From f5f8ead73a5a581a0858273bab38b594adb81076 Mon Sep 17 00:00:00 2001
From: Wai Yi Leung <w.y.leung@e-sensei.nl>
Date: Tue, 6 Oct 2015 10:50:53 +0200
Subject: [PATCH] Change commandLine to cmdLine according to the new specs
---
.../lumc/sasc/biopet/extensions/tools/KrakenReportToJson.scala | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/KrakenReportToJson.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/KrakenReportToJson.scala
index d6343a7da..5c5582a4c 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/KrakenReportToJson.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/KrakenReportToJson.scala
@@ -31,7 +31,7 @@ class KrakenReportToJson(val root: Configurable) extends ToolCommandFuntion with
override def defaultCoreMemory = 1.0
- override def commandLine = super.commandLine + required("-i", inputReport) + required("-o", output)
+ override def cmdLine = super.cmdLine + required("-i", inputReport) + required("-o", output)
def summaryStats: Map[String, Any] = {
val map = ConfigUtils.fileToConfigMap(output)
--
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