Commit b40b3f8d authored by Peter van 't Hof's avatar Peter van 't Hof

Make it possible to disable HTML report

parent 1f2295c2
......@@ -126,17 +126,21 @@ 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 _ =>
val writeHtmlReport: Boolean = config("write_html_report", default = true)
if (writeHtmlReport) {
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)
}
report.jobOutputFile = new File(report.outputDir, ".report.out")
add(report)
}
}
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment