diff --git a/public/bam2wig/pom.xml b/public/bam2wig/pom.xml
index 894cfbdb6c9b742249d4d2560e4c7540e2545feb..4ee5fd2681e87e9a999c4cfad22413dbd67a0bab 100644
--- a/public/bam2wig/pom.xml
+++ b/public/bam2wig/pom.xml
@@ -40,6 +40,11 @@
<artifactId>BiopetCore</artifactId>
<version>${project.version}</version>
</dependency>
+ <dependency>
+ <groupId>nl.lumc.sasc</groupId>
+ <artifactId>BiopetExtensions</artifactId>
+ <version>${project.version}</version>
+ </dependency>
</dependencies>
</project>
\ No newline at end of file
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/Md5sum.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/Md5sum.scala
similarity index 97%
rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/Md5sum.scala
rename to public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/Md5sum.scala
index 19f41bf3e59e8ec48eb7d87638e2c658819a83d3..90e577e01804ac1884d71de9613e3416d837fc92 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/Md5sum.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/Md5sum.scala
@@ -13,7 +13,7 @@
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
-package nl.lumc.sasc.biopet.extensions
+package nl.lumc.sasc.biopet.core.extensions
import java.io.File
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
index c59438133af902b84edf83b87a5e02e03f0dc58a..52c77fe8a63a090f2c4bb776da39647f9a35379e 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.core.summary
import java.io.File
import nl.lumc.sasc.biopet.core._
-import nl.lumc.sasc.biopet.extensions.Md5sum
+import nl.lumc.sasc.biopet.core.extensions.Md5sum
import scala.collection.mutable
diff --git a/public/biopet-extentsions/pom.xml b/public/biopet-extentsions/pom.xml
new file mode 100644
index 0000000000000000000000000000000000000000..cb5afbe9b02186ef0cf213d1ebb46f29a4148de4
--- /dev/null
+++ b/public/biopet-extentsions/pom.xml
@@ -0,0 +1,34 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <parent>
+ <artifactId>Biopet</artifactId>
+ <groupId>nl.lumc.sasc</groupId>
+ <version>0.5.0-SNAPSHOT</version>
+ </parent>
+ <modelVersion>4.0.0</modelVersion>
+
+ <artifactId>BiopetExtensions</artifactId>
+
+ <dependencies>
+ <dependency>
+ <groupId>nl.lumc.sasc</groupId>
+ <artifactId>BiopetCore</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.testng</groupId>
+ <artifactId>testng</artifactId>
+ <version>6.8</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.scalatest</groupId>
+ <artifactId>scalatest_2.10</artifactId>
+ <version>2.2.1</version>
+ <scope>test</scope>
+ </dependency>
+ </dependencies>
+
+</project>
\ No newline at end of file
diff --git a/public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/extensions/breakdancer/breakdancer2vcf.py b/public/biopet-extentsions/src/main/resources/nl/lumc/sasc/biopet/extensions/breakdancer/breakdancer2vcf.py
similarity index 100%
rename from public/biopet-core/src/main/resources/nl/lumc/sasc/biopet/extensions/breakdancer/breakdancer2vcf.py
rename to public/biopet-extentsions/src/main/resources/nl/lumc/sasc/biopet/extensions/breakdancer/breakdancer2vcf.py
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala
similarity index 100%
rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bgzip.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
similarity index 100%
rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala
similarity index 100%
rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala
similarity index 100%
rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala
similarity index 100%
rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
similarity index 100%
rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
similarity index 100%
rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala
similarity index 100%
rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala
similarity index 100%
rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala
similarity index 100%
rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/HtseqCount.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/HtseqCount.scala
similarity index 100%
rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/HtseqCount.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/HtseqCount.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala
similarity index 100%
rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala
similarity index 100%
rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
similarity index 100%
rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
similarity index 100%
rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/Sha1sum.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sha1sum.scala
similarity index 100%
rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/Sha1sum.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sha1sum.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
similarity index 100%
rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
similarity index 100%
rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
similarity index 100%
rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala
similarity index 100%
rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala
similarity index 100%
rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
similarity index 100%
rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala
similarity index 100%
rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala
similarity index 100%
rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/Bcftools.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/Bcftools.scala
similarity index 100%
rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/Bcftools.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/Bcftools.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala
similarity index 100%
rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/Bedtools.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/Bedtools.scala
similarity index 100%
rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/Bedtools.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/Bedtools.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
similarity index 100%
rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsGroupby.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsGroupby.scala
similarity index 100%
rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsGroupby.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsGroupby.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala
similarity index 100%
rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/Breakdancer.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/Breakdancer.scala
similarity index 100%
rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/Breakdancer.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/Breakdancer.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerCaller.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerCaller.scala
similarity index 100%
rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerCaller.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerCaller.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerConfig.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerConfig.scala
similarity index 100%
rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerConfig.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerConfig.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala
similarity index 100%
rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/Bwa.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/Bwa.scala
similarity index 100%
rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/Bwa.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/Bwa.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
similarity index 100%
rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
similarity index 100%
rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
similarity index 100%
rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala
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rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala
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rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala
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diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferAnalyze.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferAnalyze.scala
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rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferAnalyze.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferCall.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferCall.scala
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diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala
