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Argument to disable queueJobReport entirely 

-- Minor improvements to RodPerformanceGoals
This commit is contained in:
Mark DePristo 2011-08-25 13:32:03 -04:00
parent d65faf509c
commit 0f4be2c4a4
2 changed files with 9 additions and 3 deletions
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6
public/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala
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@ -115,8 +115,10 @@ class QCommandLine extends CommandLineProgram with Logging {
// walk over each script, calling onExecutionDone // walk over each script, calling onExecutionDone
for (script <- allQScripts) { for (script <- allQScripts) {
script.onExecutionDone(qGraph.getFunctionsAndStatus(script.functions), qGraph.success) script.onExecutionDone(qGraph.getFunctionsAndStatus(script.functions), qGraph.success)
logger.info("Writing JobLogging GATKReport to file " + settings.jobReportFile) if ( ! settings.disableJobReport ) {
QJobReport.printReport(qGraph.getFunctionsAndStatus(script.functions), settings.jobReportFile) logger.info("Writing JobLogging GATKReport to file " + settings.jobReportFile)
QJobReport.printReport(qGraph.getFunctionsAndStatus(script.functions), settings.jobReportFile)
// todo -- execute Rscript here once generic RScript execution system is implemented }
} }
if (!qGraph.success) { if (!qGraph.success) {

6
public/scala/src/org/broadinstitute/sting/queue/engine/QGraphSettings.scala
View File

@ -26,8 +26,8 @@ package org.broadinstitute.sting.queue.engine
import java.io.File import java.io.File
import org.broadinstitute.sting.queue.QSettings import org.broadinstitute.sting.queue.QSettings
import org.broadinstitute.sting.commandline.{ArgumentCollection, Argument}
import org.broadinstitute.sting.queue.util.SystemUtils import org.broadinstitute.sting.queue.util.SystemUtils
import org.broadinstitute.sting.commandline.{Advanced, ArgumentCollection, Argument}
/** /**
* Command line options for a QGraph. * Command line options for a QGraph.
@ -72,6 +72,10 @@ class QGraphSettings {
@Argument(fullName="jobReport", shortName="jobReport", doc="File where we will write the Queue job report", required=false) @Argument(fullName="jobReport", shortName="jobReport", doc="File where we will write the Queue job report", required=false)
var jobReportFile: File = new File("queue_jobreport.gatkreport.txt") var jobReportFile: File = new File("queue_jobreport.gatkreport.txt")
@Advanced
@Argument(fullName="disableJobReport", shortName="disabpleJobReport", doc="If provided, we will not create a job report", required=false)
var disableJobReport: Boolean = false
@ArgumentCollection @ArgumentCollection
val qSettings = new QSettings val qSettings = new QSettings
} }