Commit 85779d49 authored by Peter van 't Hof's avatar Peter van 't Hof

Fix report

parent 9f2f0a11
......@@ -104,19 +104,6 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
}
logger.info(s"Preprocessing done for $totalCount functions")
logger.info("Adding report")
this match {
case q: MultiSampleQScript if q.onlySamples.nonEmpty && !q.samples.forall(x => q.onlySamples.contains(x._1)) =>
logger.info("Write report is skipped because sample flag is used")
case _ => reportClass.foreach { report =>
for (f <- functions) f match {
case w: WriteSummary => report.deps :+= w.jobOutputFile
case _ =>
}
add(report)
}
}
val logDir = new File(outputDir, ".log" + File.separator + qSettings.runName.toLowerCase)
if (outputDir.getParentFile.canWrite || (outputDir.exists && outputDir.canWrite))
......@@ -139,6 +126,20 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
}
})
logger.info("Adding report")
this match {
case q: MultiSampleQScript if q.onlySamples.nonEmpty && !q.samples.forall(x => q.onlySamples.contains(x._1)) =>
logger.info("Write report is skipped because sample flag is used")
case _ => reportClass.foreach { report =>
for (f <- functions) f match {
case w: WriteSummary => report.deps :+= w.jobOutputFile
case _ =>
}
report.jobOutputFile = new File(report.outputDir, ".report.out")
add(report)
}
}
if (!skipWriteDependencies) WriteDependencies.writeDependencies(
functions,
new File(logDir, "graph"))
......
......@@ -38,8 +38,6 @@ object MappingReport extends ReportBuilder {
override def extFiles = super.extFiles ++ List("js/gears.js", "js/krona-2.0.js", "img/krona/loading.gif", "img/krona/hidden.png", "img/krona/favicon.ico")
.map(x => ExtFile("/nl/lumc/sasc/biopet/pipelines/gears/report/ext/" + x, x))
summary.getStatsSize(runId, Right("gears"), Some(Right("krakenreport")),
sample = sampleId.map(Left(_)), library = libId.map(Left(_)))
def krakenExecuted: Boolean = Await.result(summary.getStatsSize(runId, Right("gears"), Some(Right("krakenreport")),
sample = sampleId.map(Left(_)), library = libId.map(Left(_))), Duration.Inf) >= 1
......
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