From a90b06da5f58a045f4a89458211ec097c14cee7c Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Tue, 29 Jul 2014 15:03:05 +0200
Subject: [PATCH] Update base BiopetQScript command line argument names
---
.../main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
index 9a1accb31..01be09e97 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
@@ -8,10 +8,11 @@ import org.broadinstitute.gatk.queue.QSettings
import org.broadinstitute.gatk.queue.function.QFunction
trait BiopetQScript extends Configurable {
- @Argument(doc = "Config Json file", shortName = "config", required = false)
+
+ @Argument(doc = "JSON config file(s)", fullName = "config_file", shortName = "conf", required = false)
val configfiles: List[File] = Nil
- @Argument(doc = "Output directory", shortName = "outputDir", required = true)
+ @Argument(doc = "Output directory", fullName = "output_directory", shortName = "outDir", required = true)
var outputDir: String = _
var outputFiles: Map[String, File] = Map()
--
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