Commit 0d5df191 authored by Peter van 't Hof's avatar Peter van 't Hof

Fixed jobOutputFile

parent 10524ce8
......@@ -78,6 +78,13 @@ trait BiopetQScript extends Configurable with GatkLogging {
case f: ScatterGatherableFunction => f.scatterCount = 1
case _ =>
}
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(add(_))
}
for (function <- functions) function match {
case f: BiopetCommandLineFunction =>
f.preProcessExecutable()
......@@ -96,11 +103,11 @@ trait BiopetQScript extends Configurable with GatkLogging {
else if (!i.file.canRead()) Logging.addError(s"Input file can not be read: ${i.file}")
}
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(add(_))
}
functions.filter(_.jobOutputFile == null).foreach(f => {
if (f.jobOutputFile == null && f.firstOutput != null)
f.jobOutputFile = new File(f.firstOutput.getAbsoluteFile.getParent, "." + f.firstOutput.getName + "." + configName + ".out")
else throw new IllegalStateException(s"Can't generate a jobOutputFile for $f")
})
if (logger.isDebugEnabled) WriteDependencies.writeDependencies(functions, new File(outputDir, s".log/${qSettings.runName}.deps.json"))
......
......@@ -58,9 +58,6 @@ trait CommandLineResources extends CommandLineFunction with Configurable {
case e: NullPointerException => null
}
if (jobOutputFile == null && firstOutput != null)
jobOutputFile = new File(firstOutput.getAbsoluteFile.getParent, "." + firstOutput.getName + "." + configName + ".out")
nCoresRequest = Option(threads)
/** The 1e retry does not yet upgrade the memory */
......
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