diff --git a/external-example/.gitignore b/external-example/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..77146859b6e12b32e90cc6f6d388ebc878d548d6
--- /dev/null
+++ b/external-example/.gitignore
@@ -0,0 +1,14 @@
+# Project-related
+dependency-reduced-pom.xml
+git.properties
+
+# gedit
+*~
+# Vim
+*.swp
+# IntelliJ
+.idea/*
+*.iml
+target/
+public/target/
+protected/target/
diff --git a/external-example/README.md b/external-example/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..956c6ccf2746212b45f3650ef917147bdd9ed800
--- /dev/null
+++ b/external-example/README.md
@@ -0,0 +1 @@
+Test implementation of Magpie 2.0
\ No newline at end of file
diff --git a/external-example/pom.xml b/external-example/pom.xml
new file mode 100644
index 0000000000000000000000000000000000000000..da0d2258fc90fe3cc9a49b76504be5388c683fa1
--- /dev/null
+++ b/external-example/pom.xml
@@ -0,0 +1,294 @@
+<?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>
+
+ <!--TODO: replace groupId -->
+ <groupId>org.example.group</groupId>
+
+ <!--TODO: replace artifactId -->
+ <artifactId>ExternalExample</artifactId>
+
+ <!--TODO: replace version, for a new pipeline it's advised to start with '0.1.0-SNAPSHOT' -->
+ <version>0.1.0-SNAPSHOT</version>
+
+ <properties>
+ <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+ <scoverage.plugin.version>1.0.4</scoverage.plugin.version>
+ <sting.shade.phase>package</sting.shade.phase>
+
+ <!--
+ TODO: replace app.main.class, this is the class that get executed when running the jar file
+ This can be any executable that have a main method. In Biopet any pipeline can be used as direct executable.
+ Value for direct pipeline: 'org.example.group.pipelines.SimplePipeline'
+ In the given example is an extension of the biopet executable. In this example there are multiple pipelines in 1 executable.
+
+ It's also possible to make your own main function and call the main function with it's argument of the pipeline from there.
+ -->
+ <app.main.class>org.example.group.ExecutableExample</app.main.class>
+ </properties>
+
+ <dependencies>
+ <!--
+ In here maven dependencies can be placed, when importing a biopet pipeline 'Biopet-Framework' is not required.
+ When only using the framework without pipeline you need to import BiopetFramework.
+ It's advised to not use different versions of the pipeline and the framework.
+ -->
+ <dependency>
+ <groupId>nl.lumc.sasc</groupId>
+ <artifactId>BiopetCore</artifactId>
+
+ <!--TODO: replace version of pipeline to a fixed version -->
+ <version>0.5.0-SNAPSHOT</version>
+ </dependency>
+ <dependency>
+ <groupId>nl.lumc.sasc</groupId>
+ <artifactId>BiopetExtensions</artifactId>
+ <version>0.5.0-SNAPSHOT</version>
+ </dependency>
+ <dependency>
+ <groupId>nl.lumc.sasc</groupId>
+ <artifactId>Shiva</artifactId>
+
+ <!--TODO: replace version of pipeline to a fixed version -->
+ <version>0.5.0-SNAPSHOT</version>
+ </dependency>
+ </dependencies>
+
+ <build>
+ <sourceDirectory>${basedir}/src/main/scala</sourceDirectory>
+ <testSourceDirectory>${basedir}/src/test/scala</testSourceDirectory>
+ <testResources>
+ <testResource>
+ <directory>${basedir}/src/test/resources</directory>
+ <includes>
+ <include>**/*</include>
+ </includes>
+ </testResource>
+ </testResources>
+ <resources>
+ <resource>
+ <directory>${basedir}/src/main/resources</directory>
+ <includes>
+ <include>**/*</include>
+ </includes>
+ </resource>
+ </resources>
+ <plugins>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-shade-plugin</artifactId>
+ <version>2.4.1</version>
+ <configuration>
+ <!--suppress MavenModelInspection -->
+ <finalName>${project.artifactId}-${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>
+ <!--suppress MavenModelInspection -->
+ <X-Compile-Source-JDK>${maven.compile.source}</X-Compile-Source-JDK>
+ <!--suppress MavenModelInspection -->
+ <X-Compile-Target-JDK>${maven.compile.target}</X-Compile-Target-JDK>