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rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferRPKM.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferRPKM.scala
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rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferRPKM.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/Delly.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/Delly.scala
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diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/DellyCaller.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/DellyCaller.scala
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diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala
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diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/Gatk.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/Gatk.scala
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rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/Gatk.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVTools.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVTools.scala
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diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
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rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala
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diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/KrakenReport.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/KrakenReport.scala
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rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/KrakenReport.scala
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diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2.scala
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rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2.scala
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diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala
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rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/AddOrReplaceReadGroups.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/AddOrReplaceReadGroups.scala
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rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/AddOrReplaceReadGroups.scala
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diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BedToIntervalList.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BedToIntervalList.scala
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diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala
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diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
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rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
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rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
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rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectMultipleMetrics.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectMultipleMetrics.scala
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rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectMultipleMetrics.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectMultipleMetrics.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala
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rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala
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diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectTargetedPcrMetrics.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectTargetedPcrMetrics.scala
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diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectWgsMetrics.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectWgsMetrics.scala
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rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectWgsMetrics.scala
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diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/GatherBamFiles.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/GatherBamFiles.scala
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rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/GatherBamFiles.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/GatherBamFiles.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
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diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala
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rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala
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diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
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diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/ReorderSam.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/ReorderSam.scala
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diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala
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diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortSam.scala
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diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala
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diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaFlagstat.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaFlagstat.scala
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diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaIndex.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaIndex.scala
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diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMarkdup.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMarkdup.scala
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diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMerge.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMerge.scala
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diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaView.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaView.scala
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diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/Samtools.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/Samtools.scala
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diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala
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diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala
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diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsView.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsView.scala
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rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsView.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsView.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/Seqtk.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/Seqtk.scala
similarity index 100%
rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/Seqtk.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/Seqtk.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala
similarity index 100%
rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Mpileup2cns.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Mpileup2cns.scala
similarity index 100%
rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Mpileup2cns.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Mpileup2cns.scala
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Varscan.scala b/public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Varscan.scala
similarity index 100%
rename from public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Varscan.scala
rename to public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Varscan.scala
diff --git a/public/biopet-extentsions/src/test/resources/log4j.properties b/public/biopet-extentsions/src/test/resources/log4j.properties
new file mode 100644
index 0000000000000000000000000000000000000000..501af67582a546db584c8538b28cb6f9e07f1692
--- /dev/null
+++ b/public/biopet-extentsions/src/test/resources/log4j.properties
@@ -0,0 +1,25 @@
+#
+# Biopet is built on top of GATK Queue for building bioinformatic
+# pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+# SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+# should also be able to execute Biopet tools and pipelines.
