Commit a13b0d1d authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added version to varscan

parent 3fb6b5f8
...@@ -39,6 +39,8 @@ class Mpileup2cns(val root: Configurable) extends Varscan { ...@@ -39,6 +39,8 @@ class Mpileup2cns(val root: Configurable) extends Varscan {
var vcfSampleList: Option[File] = config("vcf_sample_list") var vcfSampleList: Option[File] = config("vcf_sample_list")
var variants: Option[Int] = config("variants") var variants: Option[Int] = config("variants")
override def defaultCoreMemory = 6.0
override def beforeGraph(): Unit = { override def beforeGraph(): Unit = {
val validValues: Set[Int] = Set(0, 1) val validValues: Set[Int] = Set(0, 1)
// check for boolean vars that are passed as ints // check for boolean vars that are passed as ints
......
...@@ -15,20 +15,15 @@ ...@@ -15,20 +15,15 @@
*/ */
package nl.lumc.sasc.biopet.extensions.varscan package nl.lumc.sasc.biopet.extensions.varscan
import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction import nl.lumc.sasc.biopet.core.{ Version, BiopetJavaCommandLineFunction }
abstract class Varscan extends BiopetJavaCommandLineFunction { abstract class Varscan extends BiopetJavaCommandLineFunction with Version {
override def subPath = "varscan" :: super.subPath override def subPath = "varscan" :: super.subPath
jarFile = config("varscan_jar") jarFile = config("varscan_jar")
/** def versionCommand = super.commandLine
* TODO: test version def versionRegex = """VarScan v(.*)""".r
* override def versionCommand = super.commandLine
* override val versionRegex = """VarScan v(.*)""".r
*/
override def defaultCoreMemory = 5.0
} }
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