+ </manifestEntries>
+ </transformer>
+ </transformers>
+ <filters>
+ </filters>
+ </configuration>
+ <executions>
+ <execution>
+ <phase>package</phase>
+ <goals>
+ <goal>shade</goal>
+ </goals>
+ </execution>
+ </executions>
+ </plugin>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-surefire-plugin</artifactId>
+ <version>2.18.1</version>
+ <configuration>
+ <forkCount>1C</forkCount>
+ <workingDirectory>${project.build.directory}</workingDirectory>
+ </configuration>
+ </plugin>
+ <plugin>
+ <artifactId>maven-dependency-plugin</artifactId>
+ <version>2.10</version>
+ <executions>
+ <execution>
+ <id>copy-installed</id>
+ <phase>prepare-package</phase>
+ <goals>
+ <goal>list</goal>
+ </goals>
+ <configuration>
+ <outputFile>${project.build.outputDirectory}/dependency_list.txt</outputFile>
+ </configuration>
+ </execution>
+ </executions>
+ </plugin>
+ <plugin>
+ <groupId>net.alchim31.maven</groupId>
+ <artifactId>scala-maven-plugin</artifactId>
+ <version>3.2.0</version>
+ <executions>
+ <execution>
+ <id>scala-compile</id>
+ <goals>
+ <goal>compile</goal>
+ <goal>testCompile</goal>
+ </goals>
+ <configuration>
+ <args>
+ <arg>-dependencyfile</arg>
+ <arg>${project.build.directory}/.scala_dependencies</arg>
+ <arg>-deprecation</arg>
+ <arg>-feature</arg>
+ </args>
+ </configuration>
+ </execution>
+ </executions>
+ <!-- ... (see other usage or goals for details) ... -->
+ </plugin>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-jar-plugin</artifactId>
+ <version>2.5</version>
+ <executions>
+ <execution>
+ <goals>
+ <goal>test-jar</goal>
+ </goals>
+ </execution>
+ </executions>
+ <configuration>
+ <archive>
+ <manifest>
+ <addDefaultImplementationEntries>true</addDefaultImplementationEntries>
+ <addDefaultSpecificationEntries>true</addDefaultSpecificationEntries>
+ </manifest>
+ </archive>
+ </configuration>
+ </plugin>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-compiler-plugin</artifactId>
+ <version>2.3.2</version>
+ <configuration>
+ <showDeprecation>true</showDeprecation>
+ </configuration>
+ </plugin>
+ <plugin>
+ <groupId>org.scalariform</groupId>
+ <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>
+ </executions>
+ </plugin>
+ <plugin>
+ <groupId>pl.project13.maven</groupId>
+ <artifactId>git-commit-id-plugin</artifactId>
+ <version>2.1.10</version>
+ <executions>
+ <execution>
+ <goals>
+ <goal>revision</goal>
+ </goals>
+ </execution>
+ </executions>
+ <configuration>
+ <prefix>git</prefix>
+ <dateFormat>dd.MM.yyyy '@' HH:mm:ss z</dateFormat>
+ <verbose>false</verbose>
+ <!-- TODO: This directory need to be changed depening where your .git folder is relative from this pom.xml -->
+ <dotGitDirectory>${basedir}/../.git</dotGitDirectory>
+ <useNativeGit>true</useNativeGit>
+ <skipPoms>false</skipPoms>
+ <generateGitPropertiesFile>true</generateGitPropertiesFile>
+ <generateGitPropertiesFilename>src/main/resources/git.properties</generateGitPropertiesFilename>
+ <failOnNoGitDirectory>false</failOnNoGitDirectory>
+ <abbrevLength>8</abbrevLength>
+ <skip>false</skip>
+ <gitDescribe>
+ <skip>false</skip>
+ <always>false</always>
+ <abbrev>8</abbrev>
+ <dirty>-dirty</dirty>
+ <forceLongFormat>false</forceLongFormat>
+ </gitDescribe>
+ </configuration>
+ </plugin>
+ <plugin>
+ <groupId>com.mycila</groupId>
+ <artifactId>license-maven-plugin</artifactId>
+ <version>2.6</version>
+ <configuration>
+ <excludes>
+ <exclude>**/*git*</exclude>
+ <exclude>**/License*</exclude>
+ <exclude>**/*.bam</exclude>
+ <exclude>**/*.bai</exclude>
+ <exclude>**/*.gtf</exclude>
+ <exclude>**/*.fq</exclude>
+ <exclude>**/*.sam</exclude>
+ <exclude>**/*.bed</exclude>
+ <exclude>**/*.refFlat</exclude>
+ <exclude>**/*.R</exclude>
+ <exclude>**/*.rscript</exclude>
+ </excludes>
+ </configuration>
+ </plugin>
+ <plugin>
+ <groupId>org.scoverage</groupId>
+ <artifactId>scoverage-maven-plugin</artifactId>
