Commit b8830d55 authored by Sander Bollen's avatar Sander Bollen
Browse files

use correct location for time limit

parent fac95be4
......@@ -58,11 +58,6 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
*/
var jobDelayTime: Option[Int] = config("job_delay_time")
/**
* wall clock time limit in seconds for a job
*/
var jobWallClockTimeLimit: Option[Int] = config("job_wall_time_limit")
// This overrides the default "sh" from queue. For Biopet the default is "bash"
updateJobRun = {
case jt: JobTemplate =>
......@@ -104,7 +99,6 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
_pipesJobs.foreach(_.beforeGraph())
_pipesJobs.foreach(_.internalBeforeGraph())
jobWallClockTimeLimit.foreach(x => jobNativeArgs = jobNativeArgs.toList ::: List(s"-l h_rt=$x"))
}
......
......@@ -18,7 +18,7 @@ import java.io.File
import htsjdk.samtools.reference.IndexedFastaSequenceFile
import nl.lumc.sasc.biopet.core.summary.{ Summarizable, SummaryQScript }
import nl.lumc.sasc.biopet.utils.config.{Config, Configurable}
import nl.lumc.sasc.biopet.utils.config.{ Config, Configurable }
import nl.lumc.sasc.biopet.utils.{ ConfigUtils, FastaUtils, Logging }
import scala.collection.JavaConversions._
......
......@@ -55,8 +55,8 @@ class Cnmops(val root: Configurable) extends RscriptCommandLineFunction with Ver
*/
def versionCheck: Boolean = {
getVersion.flatMap(getSemanticVersion(_)) match {
case Some(version) => (version.major == 1 && version.minor >= 18) || version.major >= 2
case _ => false
case Some(version) => (version.major == 1 && version.minor >= 18) || version.major >= 2
case _ => false
}
}
......@@ -74,7 +74,7 @@ class Cnmops(val root: Configurable) extends RscriptCommandLineFunction with Ver
lazy val outputCnv: File = {
outputDir match {
case Some(dir) => new File(dir, "cnv.txt")
case _ => throw new IllegalArgumentException("Unexpected error when trying to set cn.MOPS CNV output")
case _ => throw new IllegalArgumentException("Unexpected error when trying to set cn.MOPS CNV output")
}
}
......@@ -82,15 +82,15 @@ class Cnmops(val root: Configurable) extends RscriptCommandLineFunction with Ver
lazy val outputCnr: File = {
outputDir match {
case Some(dir) => new File(dir, "cnr.txt")
case _ => throw new IllegalArgumentException("Unexpected error when trying to set cn.MOPS CNR output")
case _ => throw new IllegalArgumentException("Unexpected error when trying to set cn.MOPS CNR output")
}
}
@Output(doc = "Raw output")
lazy val rawOutput: File = {
outputDir match {
case Some(dir) => new File(dir, "rawoutput.txt")
case _ => throw new IllegalArgumentException("Unexpected error when trying to set cn.MOPS raw output")
case Some(dir) => new File(dir, "rawoutput.txt")
case _ => throw new IllegalArgumentException("Unexpected error when trying to set cn.MOPS raw output")
}
}
......
......@@ -22,6 +22,8 @@ import org.broadinstitute.gatk.utils.commandline._
class FreeC(val root: Configurable) extends BiopetCommandLineFunction with Reference with Version {
override def defaults = Map("max_walltime_limit" -> 7200)
@Input(doc = "BAMfile", required = true)
var input: File = _
......@@ -127,9 +129,6 @@ class FreeC(val root: Configurable) extends BiopetCommandLineFunction with Refer
override def defaultThreads = 4
override def defaultCoreMemory = 50
// wallclock time limit in seconds
jobWallClockTimeLimit = config("job_wall_time_limit", namespace = "freec", default = 7200)
private var configFile: File = _
override def beforeGraph {
......
package nl.lumc.sasc.biopet.pipelines.kopisu.methods
import htsjdk.samtools.{SAMSequenceDictionary, SamReaderFactory}
import htsjdk.samtools.{ SAMSequenceDictionary, SamReaderFactory }
import nl.lumc.sasc.biopet.core.Reference
import nl.lumc.sasc.biopet.extensions.Cnmops
import nl.lumc.sasc.biopet.utils.config.Configurable
......
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