pom.xml

<?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>
    <parent>
        <groupId>org.sonatype.oss</groupId>
        <artifactId>oss-parent</artifactId>
        <version>9</version>
    </parent>
    <groupId>nl.systemsgenetics</groupId>
    <artifactId>systemsgenetics</artifactId>
    <version>1.0.4-SNAPSHOT</version>
    <packaging>pom</packaging>
    <properties>
        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
        <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
        <maven.compiler.source>11</maven.compiler.source>
        <maven.compiler.target>11</maven.compiler.target>
    </properties>
<!--    Added the following dependencies to circumvent difficulties when using the cobertura-maven-plugin
        that is used for determining the covarage (this is used on the Jenkins server). -->
    <dependencies>
        <dependency>
            <groupId>net.sourceforge.cobertura</groupId>
            <artifactId>cobertura</artifactId>
            <version>2.1.1</version>
            <exclusions>
                <exclusion>
                    <groupId>ch.qos.logback</groupId>
                    <artifactId>logback-classic</artifactId>
                </exclusion>
                <exclusion>
                    <artifactId>tools</artifactId>
                    <groupId>com.sun</groupId>
                </exclusion>
            </exclusions>
        </dependency>
    </dependencies>
    <build>
        <pluginManagement>
            <plugins>
                <!-- use java 1.6 -->
                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-compiler-plugin</artifactId>
                    <version>3.8.1</version>
                </plugin>
                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-site-plugin</artifactId>
                    <version>3.8.2</version>
                </plugin>
                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-javadoc-plugin</artifactId>
                    <version>3.1.1</version>
                    <configuration>
                        <additionalparam>-Xdoclint:none</additionalparam>
                    </configuration>
                </plugin>
            </plugins>
        </pluginManagement>
    </build>
    <repositories>
        <repository>
            <id>TUDelft</id>
            <name>TUDelft</name>
            <url>https://simulation.tudelft.nl/maven/</url>
        </repository>
        <repository>
            <id>Maven Central</id>
            <name>Maven Central</name>
            <url>https://repo1.maven.org/maven2/</url>
        </repository>
    </repositories>
    <modules>
        <module>genetica-libraries</module>
        <module>imputation-tool</module>
        <module>eqtl-mapping-pipeline</module>
        <module>Genotype-IO</module>
        <module>GadoCommandline</module>
        <module>Genotype-Harmonizer</module>
        <module>eqtl-functional-enrichment</module>
        <module>GeneticRiskScoreCalculator</module>
        <module>BinaryMetaAnalyzer</module>
        <module>eQTLInteractionAnalyser</module>
        <module>javaPoCA</module>
        <module>cellTypeSpecificAlleleSpecificExpression</module>
        <module>MetaGenomicDataProcessing</module>
        <module>GeneNetworkBackend</module>
        <module>Decon2/Decon-eQTL</module>
        <module>FunctionEnrichmentOfTransQtls</module>
        <module>Downstreamer</module>
        <module>PatricksToolbox</module>
        <module>mbQTL</module>
        <module>Datg</module>
    </modules>
</project>