Commit aea6651a authored by Peter van 't Hof's avatar Peter van 't Hof Committed by GitHub

Merge pull request #17 from biopet/fix-BIOPET-521

one log line
parents 6abbb191 103babcf
......@@ -93,14 +93,19 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
}
logger.info("Running pre commands")
for (function <- functions) function match {
case f: BiopetCommandLineFunction =>
f.preProcessExecutable()
f.beforeGraph()
f.internalBeforeGraph()
f.commandLine
case f: WriteSummary => f.init()
case _ =>
var count = 0
for (function <- functions) {
function match {
case f: BiopetCommandLineFunction =>
f.preProcessExecutable()
f.beforeGraph()
f.internalBeforeGraph()
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)
......
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