diff --git a/biopet-framework/pom.xml b/biopet-framework/pom.xml
index 69c3c3ff4f7ac147c87ade7ec0c9a0c790090a33..ac2879e75dea217e25cc42adf3e9b0aae80cd277 100644
--- a/biopet-framework/pom.xml
+++ b/biopet-framework/pom.xml
@@ -1,36 +1,35 @@
<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">
- <modelVersion>4.0.0</modelVersion>
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
- <groupId>nl.lumc.sasc</groupId>
- <artifactId>BiopetFramework</artifactId>
- <version>0.2.0-DEV</version>
- <packaging>jar</packaging>
+ <groupId>nl.lumc.sasc</groupId>
+ <artifactId>BiopetFramework</artifactId>
+ <version>0.2.0-DEV</version>
+ <packaging>jar</packaging>
- <name>BiopetFramework</name>
- <url>http://maven.apache.org</url>
+ <name>BiopetFramework</name>
+ <url>http://maven.apache.org</url>
+
+ <properties>
+ <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+ <sting.unpack.phase>prepare-package</sting.unpack.phase>
+ <sting.shade.phase>package</sting.shade.phase>
+ <app.main.class>nl.lumc.sasc.biopet.core.BiopetExecutable</app.main.class>
+ </properties>
- <properties>
- <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
- <sting.unpack.phase>prepare-package</sting.unpack.phase>
- <sting.shade.phase>package</sting.shade.phase>
- <sting.binary-dist.name>SASC-Pipelines</sting.binary-dist.name>
- <app.main.class>nl.lumc.sasc.biopet.core.BiopetExecutable</app.main.class>
- </properties>
-
<repositories>
<repository>
<id>biojava-maven-repo</id>
<name>BioJava repository</name>
- <url>http://www.biojava.org/download/maven/</url>
+ <url>http://www.biojava.org/download/maven/</url>
</repository>
</repositories>
<dependencies>
<dependency>
- <groupId>org.testng</groupId>
- <artifactId>testng</artifactId>
- <version>6.8</version>
- <scope>test</scope>
+ <groupId>org.testng</groupId>
+ <artifactId>testng</artifactId>
+ <version>6.8</version>
+ <scope>test</scope>
</dependency>
<dependency>
<groupId>org.scalatest</groupId>
@@ -68,9 +67,9 @@
<version>18.0</version>
</dependency>
<dependency>
- <groupId>com.github.scopt</groupId>
- <artifactId>scopt_2.10</artifactId>
- <version>3.2.0</version>
+ <groupId>com.github.scopt</groupId>
+ <artifactId>scopt_2.10</artifactId>
+ <version>3.2.0</version>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
@@ -81,16 +80,16 @@
<build>
<resources>
<resource>
- <directory>src/main/scripts</directory>
- <includes>
- <include>**/*</include>
- </includes>
+ <directory>src/main/scripts</directory>
+ <includes>
+ <include>**/*</include>
+ </includes>
</resource>
<resource>
- <directory>src/main/resources</directory>
- <includes>
- <include>**/*</include>
- </includes>
+ <directory>src/main/resources</directory>
+ <includes>
+ <include>**/*</include>
+ </includes>
</resource>
</resources>
<plugins>
@@ -102,7 +101,7 @@
<execution>
<goals>
<goal>revision</goal>
- </goals>
+ </goals>
</execution>
</executions>
@@ -141,9 +140,10 @@
</goals>
<configuration>
<args>
-<!-- <arg>-make:transitive</arg>-->
<arg>-dependencyfile</arg>
<arg>${project.build.directory}/.scala_dependencies</arg>
+ <arg>-deprecation</arg>
+ <arg>-feature</arg>
</args>
</configuration>
</execution>
@@ -154,7 +154,7 @@
<artifactId>maven-jar-plugin</artifactId>
<version>2.5</version>
<configuration>
- <archive>
+ <archive>
<manifest>
<addDefaultImplementationEntries>true</addDefaultImplementationEntries>
<addDefaultSpecificationEntries>true</addDefaultSpecificationEntries>
@@ -163,50 +163,50 @@
</configuration>
</plugin>
<plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-shade-plugin</artifactId>
- <version>2.3</version>
- <configuration>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-shade-plugin</artifactId>
+ <version>2.3</version>
+ <configuration>
<finalName>Biopet-${project.version}-${git.commit.id.abbrev}</finalName>
<transformers>
- <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
- <manifestEntries>
- <Main-Class>${app.main.class}</Main-Class>
- <X-Compile-Source-JDK>${maven.compile.source}</X-Compile-Source-JDK>
- <X-Compile-Target-JDK>${maven.compile.target}</X-Compile-Target-JDK>
- </manifestEntries>
- </transformer>
+ <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
+ <manifestEntries>
+ <Main-Class>${app.main.class}</Main-Class>
+ <X-Compile-Source-JDK>${maven.compile.source}</X-Compile-Source-JDK>
+ <X-Compile-Target-JDK>${maven.compile.target}</X-Compile-Target-JDK>
+ </manifestEntries>
+ </transformer>
</transformers>
<filters>
<filter>
- <artifact>org.broadinstitute.gatk:gatk-queue-package-distribution</artifact>
- <includes>
- <include>*/**</include>
- <include>org/simpleframework/**</include>
- <include>org/jets3t/**</include>
- <include>com/sun/**</include>
- <include>org/ggf/**</include>
- <include>picard/**</include>
