Commit 6569f666 authored by Peter van 't Hof's avatar Peter van 't Hof Committed by GitHub

Merge branch 'develop' into fix-BIOPET-558

parents b61ac974 aea6651a
...@@ -93,14 +93,19 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript => ...@@ -93,14 +93,19 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
} }
logger.info("Running pre commands") logger.info("Running pre commands")
for (function <- functions) function match { var count = 0
case f: BiopetCommandLineFunction => for (function <- functions) {
f.preProcessExecutable() function match {
f.beforeGraph() case f: BiopetCommandLineFunction =>
f.internalBeforeGraph() f.preProcessExecutable()
f.commandLine f.beforeGraph()
case f: WriteSummary => f.init() f.internalBeforeGraph()
case _ => f.commandLine
case f: WriteSummary => f.init()
case _ =>
}
count += 1
if (count % 500 == 0) logger.info(s"Preprocessing done for ${count} jobs out of ${functions.length} total")
} }
val logDir = new File(outputDir, ".log" + File.separator + qSettings.runName.toLowerCase) val logDir = new File(outputDir, ".log" + File.separator + qSettings.runName.toLowerCase)
......
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