From b36e7c853814f26d67e56377dd583cbc5b0fcc1d Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 5 Feb 2015 15:13:27 +0100
Subject: [PATCH] Enables manual set of jobOutputFile
---
.../sasc/biopet/core/BiopetCommandLineFunctionTrait.scala | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
index 97cc2bd46..a76bd7e3a 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
@@ -53,7 +53,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
override def freezeFieldValues() {
checkExecutable
afterGraph
- jobOutputFile = new File(firstOutput.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 > 1) nCoresRequest = Option(threads)
@@ -63,7 +63,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
if (vmem.isEmpty && defaultVmem.nonEmpty) vmem = Some(defaultVmem)
}
if (vmem != null) jobResourceRequests :+= "h_vmem=" + vmem
- jobName = configName + ":" + firstOutput.getName
+ jobName = configName + ":" + (if (firstOutput != null) firstOutput.getName else jobOutputFile)
super.freezeFieldValues()
}
--
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