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 ...@@ -52,9 +52,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
checkExecutable checkExecutable
afterGraph afterGraph
super.freezeFieldValues() if (jobOutputFile == null) jobOutputFile = new File(firstOutput.getAbsoluteFile.getParent + "/." + firstOutput.getName + "." + configName + ".out")
if (jobOutputFile == null) jobOutputFile = new File(firstOutput.getParent + "/." + firstOutput.getName + "." + configName + ".out")
if (threads == 0) threads = getThreads(defaultThreads) if (threads == 0) threads = getThreads(defaultThreads)
if (threads > 1) nCoresRequest = Option(threads) if (threads > 1) nCoresRequest = Option(threads)
...@@ -65,6 +63,8 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab ...@@ -65,6 +63,8 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
} }
if (vmem.isDefined) jobResourceRequests :+= "h_vmem=" + vmem.get if (vmem.isDefined) jobResourceRequests :+= "h_vmem=" + vmem.get
jobName = configName + ":" + (if (firstOutput != null) firstOutput.getName else jobOutputFile) jobName = configName + ":" + (if (firstOutput != null) firstOutput.getName else jobOutputFile)
super.freezeFieldValues()
} }
protected def checkExecutable { protected def checkExecutable {
......
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