From fcaccd905c41565e670501b3c66a5e7d74f95826 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 12 Jun 2014 21:10:38 +0200
Subject: [PATCH] Extends directly on Python
---
.../sasc/biopet/pipelines/flexiprep/scripts/FastqSync.scala | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqSync.scala b/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqSync.scala
index 4b5f179c7..3defa15fc 100644
--- a/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqSync.scala
+++ b/flexiprep/src/main/java/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqSync.scala
@@ -7,10 +7,10 @@ import org.broadinstitute.sting.queue.function.CommandLineFunction
import org.broadinstitute.sting.commandline._
import java.io.File
-class FastqSync(val globalConfig: Config) extends CommandLineFunction with Python {
+class FastqSync(val globalConfig: Config) extends Python {
def this() = this(new Config(Map()))
analysisName = "fastqsync"
- val config: Config = Config.mergeConfigs(globalConfig.getAsConfig(analysisName), globalConfig)
+ val config = Config.mergeConfigs(globalConfig.getAsConfig(analysisName.toLowerCase), globalConfig)
logger.debug("Config for " + analysisName + ": " + config)
setPythonScript("__init__.py", "scripts/pyfastqc/")
--
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