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Default jobreport is now jobPrefix, so you see logs like Q-2508.jobreport.txt

This commit is contained in:
Mark DePristo 2011-08-28 19:19:45 -04:00
parent a5c65fc133
commit 61633c95a8
3 changed files with 8 additions and 4 deletions
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8
public/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala
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@ -116,9 +116,11 @@ class QCommandLine extends CommandLineProgram with Logging {
for (script <- allQScripts) { for (script <- allQScripts) {
script.onExecutionDone(qGraph.getFunctionsAndStatus(script.functions), qGraph.success) script.onExecutionDone(qGraph.getFunctionsAndStatus(script.functions), qGraph.success)
if ( ! settings.disableJobReport ) { if ( ! settings.disableJobReport ) {
logger.info("Writing JobLogging GATKReport to file " + settings.jobReportFile) val jobStringName = (QScriptUtils.?(settings.jobReportFile)).getOrElse(settings.qSettings.jobNamePrefix + ".jobreport.txt")
QJobReport.printReport(qGraph.getFunctionsAndStatus(script.functions), settings.jobReportFile) val jobReportFile = new File(jobStringName)
QJobReport.plotReport(settings.rScriptArgs, settings.jobReportFile) logger.info("Writing JobLogging GATKReport to file " + jobReportFile)
QJobReport.printReport(qGraph.getFunctionsAndStatus(script.functions), jobReportFile)
QJobReport.plotReport(settings.rScriptArgs, jobReportFile)
} }
} }

2
public/scala/src/org/broadinstitute/sting/queue/engine/QGraphSettings.scala
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@ -71,7 +71,7 @@ class QGraphSettings {
var expandedDotFile: File = _ var expandedDotFile: File = _
@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: String = _
@Advanced @Advanced
@Argument(fullName="disableJobReport", shortName="disabpleJobReport", doc="If provided, we will not create a job report", required=false) @Argument(fullName="disableJobReport", shortName="disabpleJobReport", doc="If provided, we will not create a job report", required=false)

2
public/scala/src/org/broadinstitute/sting/queue/util/QScriptUtils.scala
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@ -57,4 +57,6 @@ object QScriptUtils {
} }
def ?[A <: AnyRef](ref: A): Option[A] =
if (ref eq null) None else Some(ref)
} }