Commit 9bf128f3 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Adding log lines

parent 7b7dbee8
......@@ -122,6 +122,7 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
if (!i.file.isAbsolute) Logging.addError(s"Input file should be an absolute path: ${i.file}")
}
logger.info("Set stdout file when not set")
functions.filter(_.jobOutputFile == null).foreach(f => {
val className = if (f.getClass.isAnonymousClass) f.getClass.getSuperclass.getSimpleName else f.getClass.getSimpleName
BiopetQScript.safeOutputs(f) match {
......@@ -133,6 +134,7 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
if (!skipWriteDependencies) WriteDependencies.writeDependencies(
functions,
new File(logDir, "graph"))
else logger.debug("Write dependencies is skipped")
Logging.checkErrors()
logger.info("Script complete without errors")
......
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