Switch to only 1 maven artifact as example

external-examples/single-pipeline/pom.xml → external-example/pom.xml

@@ -4,21 +4,42 @@
          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.kg</groupId>
+    <!--TODO: replace groupId -->
+    <groupId>org.example.group</groupId>
+
+    <!--TODO: replace artifactId -->
     <artifactId>SinglePipeline</artifactId>
+
+    <!--TODO: replace version, for a new pipeline it's advised to start with '0.1.0-SNAPSHOT' -->
     <version>0.5.0-DEV</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>
-        <app.main.class>org.example.group.SinglePipeline</app.main.class>
+
+        <!--TODO: replace app.main.class, this is the class that get executed when running the jar file -->
+        <app.main.class>org.example.group.BiopetPipeline</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>BiopetFramework</artifactId>
+
+            <!--TODO: replace version of pipeline to a fixed version -->
+            <version>${project.version}</version>
+        </dependency>
         <dependency>
             <groupId>nl.lumc.sasc</groupId>
             <artifactId>Shiva</artifactId>
+
+            <!--TODO: replace version of pipeline to a fixed version -->
             <version>${project.version}</version>
         </dependency>
     </dependencies>

external-examples/single-pipeline/src/main/scala/org/example/group/SinglePipeline.scala → external-example/src/main/scala/org/example/group/BiopetPipeline.scala

@@ -9,26 +9,36 @@ import org.broadinstitute.gatk.queue.QScript
 /**
  * Created by pjvan_thof on 8/28/15.
  */
-class SinglePipeline(val root: Configurable) extends QScript with SummaryQScript {
+//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)
   }
 }
 
-object SinglePipeline extends PipelineCommand
+//TODO: Replace object Name, must be the same as the class of the pipeline
+object BiopetPipeline extends PipelineCommand

external-examples/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">
-    <parent>
-        <artifactId>BiopetRoot</artifactId>
-        <groupId>nl.lumc.sasc</groupId>
-        <version>0.5.0-DEV</version>
-    </parent>
-    <modelVersion>4.0.0</modelVersion>
-    <packaging>pom</packaging>
-
-    <artifactId>ExternalExamples</artifactId>
-
-    <modules>
-        <module>single-pipeline</module>
-    </modules>
-
-</project>
\ No newline at end of file

pom.xml

@@ -16,6 +16,6 @@
     <modules>
         <module>public</module>
         <module>protected</module>
-        <module>external-examples</module>
+        <module>external-example</module>
     </modules>
 </project>