Move variantcallers to public

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Basty.scala

-/**
- * Due to the license issue with GATK, this part of Biopet can only be used inside the
- * LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
- * on how to use this protected part of biopet or contact us at sasc@lumc.nl
- */
-package nl.lumc.sasc.biopet.pipelines.gatk
-
-import nl.lumc.sasc.biopet.core.PipelineCommand
-import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.pipelines.basty.BastyTrait
-import org.broadinstitute.gatk.queue.QScript
-
-/**
- * Basty pipeline including GATK steps
- *
- * Created by pjvan_thof on 3/4/15.
- */
-class Basty(val root: Configurable) extends QScript with BastyTrait {
-  qscript =>
-  def this() = this(null)
-
-  override def variantcallers = List("unifiedgenotyper")
-
-  override lazy val shiva = new Shiva(qscript)
-}
-
-object Basty extends PipelineCommand
\ No newline at end of file

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala

@@ -7,7 +7,7 @@ package nl.lumc.sasc.biopet.pipelines.gatk
 
 import nl.lumc.sasc.biopet.core.PipelineCommand
 import nl.lumc.sasc.biopet.extensions.gatk.broad._
-import nl.lumc.sasc.biopet.pipelines.shiva.ShivaTrait
+import nl.lumc.sasc.biopet.pipelines.shiva.{ ShivaTrait, ShivaVariantcalling }
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.QScript
 

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcalling.scala

-/**
- * Due to the license issue with GATK, this part of Biopet can only be used inside the
- * LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
- * on how to use this protected part of biopet or contact us at sasc@lumc.nl
- */
-package nl.lumc.sasc.biopet.pipelines.gatk
-
-import nl.lumc.sasc.biopet.core.PipelineCommand
-import nl.lumc.sasc.biopet.pipelines.gatk.variantcallers._
-import nl.lumc.sasc.biopet.pipelines.shiva.ShivaVariantcallingTrait
-import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.queue.QScript
-
-/**
- * ShivaVariantcalling with GATK variantcallers
- *
- * Created by pjvan_thof on 2/26/15.
- */
-class ShivaVariantcalling(val root: Configurable) extends QScript with ShivaVariantcallingTrait {
-  qscript =>
-  def this() = this(null)
-
-  /** Will generate all available variantcallers */
-  override def callersList = {
-    new HaplotypeCallerGvcf(this) ::
-      new HaplotypeCallerAllele(this) ::
-      new UnifiedGenotyperAllele(this) ::
-      new UnifiedGenotyper(this) ::
-      new HaplotypeCaller(this) ::
-      super.callersList
-  }
-}
-
-/** object to add default main method to pipeline */
-object ShivaVariantcalling extends PipelineCommand
\ No newline at end of file

protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala

@@ -12,6 +12,7 @@ import nl.lumc.sasc.biopet.utils.config.Config
 import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
 import nl.lumc.sasc.biopet.extensions.gatk.broad.{ HaplotypeCaller, UnifiedGenotyper }
 import nl.lumc.sasc.biopet.extensions.tools.{ MpileupToVcf, VcfFilter, VcfStats }
+import nl.lumc.sasc.biopet.pipelines.shiva.ShivaVariantcalling
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import org.apache.commons.io.FileUtils
 import org.broadinstitute.gatk.queue.QSettings

protected/biopet-protected-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutableProtected.scala

@@ -9,9 +9,7 @@ import nl.lumc.sasc.biopet.utils.{ BiopetExecutable, MainCommand }
 
 object BiopetExecutableProtected extends BiopetExecutable {
   def pipelines: List[MainCommand] = BiopetExecutablePublic.publicPipelines ::: List(
-    nl.lumc.sasc.biopet.pipelines.gatk.Shiva,
-    nl.lumc.sasc.biopet.pipelines.gatk.ShivaVariantcalling,
-    nl.lumc.sasc.biopet.pipelines.gatk.Basty)
+    nl.lumc.sasc.biopet.pipelines.gatk.Shiva)
 
   def tools = BiopetExecutablePublic.tools
 }
\ No newline at end of file

public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala

@@ -13,19 +13,189 @@
  * license; For commercial users or users who do not want to follow the AGPL
  * license, please contact us to obtain a separate license.
  */
+/**
+ * Due to the license issue with GATK, this part of Biopet can only be used inside the
+ * LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
+ * on how to use this protected part of biopet or contact us at sasc@lumc.nl
+ */
 package nl.lumc.sasc.biopet.pipelines.basty
 
-import nl.lumc.sasc.biopet.core.PipelineCommand
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.{ MultiSampleQScript, PipelineCommand }
+import nl.lumc.sasc.biopet.extensions.{ Cat, Raxml, RunGubbins }
+import nl.lumc.sasc.biopet.pipelines.shiva.{ Shiva, ShivaTrait }
+import nl.lumc.sasc.biopet.extensions.tools.BastyGenerateFasta
+import nl.lumc.sasc.biopet.utils.ConfigUtils
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.QScript
 
