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 => ...@@ -58,11 +58,6 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
*/ */
var jobDelayTime: Option[Int] = config("job_delay_time") 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" // This overrides the default "sh" from queue. For Biopet the default is "bash"
updateJobRun = { updateJobRun = {
case jt: JobTemplate => case jt: JobTemplate =>
...@@ -104,7 +99,6 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction => ...@@ -104,7 +99,6 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
_pipesJobs.foreach(_.beforeGraph()) _pipesJobs.foreach(_.beforeGraph())
_pipesJobs.foreach(_.internalBeforeGraph()) _pipesJobs.foreach(_.internalBeforeGraph())
jobWallClockTimeLimit.foreach(x => jobNativeArgs = jobNativeArgs.toList ::: List(s"-l h_rt=$x"))
} }
......
...@@ -18,7 +18,7 @@ import java.io.File ...@@ -18,7 +18,7 @@ import java.io.File
import htsjdk.samtools.reference.IndexedFastaSequenceFile import htsjdk.samtools.reference.IndexedFastaSequenceFile
import nl.lumc.sasc.biopet.core.summary.{ Summarizable, SummaryQScript } 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 nl.lumc.sasc.biopet.utils.{ ConfigUtils, FastaUtils, Logging }
import scala.collection.JavaConversions._ import scala.collection.JavaConversions._
......
...@@ -22,6 +22,8 @@ import org.broadinstitute.gatk.utils.commandline._ ...@@ -22,6 +22,8 @@ import org.broadinstitute.gatk.utils.commandline._
class FreeC(val root: Configurable) extends BiopetCommandLineFunction with Reference with Version { class FreeC(val root: Configurable) extends BiopetCommandLineFunction with Reference with Version {
override def defaults = Map("max_walltime_limit" -> 7200)
@Input(doc = "BAMfile", required = true) @Input(doc = "BAMfile", required = true)
var input: File = _ var input: File = _
...@@ -127,9 +129,6 @@ class FreeC(val root: Configurable) extends BiopetCommandLineFunction with Refer ...@@ -127,9 +129,6 @@ class FreeC(val root: Configurable) extends BiopetCommandLineFunction with Refer
override def defaultThreads = 4 override def defaultThreads = 4
override def defaultCoreMemory = 50 override def defaultCoreMemory = 50
// wallclock time limit in seconds
jobWallClockTimeLimit = config("job_wall_time_limit", namespace = "freec", default = 7200)
private var configFile: File = _ private var configFile: File = _
override def beforeGraph { override def beforeGraph {
......
package nl.lumc.sasc.biopet.pipelines.kopisu.methods 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.core.Reference
import nl.lumc.sasc.biopet.extensions.Cnmops import nl.lumc.sasc.biopet.extensions.Cnmops
import nl.lumc.sasc.biopet.utils.config.Configurable import nl.lumc.sasc.biopet.utils.config.Configurable
......
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