Remove unused source

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/Clever.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.extensions.clever
-
-import java.io.File
-
-import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
-import org.broadinstitute.gatk.queue.QScript
-
-class Clever(val root: Configurable) extends QScript with BiopetQScript {
-  def this() = this(null)
-
-  @Input(doc = "Input file (bam)")
-  var input: File = _
-
-  @Input(doc = "Reference")
-  var reference: File = _
-
-  @Argument(doc = "Work directory")
-  var workdir: String = _
-
-  @Argument(doc = "Current working directory")
-  var cwd: String = _
-
-  override def init() {
-  }
-
-  def biopetScript() {
-    // write the pipeline here
-    logger.info("Starting Clever Pipeline")
-
-    /// start clever and then copy the vcf into the root directory "<sample>.clever/"
-    val clever = CleverCaller(this, input, reference, cwd, workdir)
-    outputFiles += ("clever_vcf" -> clever.outputvcf)
-    add(clever)
-  }
-}
-
-object Clever extends PipelineCommand {
-  override val pipeline = "/nl/lumc/sasc/biopet/extensions/svcallers/Clever/Clever.class"
-
-  def apply(root: Configurable, input: File, runDir: String): Clever = {
-    val cleverpipeline = new Clever(root)
-    cleverpipeline.input = input
-    cleverpipeline.workdir = runDir
-    cleverpipeline.init()
-    cleverpipeline.biopetScript()
-    cleverpipeline
-  }
-
-}
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