- <include>htsjdk/**</include>
- <include>javassist/**</include>
- <include>com/google/**</include>
- <include>org/reflections/</include>
- <include>org/jgrapht/**</include>
- <include>org/broadinstitute/**</include>
- <include>org/apache/**</include>
- <include>scala/tools/nsc/reporters/**</include>
- </includes>
+ <artifact>org.broadinstitute.gatk:gatk-queue-package-distribution</artifact>
+ <includes>
+ <include>*/**</include>
+ <include>org/simpleframework/**</include>
+ <include>org/jets3t/**</include>
+ <include>com/sun/**</include>
+ <include>org/ggf/**</include>
+ <include>picard/**</include>
+ <include>htsjdk/**</include>
+ <include>javassist/**</include>
+ <include>com/google/**</include>
+ <include>org/reflections/</include>
+ <include>org/jgrapht/**</include>
+ <include>org/broadinstitute/**</include>
+ <include>org/apache/**</include>
+ <include>scala/tools/nsc/reporters/**</include>
+ </includes>
</filter>
</filters>
- </configuration>
- <executions>
- <execution>
- <phase>package</phase>
- <goals>
- <goal>shade</goal>
- </goals>
- </execution>
- </executions>
+ </configuration>
+ <executions>
+ <execution>
+ <phase>package</phase>
+ <goals>
+ <goal>shade</goal>
+ </goals>
+ </execution>
+ </executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
@@ -221,33 +221,35 @@
<artifactId>scalariform-maven-plugin</artifactId>
<version>0.1.4</version>
<executions>
- <execution>
- <phase>process-sources</phase>
- <goals>
- <goal>format</goal>
- </goals>
- <configuration>
- <rewriteArrowSymbols>false</rewriteArrowSymbols>
- <alignParameters>true</alignParameters>
- <alignSingleLineCaseStatements_maxArrowIndent>40</alignSingleLineCaseStatements_maxArrowIndent>
- <alignSingleLineCaseStatements>true</alignSingleLineCaseStatements>
- <compactStringConcatenation>false</compactStringConcatenation>
- <compactControlReadability>false</compactControlReadability>
- <doubleIndentClassDeclaration>false</doubleIndentClassDeclaration>
- <formatXml>true</formatXml>
- <indentLocalDefs>false</indentLocalDefs>
- <indentPackageBlocks>true</indentPackageBlocks>
- <indentSpaces>2</indentSpaces>
- <placeScaladocAsterisksBeneathSecondAsterisk>false</placeScaladocAsterisksBeneathSecondAsterisk>
- <preserveDanglingCloseParenthesis>true</preserveDanglingCloseParenthesis>
- <preserveSpaceBeforeArguments>false</preserveSpaceBeforeArguments>
- <rewriteArrowSymbols>false</rewriteArrowSymbols>
- <spaceBeforeColon>false</spaceBeforeColon>
- <spaceInsideBrackets>false</spaceInsideBrackets>
- <spaceInsideParentheses>false</spaceInsideParentheses>
- <spacesWithinPatternBinders>true</spacesWithinPatternBinders>
- </configuration>
- </execution>
+ <execution>
+ <phase>process-sources</phase>
+ <goals>
+ <goal>format</goal>
+ </goals>
+ <configuration>
+ <rewriteArrowSymbols>false</rewriteArrowSymbols>
+ <alignParameters>true</alignParameters>
+ <alignSingleLineCaseStatements_maxArrowIndent>40
+ </alignSingleLineCaseStatements_maxArrowIndent>
+ <alignSingleLineCaseStatements>true</alignSingleLineCaseStatements>
+ <compactStringConcatenation>false</compactStringConcatenation>
+ <compactControlReadability>false</compactControlReadability>
+ <doubleIndentClassDeclaration>false</doubleIndentClassDeclaration>
+ <formatXml>true</formatXml>
+ <indentLocalDefs>false</indentLocalDefs>
+ <indentPackageBlocks>true</indentPackageBlocks>
+ <indentSpaces>2</indentSpaces>
+ <placeScaladocAsterisksBeneathSecondAsterisk>false
+ </placeScaladocAsterisksBeneathSecondAsterisk>
+ <preserveDanglingCloseParenthesis>true</preserveDanglingCloseParenthesis>
+ <preserveSpaceBeforeArguments>false</preserveSpaceBeforeArguments>
+ <rewriteArrowSymbols>false</rewriteArrowSymbols>
+ <spaceBeforeColon>false</spaceBeforeColon>
+ <spaceInsideBrackets>false</spaceInsideBrackets>
+ <spaceInsideParentheses>false</spaceInsideParentheses>
+ <spacesWithinPatternBinders>true</spacesWithinPatternBinders>
+ </configuration>
+ </execution>
</executions>
</plugin>
</plugins>
diff --git a/pom.xml b/pom.xml
index 7e98eb6956a1390dff1a32cce1bf1ee28d581f46..732ff3d241c9af014fdd61b74aea83b3b091a430 100644
--- a/pom.xml
+++ b/pom.xml
@@ -1,12 +1,13 @@
<?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">
- <modelVersion>4.0.0</modelVersion>
- <groupId>nl.lumc.sasc</groupId>
- <artifactId>Biopet</artifactId>
- <version>0.1.3</version>
- <packaging>pom</packaging>
- <name>Biopet</name>
- <modules>
- <module>biopet-framework</module>
- </modules>
+<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">
+ <modelVersion>4.0.0</modelVersion>
+ <groupId>nl.lumc.sasc</groupId>
+ <artifactId>Biopet</artifactId>
+ <version>0.2.0-DEV</version>
+ <packaging>pom</packaging>
+ <name>Biopet</name>
+ <modules>
+ <module>biopet-framework</module>
+ </modules>
</project>