Commit 72761225 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Switch to CommandLineResources

parent 1199a39e
......@@ -14,8 +14,8 @@ class ApplyRecalibration(val root: Configurable) extends org.broadinstitute.gatk
override val defaultThreads = 3
override def beforeGraph() {
super.beforeGraph()
override def freezeFieldValues() {
super.freezeFieldValues()
nt = Option(getThreads)
memoryLimit = Option(nt.getOrElse(1) * 2)
......
......@@ -20,7 +20,6 @@ object BaseRecalibrator {
val br = new BaseRecalibrator(root)
br.input_file :+= input
br.out = output
br.beforeGraph()
br
}
}
\ No newline at end of file
......@@ -5,17 +5,19 @@
*/
package nl.lumc.sasc.biopet.extensions.gatk.broad
import nl.lumc.sasc.biopet.core.{ Reference, BiopetJavaCommandLineFunction }
import nl.lumc.sasc.biopet.core.{ CommandLineResources, 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 {
trait GatkGeneral extends CommandLineGATK with CommandLineResources with Reference {
memoryLimit = Option(3)
override def subPath = "gatk" :: super.subPath
jarFile = config("gatk_jar")
reference_sequence = referenceFasta()
override def defaultCoreMemory = 4.0
override def faiRequired = true
......@@ -33,14 +35,9 @@ trait GatkGeneral extends CommandLineGATK with BiopetJavaCommandLineFunction wit
if (config.contains("gatk_key")) gatk_key = config("gatk_key")
if (config.contains("pedigree")) pedigree = config("pedigree")
override def versionRegex = """(.*)""".r
override def versionExitcode = List(0, 1)
override def versionCommand = executable + " -jar " + jarFile + " -version"
override def getVersion = super.getVersion.collect { case v => "Gatk " + v }
//override def versionRegex = """(.*)""".r
//override def versionExitcode = List(0, 1)
//override def versionCommand = executable + " -jar " + jarFile + " -version"
override def beforeGraph(): Unit = {
super.beforeGraph()
if (reference_sequence == null) reference_sequence = referenceFasta()
}
//override def getVersion = super.getVersion.collect { case v => "Gatk " + v }
}
......@@ -38,8 +38,8 @@ class HaplotypeCaller(val root: Configurable) extends org.broadinstitute.gatk.qu
stand_emit_conf = config("stand_emit_conf", default = 0)
}
override def beforeGraph() {
super.beforeGraph()
override def freezeFieldValues() {
super.freezeFieldValues()
if (bamOutput != null && nct.getOrElse(1) > 1) {
logger.warn("BamOutput is on, nct/threads is forced to set on 1, this option is only for debug")
}
......
......@@ -28,8 +28,8 @@ class UnifiedGenotyper(val root: Configurable) extends org.broadinstitute.gatk.q
override val defaultThreads = 1
override def beforeGraph() {
super.beforeGraph()
override def freezeFieldValues() {
super.freezeFieldValues()
genotype_likelihoods_model = org.broadinstitute.gatk.tools.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.BOTH
nct = Some(getThreads)
......
......@@ -10,9 +10,6 @@ import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
class VariantEval(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.VariantEval with GatkGeneral {
override def beforeGraph() {
super.beforeGraph()
}
}
object VariantEval {
......@@ -22,7 +19,6 @@ object VariantEval {
vareval.eval = Seq(sample)
vareval.comp = Seq(compareWith)
vareval.out = output
vareval.beforeGraph()
vareval
}
......@@ -36,7 +32,6 @@ object VariantEval {
vareval.ST = ST
vareval.noEV = true
vareval.EV = EV
vareval.beforeGraph()
vareval
}
......
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