From 1c15813322efe2ecf866aee2a660cca2bf2acb7b Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 6 Apr 2015 13:05:44 +0200
Subject: [PATCH] Refactor output dir
---
.../nl/lumc/sasc/biopet/core/BiopetQScript.scala | 13 ++++---------
1 file changed, 4 insertions(+), 9 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 97b383a8a..28d47adf5 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
@@ -37,10 +37,8 @@ trait BiopetQScript extends Configurable with GatkLogging {
val configValues: List[String] = Nil
var outputDir: File = {
- Config.getValueFromMap(globalConfig.map, ConfigValueIndex(this.configName, configPath, "output_dir")) match {
- case Some(value) => new File(value.asString).getAbsoluteFile
- case _ => new File(".")
- }
+ if (config.contains("output_dir", path = Nil)) config("output_dir", path = Nil).asFile
+ else new File(".")
}
@Argument(doc = "Disable all scatters", shortName = "DSC", required = false)
@@ -64,11 +62,8 @@ trait BiopetQScript extends Configurable with GatkLogging {
* Script from queue itself, final to force some checks for each pipeline and write report
*/
final def script() {
- if (config.contains("output_dir")) outputDir = config("output_dir").asFile.getAbsoluteFile
- else {
- outputDir = new File(".").getAbsoluteFile
- BiopetQScript.addError("No output_dir defined in config")
- }
+ outputDir = config("output_dir")
+ outputDir = outputDir.getAbsoluteFile
init
biopetScript
--
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