Commit 815a271f authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added CatVariants

parent 2b63ae70
......@@ -25,7 +25,7 @@
<dependencies>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetCore</artifactId>
<artifactId>BiopetExtensions</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
......
......@@ -17,24 +17,32 @@ package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File
import nl.lumc.sasc.biopet.core.{ Reference, BiopetJavaCommandLineFunction }
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class CatVariants(val root: Configurable) extends Gatk {
val analysisType = "CatVariants"
class CatVariants(val root: Configurable) extends BiopetJavaCommandLineFunction with Reference {
@Input(doc = "", required = true)
javaMainClass = classOf[org.broadinstitute.gatk.tools.CatVariants].getClass.getName
@Input(required = true)
var inputFiles: List[File] = Nil
@Output(doc = "", required = true)
@Output(required = true)
var outputFile: File = null
override def cmdLine = super.cmdLine +
(for (file <- inputFiles) yield {
required("-V", file)
}).mkString +
required("-o", outputFile)
@Input
var reference: File = null
override def beforeGraph(): Unit = {
super.beforeGraph()
if (reference == null) reference = referenceFasta()
}
override def cmdLine = super.cmdLine +
repeat("-V", inputFiles) +
required("-out", outputFile) +
required("-R", reference)
}
object CatVariants {
......
......@@ -10,8 +10,6 @@ import org.broadinstitute.gatk.engine.phonehome.GATKRunReport
import org.broadinstitute.gatk.queue.extensions.gatk.CommandLineGATK
trait GatkGeneral extends CommandLineGATK with CommandLineResources with Reference with Version {
memoryLimit = Option(3)
var executable: String = config("java", default = "java", submodule = "java", freeVar = false)
override def subPath = "gatk" :: super.subPath
......
......@@ -21,6 +21,7 @@ import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.core.{ PipelineCommand, Reference }
import nl.lumc.sasc.biopet.extensions.Ln
import nl.lumc.sasc.biopet.extensions.delly.DellyCaller
import nl.lumc.sasc.biopet.extensions.gatk.CatVariants
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment