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
......@@ -93,7 +93,9 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
}
logger.info("Running pre commands")
for (function <- functions) function match {
var count = 0
for (function <- functions) {
function match {
case f: BiopetCommandLineFunction =>
f.preProcessExecutable()
f.beforeGraph()
......@@ -102,6 +104,9 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
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)
......
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