Remove template from framework

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/MultisamplePipelineTemplate.scala

-/**
- * 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.
- */
-package nl.lumc.sasc.biopet.pipelines
-
-import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.core.{ MultiSampleQScript, PipelineCommand }
-import org.broadinstitute.gatk.queue.QScript
-
-/** Template for a multisample pipeline */
-class MultisamplePipelineTemplate(val root: Configurable) extends QScript with MultiSampleQScript {
-  def this() = this(null)
-
-  /** Location of summary file */
-  def summaryFile: File = new File(outputDir, "MultisamplePipelineTemplate.summary.json")
-
-  /** File to add to the summary */
-  def summaryFiles: Map[String, File] = Map()
-
-  /** Pipeline settings to add to the summary */
-  def summarySettings: Map[String, Any] = Map()
-
-  /** Function to make a sample */
-  def makeSample(id: String) = new Sample(id)
-
-  /** This class will contain jobs and libraries for a sample */
-  class Sample(sampleId: String) extends AbstractSample(sampleId) {
-    /** Sample specific files for summary */
-    def summaryFiles: Map[String, File] = Map()
-
-    /** Sample specific stats for summary */
-    def summaryStats: Map[String, Any] = Map()
-
-    /** Function to make a library */
-    def makeLibrary(id: String) = new Library(id)
-
-    /** This class will contain all jobs for a library */
-    class Library(libId: String) extends AbstractLibrary(libId) {
-      /** Library specific files for summary */
-      def summaryFiles: Map[String, File] = Map()
-
-      /** Library specific stats for summary */
-      def summaryStats: Map[String, Any] = Map()
-
-      /** Method to add library jobs */
-      protected def addJobs(): Unit = {
-      }
-    }
-
-    /** Method to add sample jobs */
-    protected def addJobs(): Unit = {
-    }
-  }
-
-  /** Method where multisample jobs are added */
-  def addMultiSampleJobs(): Unit = {
-  }
-
-  /** This is executed before the script starts */
-  def init(): Unit = {
-  }
-
-  /** Method where jobs must be added */
-  def biopetScript() {
-  }
-}
-
-/** Object to let to generate a main method */
-object MultisamplePipelineTemplate extends PipelineCommand
\ No newline at end of file

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/PipelineTemplate.scala

-/**
- * 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.
- */
-package nl.lumc.sasc.biopet.pipelines
-
-import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
-import org.broadinstitute.gatk.queue.QScript
-
-/** Template for a pipeline */
-class PipelineTemplate(val root: Configurable) extends QScript with BiopetQScript {
-  def this() = this(null)
-
-  /** This is executed before the script starts */
-  def init() {
-  }
-
-  /** Method where jobs must be added */
-  def biopetScript() {
-  }
-}
-
-/** Object to let to generate a main method */
-object PipelineTemplate extends PipelineCommand