Commit 58d71f66 authored by Peter van 't Hof's avatar Peter van 't Hof Committed by GitHub

Merge branch 'develop' into Fix-BIOPET-572

parents 8106b4a6 0140969c
...@@ -126,17 +126,21 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript => ...@@ -126,17 +126,21 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
} }
}) })
logger.info("Adding report") val writeHtmlReport: Boolean = config("write_html_report", default = true)
this match {
case q: MultiSampleQScript if q.onlySamples.nonEmpty && !q.samples.forall(x => q.onlySamples.contains(x._1)) => if (writeHtmlReport) {
logger.info("Write report is skipped because sample flag is used") logger.info("Adding report")
case _ => reportClass.foreach { report => this match {
for (f <- functions) f match { case q: MultiSampleQScript if q.onlySamples.nonEmpty && !q.samples.forall(x => q.onlySamples.contains(x._1)) =>
case w: WriteSummary => report.deps :+= w.jobOutputFile logger.info("Write report is skipped because sample flag is used")
case _ => 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)
} }
} }
......
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