+ <version>${scoverage.plugin.version}</version>
+ <configuration>
+ <scalaVersion>2.10.2</scalaVersion>
+ <!-- other parameters -->
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+ <reporting>
+ <plugins>
+ <plugin>
+ <groupId>org.scoverage</groupId>
+ <artifactId>scoverage-maven-plugin</artifactId>
+ <version>${scoverage.plugin.version}</version>
+ </plugin>
+ </plugins>
+ </reporting>
+</project>
\ No newline at end of file
diff --git a/external-example/src/main/scala/org/example/group/ExecutableExample.scala b/external-example/src/main/scala/org/example/group/ExecutableExample.scala
new file mode 100644
index 0000000000000000000000000000000000000000..fe0aaa13d57d5380f8eb14bf984145992ce297e8
--- /dev/null
+++ b/external-example/src/main/scala/org/example/group/ExecutableExample.scala
@@ -0,0 +1,19 @@
+package org.example.group
+
+import nl.lumc.sasc.biopet.utils.{ BiopetExecutable, MainCommand }
+
+/**
+ * Created by pjvanthof on 30/08/15.
+ */
+object ExecutableExample extends BiopetExecutable {
+
+ /** This list defines the pipeline that are usable from the executable */
+ def pipelines: List[MainCommand] = List(
+ org.example.group.pipelines.MultisamplePipeline,
+ org.example.group.pipelines.BiopetPipeline,
+ org.example.group.pipelines.SimplePipeline
+ )
+
+ /** This list defines the (biopet)tools that are usable from the executable */
+ def tools: List[MainCommand] = Nil
+}
diff --git a/external-example/src/main/scala/org/example/group/pipelines/BiopetPipeline.scala b/external-example/src/main/scala/org/example/group/pipelines/BiopetPipeline.scala
new file mode 100644
index 0000000000000000000000000000000000000000..6099047a6e5153c15df565d3e70179006ef4ceac
--- /dev/null
+++ b/external-example/src/main/scala/org/example/group/pipelines/BiopetPipeline.scala
@@ -0,0 +1,47 @@
+package org.example.group.pipelines
+
+import nl.lumc.sasc.biopet.core.PipelineCommand
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import nl.lumc.sasc.biopet.core.summary.SummaryQScript
+import nl.lumc.sasc.biopet.pipelines.shiva.Shiva
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.queue.QScript
+
+/**
+ * Created by pjvan_thof on 8/28/15.
+ */
+//TODO: Replace class Name
+class BiopetPipeline(val root: Configurable) extends QScript with SummaryQScript {
+ def this() = this(null)
+
+ /** Only required when using [[SummaryQScript]] */
+ def summaryFile = new File(outputDir, "magpie.summary.json")
+
+ /** Only required when using [[SummaryQScript]] */
+ def summaryFiles: Map[String, File] = Map()
+
+ /** Only required when using [[SummaryQScript]] */
+ def summarySettings = Map()
+
+ // This method can be used to initialize some classes where needed
+ def init(): Unit = {
+ }
+
+ // This method is the actual pipeline
+ def biopetScript: Unit = {
+
+ // Executing a biopet pipeline inside
+ val shiva = new Shiva(this)
+ shiva.init()
+ shiva.biopetScript()
+ addAll(shiva.functions)
+
+ /* Only required when using [[SummaryQScript]] */
+ addSummaryQScript(shiva)
+
+ // From here you can use the output files of shiva as input file of other jobs
+ }
+}
+
+//TODO: Replace object Name, must be the same as the class of the pipeline
+object BiopetPipeline extends PipelineCommand
diff --git a/external-example/src/main/scala/org/example/group/pipelines/MultisamplePipeline.scala b/external-example/src/main/scala/org/example/group/pipelines/MultisamplePipeline.scala
new file mode 100644
index 0000000000000000000000000000000000000000..ee66d89663c22868958720615a83c5d72f85e8f7
--- /dev/null
+++ b/external-example/src/main/scala/org/example/group/pipelines/MultisamplePipeline.scala
@@ -0,0 +1,64 @@
+package org.example.group.pipelines
+
+import nl.lumc.sasc.biopet.core.{ PipelineCommand, MultiSampleQScript }
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.queue.QScript
+
+/**
+ * Created by pjvanthof on 30/08/15.
