Commit a93b0bbd authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix bug on relative files

parent 45200c55
......@@ -52,9 +52,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
checkExecutable
afterGraph
super.freezeFieldValues()
if (jobOutputFile == null) jobOutputFile = new File(firstOutput.getParent + "/." + firstOutput.getName + "." + configName + ".out")
if (jobOutputFile == null) jobOutputFile = new File(firstOutput.getAbsoluteFile.getParent + "/." + firstOutput.getName + "." + configName + ".out")
if (threads == 0) threads = getThreads(defaultThreads)
if (threads > 1) nCoresRequest = Option(threads)
......@@ -65,6 +63,8 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
}
if (vmem.isDefined) jobResourceRequests :+= "h_vmem=" + vmem.get
jobName = configName + ":" + (if (firstOutput != null) firstOutput.getName else jobOutputFile)
super.freezeFieldValues()
}
protected def checkExecutable {
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment