Commit 6300d051 authored by Sander Bollen's avatar Sander Bollen
Browse files

Merge branch 'feature-gatk_et_option' into 'develop'

Add et option to gatk jobs

Added the et option to gatk.

@a.h.b.bollen: could you maybe test this? I don't have a key

See merge request !169
parents d5ae90cf a715d472
......@@ -5,7 +5,8 @@
*/
package nl.lumc.sasc.biopet.extensions.gatk.broad
import nl.lumc.sasc.biopet.core.{ BiopetJavaCommandLineFunction, Reference }
import nl.lumc.sasc.biopet.core.{ Reference, BiopetJavaCommandLineFunction }
import org.broadinstitute.gatk.engine.phonehome.GATKRunReport
import org.broadinstitute.gatk.queue.extensions.gatk.CommandLineGATK
trait GatkGeneral extends CommandLineGATK with BiopetJavaCommandLineFunction with Reference {
......@@ -20,6 +21,15 @@ trait GatkGeneral extends CommandLineGATK with BiopetJavaCommandLineFunction wit
if (config.contains("intervals")) intervals = config("intervals").asFileList
if (config.contains("exclude_intervals")) excludeIntervals = config("exclude_intervals").asFileList
Option(config("et").value) match {
case Some("NO_ET") => et = GATKRunReport.PhoneHomeOption.NO_ET
case Some("AWS") => et = GATKRunReport.PhoneHomeOption.AWS
case Some("STDOUT") => et = GATKRunReport.PhoneHomeOption.STDOUT
case Some(x) => throw new IllegalArgumentException(s"Unknown et option for gatk: $x")
case _ =>
}
if (config.contains("gatk_key")) gatk_key = config("gatk_key")
if (config.contains("pedigree")) pedigree = config("pedigree")
......
......@@ -49,6 +49,8 @@ abstract class Gatk extends BiopetJavaCommandLineFunction with Reference {
@Input(required = false)
var pedigree: List[File] = config("pedigree", default = Nil)
var et: Option[String] = config("et")
override def versionRegex = """(.*)""".r
override def versionExitcode = List(0, 1)
override def versionCommand = executable + " -jar " + jarFile + " -version"
......@@ -65,6 +67,7 @@ abstract class Gatk extends BiopetJavaCommandLineFunction with Reference {
required("-T", analysisType) +
required("-R", reference) +
optional("-K", gatkKey) +
optional("-et", et) +
repeat("-I", intervals) +
repeat("-XL", excludeIntervals) +
repeat("-ped", pedigree)
......
Supports Markdown
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