944b
......@@ -2,9 +2,9 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.core.{BiopetJavaCommandLineFunction, Reference, Version}
import nl.lumc.sasc.biopet.core.{ BiopetJavaCommandLineFunction, Reference, Version }
import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
import org.broadinstitute.gatk.utils.commandline.{Argument, Gather, Input, Output}
import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Input, Output }
trait CommandLineGATK extends BiopetJavaCommandLineFunction with Reference with Version {
analysisName = "CommandLineGATK"
......@@ -320,6 +320,8 @@ trait CommandLineGATK extends BiopetJavaCommandLineFunction with Reference with
override def versionExitcode = List(0, 1)
def versionCommand = executable + " -jar " + jarFile + " -version"
override def dictRequired = true
override def beforeGraph() {
super.beforeGraph()
if (reference_sequence != null) reference_sequence = referenceFasta()
......
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