+#
+# Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+#
+# Contact us at: sasc@lumc.nl
+#
+# A dual licensing mode is applied. The source code within this project that are
+# not part of GATK Queue is freely available for non-commercial use under an AGPL
+# license; For commercial users or users who do not want to follow the AGPL
+# license, please contact us to obtain a separate license.
+#
+
+# Set root logger level to DEBUG and its only appender to A1.
+log4j.rootLogger=ERROR, A1
+
+# A1 is set to be a ConsoleAppender.
+log4j.appender.A1=org.apache.log4j.ConsoleAppender
+
+# A1 uses PatternLayout.
+log4j.appender.A1.layout=org.apache.log4j.PatternLayout
+log4j.appender.A1.layout.ConversionPattern=%-5p [%d] [%C{1}] - %m%n
\ No newline at end of file
diff --git a/public/biopet-core/src/test/resources/picard.alignmentMetrics b/public/biopet-extentsions/src/test/resources/nl/lumc/sasc/biopet/extensions/picard/picard.alignmentMetrics
similarity index 100%
rename from public/biopet-core/src/test/resources/picard.alignmentMetrics
rename to public/biopet-extentsions/src/test/resources/nl/lumc/sasc/biopet/extensions/picard/picard.alignmentMetrics
diff --git a/public/biopet-core/src/test/resources/picard.dedup.metrics b/public/biopet-extentsions/src/test/resources/nl/lumc/sasc/biopet/extensions/picard/picard.dedup.metrics
similarity index 100%
rename from public/biopet-core/src/test/resources/picard.dedup.metrics
rename to public/biopet-extentsions/src/test/resources/nl/lumc/sasc/biopet/extensions/picard/picard.dedup.metrics
diff --git a/public/biopet-core/src/test/resources/picard.insertsizemetrics b/public/biopet-extentsions/src/test/resources/nl/lumc/sasc/biopet/extensions/picard/picard.insertsizemetrics
similarity index 100%
rename from public/biopet-core/src/test/resources/picard.insertsizemetrics
rename to public/biopet-extentsions/src/test/resources/nl/lumc/sasc/biopet/extensions/picard/picard.insertsizemetrics
diff --git a/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/extensions/GsnapTest.scala b/public/biopet-extentsions/src/test/scala/nl/lumc/sasc/biopet/extensions/GsnapTest.scala
similarity index 100%
rename from public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/extensions/GsnapTest.scala
rename to public/biopet-extentsions/src/test/scala/nl/lumc/sasc/biopet/extensions/GsnapTest.scala
diff --git a/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/extensions/HtseqCountTest.scala b/public/biopet-extentsions/src/test/scala/nl/lumc/sasc/biopet/extensions/HtseqCountTest.scala
similarity index 100%
rename from public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/extensions/HtseqCountTest.scala
rename to public/biopet-extentsions/src/test/scala/nl/lumc/sasc/biopet/extensions/HtseqCountTest.scala
diff --git a/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/extensions/LnTest.scala b/public/biopet-extentsions/src/test/scala/nl/lumc/sasc/biopet/extensions/LnTest.scala
similarity index 100%
rename from public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/extensions/LnTest.scala
rename to public/biopet-extentsions/src/test/scala/nl/lumc/sasc/biopet/extensions/LnTest.scala
diff --git a/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetricsTest.scala b/public/biopet-extentsions/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetricsTest.scala
similarity index 92%
rename from public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetricsTest.scala
rename to public/biopet-extentsions/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetricsTest.scala
index 49edf90b2eaf52f3c48757c060a705a9a72d2f77..48a6bade41d2fdd65faacceb40c6dc750cac841f 100644
--- a/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetricsTest.scala
+++ b/public/biopet-extentsions/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetricsTest.scala
@@ -31,7 +31,7 @@ class CollectAlignmentSummaryMetricsTest extends TestNGSuite with Matchers {
@Test
