Commit 76992696 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Update catvariants

parent 556ca42a
......@@ -2,11 +2,11 @@ package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File
import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import nl.lumc.sasc.biopet.core.{BiopetJavaCommandLineFunction, Reference}
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Input, Output }
import org.broadinstitute.gatk.utils.commandline.{Argument, Gather, Input, Output}
class CatVariants(val root: Configurable) extends BiopetJavaCommandLineFunction {
class CatVariants(val root: Configurable) extends BiopetJavaCommandLineFunction with Reference {
analysisName = "CatVariants"
javaMainClass = "org.broadinstitute.gatk.tools.CatVariants"
......@@ -44,6 +44,11 @@ class CatVariants(val root: Configurable) extends BiopetJavaCommandLineFunction
@Gather(classOf[org.broadinstitute.gatk.queue.function.scattergather.SimpleTextGatherFunction])
var log_to_file: File = _
override def beforeGraph() = {
super.beforeGraph()
if (reference == null) reference = referenceFasta()
}
override def cmdLine = super.cmdLine +
required("-R", reference, spaceSeparated = true, escape = true, format = "%s") +
repeat("-V", variant, spaceSeparated = true, escape = true, format = "%s") +
......
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