+ */
+class MultisamplePipeline(val root: Configurable) extends QScript with MultiSampleQScript {
+ qscript =>
+ def this() = this(null)
+
+ def init: Unit = {
+ }
+
+ def biopetScript: Unit = {
+ addSamplesJobs() // This executes jobs for all samples
+ }
+
+ def addMultiSampleJobs: Unit = {
+ // this code will be executed after all code of all samples is executed
+ }
+
+ def summaryFile: File = new File(outputDir, "MultisamplePipeline.summary.json")
+
+ //TODO: Add summary
+ def summaryFiles: Map[String, File] = Map()
+
+ //TODO: Add summary
+ def summarySettings: Map[String, Any] = Map()
+
+ def makeSample(id: String) = new Sample(id)
+ class Sample(sampleId: String) extends AbstractSample(sampleId) {
+
+ def makeLibrary(id: String) = new Library(id)
+ class Library(libId: String) extends AbstractLibrary(libId) {
+ //TODO: Add summary
+ def summaryFiles: Map[String, File] = Map()
+
+ //TODO: Add summary
+ def summaryStats: Map[String, Any] = Map()
+
+ def addJobs: Unit = {
+ //TODO: add library specific jobs
+ }
+ }
+
+ //TODO: Add summary
+ def summaryFiles: Map[String, File] = Map()
+
+ //TODO: Add summary
+ def summaryStats: Map[String, Any] = Map()
+
+ def addJobs: Unit = {
+ addPerLibJobs() // This add jobs for each library
+ //TODO: add sample specific jobs
+ }
+ }
+
+}
+
+object MultisamplePipeline extends PipelineCommand
\ No newline at end of file
diff --git a/external-example/src/main/scala/org/example/group/pipelines/SimplePipeline.scala b/external-example/src/main/scala/org/example/group/pipelines/SimplePipeline.scala
new file mode 100644
index 0000000000000000000000000000000000000000..f24b0f6152a03979d74c2f7337760cdc06c9e3be
--- /dev/null
+++ b/external-example/src/main/scala/org/example/group/pipelines/SimplePipeline.scala
@@ -0,0 +1,38 @@
+package org.example.group.pipelines
+
+import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import nl.lumc.sasc.biopet.extensions.{ Gzip, Cat }
+import org.broadinstitute.gatk.queue.QScript
+
+/**
+ * Created by pjvanthof on 30/08/15.
+ */
+//TODO: Replace class name, must be the same as the class of the pipeline
+class SimplePipeline(val root: Configurable) extends QScript with BiopetQScript {
+ // A constructor without arguments is needed if this pipeline is a root pipeline
+ def this() = this(null)
+
+ @Input(required = true)
+ var inputFile: File = null
+
+ /** This method can be used to initialize some classes where needed */
+ def init(): Unit = {
+ }
+
+ /** This method is the actual pipeline */
+ def biopetScript: Unit = {
+ val cat = new Cat(this)
+ cat.input :+= inputFile
+ cat.output = new File(outputDir, "file.out")
+ add(cat)
+
+ val gzip = new Gzip(this)
+ gzip.input :+= cat.output
+ gzip.output = new File(outputDir, "file.out.gz")
+ add(gzip)
+ }
+}
+
+//TODO: Replace object name, must be the same as the class of the pipeline
+object SimplePipeline extends PipelineCommand
diff --git a/pom.xml b/pom.xml
index 9390bf9a13c0362d75f158b08d2e99d3ad8d181f..143a9095a763bbdcc323dc6e4299e534e5f0bc33 100644
--- a/pom.xml
+++ b/pom.xml
@@ -16,5 +16,6 @@
<modules>
<module>public</module>
<module>protected</module>
+ <module>external-example</module>
</modules>
</project>