-/**
- * Basty implementation without GATK parts
- *
- * Created by pjvan_thof on 3/4/15.
- */
-class Basty(val root: Configurable) extends QScript with BastyTrait {
+class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
+  qscript =>
+
   def this() = this(null)
+
+  case class FastaOutput(variants: File, consensus: File, consensusVariants: File)
+
+  def variantcallers = List("unifiedgenotyper")
+
+  override def defaults = Map(
+    "ploidy" -> 1,
+    "variantcallers" -> variantcallers
+  )
+
+  lazy val shiva: ShivaTrait = new Shiva(qscript)
+
+  def summaryFile: File = new File(outputDir, "Basty.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) {
+    //TODO: Add summary
+    def summaryFiles: Map[String, File] = Map()
+
+    //TODO: Add summary
+    def summaryStats: Map[String, Any] = Map()
+
+    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()
+
+      protected def addJobs(): Unit = {}
+    }
+
+    var output: FastaOutput = _
+    var outputSnps: FastaOutput = _
+
+    protected def addJobs(): Unit = {
+      addPerLibJobs()
+      output = addGenerateFasta(sampleId, sampleDir)
+      outputSnps = addGenerateFasta(sampleId, sampleDir, snpsOnly = true)
+    }
+  }
+
+  def init() {
+    shiva.outputDir = outputDir
+    shiva.init()
+  }
+
+  def biopetScript() {
+    shiva.biopetScript()
+    addAll(shiva.functions)
+    addSummaryQScript(shiva)
+
+    inputFiles :::= shiva.inputFiles
+
+    addSamplesJobs()
+  }
+
+  def addMultiSampleJobs(): Unit = {
+    val refVariants = addGenerateFasta(null, new File(outputDir, "fastas" + File.separator + "reference"), outputName = "reference")
+    val refVariantSnps = addGenerateFasta(null, new File(outputDir, "fastas" + File.separator + "reference"), outputName = "reference", snpsOnly = true)
+
+    val catVariants = Cat(this, refVariants.variants :: samples.map(_._2.output.variants).toList,
+      new File(outputDir, "fastas" + File.separator + "variant.fasta"))
+    add(catVariants)
+    val catVariantsSnps = Cat(this, refVariantSnps.variants :: samples.map(_._2.outputSnps.variants).toList,
+      new File(outputDir, "fastas" + File.separator + "variant.snps_only.fasta"))
+    add(catVariantsSnps)
+
+    val catConsensus = Cat(this, refVariants.consensus :: samples.map(_._2.output.consensus).toList,
+      new File(outputDir, "fastas" + File.separator + "consensus.fasta"))
+    add(catConsensus)
+    val catConsensusSnps = Cat(this, refVariantSnps.consensus :: samples.map(_._2.outputSnps.consensus).toList,
+      new File(outputDir, "fastas" + File.separator + "consensus.snps_only.fasta"))
+    add(catConsensusSnps)
+
+    val catConsensusVariants = Cat(this, refVariants.consensusVariants :: samples.map(_._2.output.consensusVariants).toList,
+      new File(outputDir, "fastas" + File.separator + "consensus.variant.fasta"))
+    add(catConsensusVariants)
+    val catConsensusVariantsSnps = Cat(this, refVariantSnps.consensusVariants :: samples.map(_._2.outputSnps.consensusVariants).toList,
+      new File(outputDir, "fastas" + File.separator + "consensus.variant.snps_only.fasta"))
+    add(catConsensusVariantsSnps)
+
+    val seed: Int = config("seed", default = 12345)
+    def addTreeJobs(variants: File, concensusVariants: File, outputDir: File, outputName: String) {
+      val dirSufixRaxml = new File(outputDir, "raxml")
+      val dirSufixGubbins = new File(outputDir, "gubbins")
+
+      val raxmlMl = new Raxml(this)
+      raxmlMl.input = variants
+      raxmlMl.m = config("raxml_ml_model", default = "GTRGAMMAX")
+      raxmlMl.p = Some(seed)
+      raxmlMl.n = outputName + "_ml"
+      raxmlMl.w = dirSufixRaxml
+      raxmlMl.N = config("ml_runs", default = 20, namespace = "raxml")
+      add(raxmlMl)
+
+      val r = new scala.util.Random(seed)
+      val numBoot = config("boot_runs", default = 100, namespace = "raxml").asInt
+      val bootList = for (t <- 0 until numBoot) yield {
+        val raxmlBoot = new Raxml(this)
+        raxmlBoot.input = variants
+        raxmlBoot.m = config("raxml_ml_model", default = "GTRGAMMAX")
+        raxmlBoot.p = