Commit 9f2f0a11 authored by Peter van 't Hof's avatar Peter van 't Hof

Fix report deps

parent 166530dc
......@@ -86,18 +86,6 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
}
}
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)
}
}
logger.info("Running pre commands")
var count = 0
val totalCount = functions.size
......@@ -116,6 +104,19 @@ 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))
......
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