From 6e5f147833762f204b04ab8817a1c32144c07d04 Mon Sep 17 00:00:00 2001
From: Sander Bollen <a.h.b.bollen@lumc.nl>
Date: Fri, 8 Apr 2016 14:53:39 +0200
Subject: [PATCH] well.. it compiles
---
.../src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala | 2 +-
.../sasc/biopet/pipelines/tinycap/TinyCapTest.scala | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
rename public/tinycap/src/test/scala/nl/{lucm => lumc}/sasc/biopet/pipelines/tinycap/TinyCapTest.scala (98%)
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
index 8f32e947b..d40690df7 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
@@ -85,7 +85,7 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction with Vers
/** return commandline to execute */
def cmdLine = required(executable) +
- optional("--java", java_exe) +
+ optional("--java", javaExe) +
optional("--threads", threads) +
optional("--contaminants", contaminants) +
optional("--adapters", adapters) +
diff --git a/public/tinycap/src/test/scala/nl/lucm/sasc/biopet/pipelines/tinycap/TinyCapTest.scala b/public/tinycap/src/test/scala/nl/lumc/sasc/biopet/pipelines/tinycap/TinyCapTest.scala
similarity index 98%
rename from public/tinycap/src/test/scala/nl/lucm/sasc/biopet/pipelines/tinycap/TinyCapTest.scala
rename to public/tinycap/src/test/scala/nl/lumc/sasc/biopet/pipelines/tinycap/TinyCapTest.scala
index b8ec5c3ab..7275b4349 100644
--- a/public/tinycap/src/test/scala/nl/lucm/sasc/biopet/pipelines/tinycap/TinyCapTest.scala
+++ b/public/tinycap/src/test/scala/nl/lumc/sasc/biopet/pipelines/tinycap/TinyCapTest.scala
@@ -35,7 +35,7 @@ class TinyCapTest extends TestNGSuite with Matchers {
def initPipeline(map: Map[String, Any]): TinyCap = {
new TinyCap() {
- override def configName = "tinycap"
+ override def configNamespace = "tinycap"
override def globalConfig = new Config(map)
--
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