def summaryData(): Unit = {
- val file = new File(Paths.get(getClass.getResource("/picard.alignmentMetrics").toURI).toString)
+ val file = new File(Paths.get(getClass.getResource("picard.alignmentMetrics").toURI).toString)
val job = new CollectAlignmentSummaryMetrics(null)
job.output = file
diff --git a/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetricsTest.scala b/public/biopet-extentsions/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetricsTest.scala
similarity index 92%
rename from public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetricsTest.scala
rename to public/biopet-extentsions/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetricsTest.scala
index 52a0f2d3f39ad72151b9ff4d445aa609e82bbfc2..88f2b330f7e70d2da8f48c222408500d2cb83ea0 100644
--- a/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetricsTest.scala
+++ b/public/biopet-extentsions/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetricsTest.scala
@@ -31,7 +31,7 @@ class CollectInsertSizeMetricsTest extends TestNGSuite with Matchers {
@Test
def summaryData(): Unit = {
- val file = new File(Paths.get(getClass.getResource("/picard.insertsizemetrics").toURI).toString)
+ val file = new File(Paths.get(getClass.getResource("picard.insertsizemetrics").toURI).toString)
val job = new CollectInsertSizeMetrics(null)
job.output = file
diff --git a/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicatesTest.scala b/public/biopet-extentsions/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicatesTest.scala
similarity index 92%
rename from public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicatesTest.scala
rename to public/biopet-extentsions/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicatesTest.scala
index 9b6d9b575ea5d0a2a5a69cb77f2fa575926a2294..23cfcddc5f3ff58a15e867a853e760684794d4c9 100644
--- a/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicatesTest.scala
+++ b/public/biopet-extentsions/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicatesTest.scala
@@ -31,7 +31,7 @@ class MarkDuplicatesTest extends TestNGSuite with Matchers {
@Test
def summaryData(): Unit = {
- val file = new File(Paths.get(getClass.getResource("/picard.dedup.metrics").toURI).toString)
+ val file = new File(Paths.get(getClass.getResource("picard.dedup.metrics").toURI).toString)
val job = new MarkDuplicates(null)
job.outputMetrics = file
diff --git a/public/biopet-tools-extensions/pom.xml b/public/biopet-tools-extensions/pom.xml
index 2ba2b83be5f112bdab087acb51ee2ebd18496dd9..e8ef9d9a7b4f21a2dada57c3cb1cfcfe0299dd12 100644
--- a/public/biopet-tools-extensions/pom.xml
+++ b/public/biopet-tools-extensions/pom.xml
@@ -15,12 +15,17 @@
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetCore</artifactId>
- <version>0.5.0-SNAPSHOT</version>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>nl.lumc.sasc</groupId>
+ <artifactId>BiopetExtensions</artifactId>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetTools</artifactId>
- <version>0.5.0-SNAPSHOT</version>
+ <version>${project.version}</version>
</dependency>
</dependencies>
diff --git a/public/kopisu/pom.xml b/public/kopisu/pom.xml
index 66cab779dc5882949dabd9adf7e05068ddfaa343..21f4f0c60dab41cf8d7d7800e8e8ac7654ed6d81 100644
--- a/public/kopisu/pom.xml
+++ b/public/kopisu/pom.xml
@@ -38,5 +38,10 @@
<artifactId>BiopetCore</artifactId>
<version>${project.version}</version>
</dependency>
+ <dependency>
+ <groupId>nl.lumc.sasc</groupId>
+ <artifactId>BiopetExtensions</artifactId>
+ <version>${project.version}</version>
+ </dependency>
</dependencies>
</project>
diff --git a/public/pom.xml b/public/pom.xml
index 0381fd1a825589064d8a46a5626c127dc7b53c74..ca015ae7f87bb3466bc54e50f85ec1d371f18a44 100644
--- a/public/pom.xml
+++ b/public/pom.xml
@@ -44,6 +44,7 @@
<module>biopet-utils</module>
<module>biopet-tools</module>
<module>biopet-tools-extensions</module>
+ <module>biopet-extentsions</module>
</modules>
<properties>