From d5b3661d6a309b00cf5f9a09aa6e4af9280a3660 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 13 Feb 2015 16:46:33 +0100
Subject: [PATCH] Fix output dirs
---
public/flexiprep/Flexiprep.iml | 13 +++++++++++--
.../sasc/biopet/pipelines/mapping/Mapping.scala | 2 +-
2 files changed, 12 insertions(+), 3 deletions(-)
diff --git a/public/flexiprep/Flexiprep.iml b/public/flexiprep/Flexiprep.iml
index 54fb96649..791476d63 100644
--- a/public/flexiprep/Flexiprep.iml
+++ b/public/flexiprep/Flexiprep.iml
@@ -6,6 +6,8 @@
<content url="file://$MODULE_DIR$">
<sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" />
<sourceFolder url="file://$MODULE_DIR$/src/main/scala" isTestSource="false" />
+ <sourceFolder url="file://$MODULE_DIR$/src/test/resources" type="java-test-resource" />
+ <sourceFolder url="file://$MODULE_DIR$/src/test/scala" isTestSource="true" />
<excludeFolder url="file://$MODULE_DIR$/target" />
</content>
<orderEntry type="inheritedJdk" />
@@ -16,7 +18,6 @@
<orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-public:3.3" level="project" />
<orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-engine:3.3" level="project" />
<orderEntry type="library" name="Maven: org.scala-lang:scala-compiler:2.10.2" level="project" />
- <orderEntry type="library" name="Maven: org.scala-lang:scala-reflect:2.10.2" level="project" />
<orderEntry type="library" name="Maven: log4j:log4j:1.2.15" level="project" />
<orderEntry type="library" name="Maven: net.sf.jgrapht:jgrapht:0.8.3" level="project" />
<orderEntry type="library" name="Maven: org.apache.commons:commons-email:1.2" level="project" />
@@ -82,11 +83,19 @@
<orderEntry type="library" name="Maven: io.argonaut:argonaut_2.11:6.1-M4" level="project" />
<orderEntry type="library" name="Maven: org.scalaz:scalaz-core_2.11:7.1.0" level="project" />
<orderEntry type="library" name="Maven: org.scala-lang.modules:scala-parser-combinators_2.11:1.0.2" level="project" />
- <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-xml_2.11:1.0.2" level="project" />
<orderEntry type="library" name="Maven: com.github.julien-truffaut:monocle-core_2.11:0.5.0" level="project" />
<orderEntry type="library" name="Maven: org.biojava:biojava3-core:3.1.0" level="project" />
<orderEntry type="library" name="Maven: org.biojava:biojava3-sequencing:3.1.0" level="project" />
<orderEntry type="library" name="Maven: com.google.guava:guava:18.0" level="project" />
<orderEntry type="library" name="Maven: com.github.scopt:scopt_2.10:3.2.0" level="project" />
+ <orderEntry type="library" scope="TEST" name="Maven: org.testng:testng:6.8" level="project" />
+ <orderEntry type="library" name="Maven: junit:junit:4.10" level="project" />
+ <orderEntry type="library" name="Maven: org.hamcrest:hamcrest-core:1.1" level="project" />
+ <orderEntry type="library" scope="TEST" name="Maven: org.beanshell:bsh:2.0b4" level="project" />
+ <orderEntry type="library" scope="TEST" name="Maven: com.beust:jcommander:1.27" level="project" />
+ <orderEntry type="library" scope="TEST" name="Maven: org.yaml:snakeyaml:1.6" level="project" />
+ <orderEntry type="library" scope="TEST" name="Maven: org.scalatest:scalatest_2.11:2.2.1" level="project" />
+ <orderEntry type="library" name="Maven: org.scala-lang:scala-reflect:2.11.2" level="project" />
+ <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-xml_2.11:1.0.2" level="project" />
</component>
</module>
\ No newline at end of file
diff --git a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
index c83014c44..2db8a8f84 100644
--- a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+++ b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
@@ -176,7 +176,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
var R2 = fastqfile._2
var deps: List[File] = Nil
if (!skipFlexiprep) {
- val flexiout = flexiprep.runTrimClip(R1, R2, chunkDir + "flexiprep/", chunkDir)
+ val flexiout = flexiprep.runTrimClip(R1, R2, new File(chunkDir, "flexiprep"), chunkDir)
logger.debug(chunkDir + " - " + flexiout)
R1 = flexiout._1
if (paired) R2 = flexiout._2
--
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