From eb5f93272c3a20a83cc9ea6eefbd68fc217a7bc4 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 12 Feb 2015 18:17:35 +0100
Subject: [PATCH] Make outputDir always absolute
---
.../main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
index 3ae6780e4..91a9da2a3 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
@@ -35,7 +35,7 @@ trait BiopetQScript extends Configurable with GatkLogging {
var outputDir: File = {
Config.getValueFromMap(globalConfig.map, ConfigValueIndex(this.configName, configPath, "output_dir")) match {
- case Some(value) => new File(value.asString)
+ case Some(value) => new File(value.asString).getAbsoluteFile
case _ => new File(".")
}
}
@@ -61,7 +61,7 @@ trait BiopetQScript extends Configurable with GatkLogging {
* Script from queue itself, final to force some checks for each pipeline and write report
*/
final def script() {
- outputDir = config("output_dir")
+ outputDir = config("output_dir").asFile.getAbsoluteFile
init
biopetScript
--
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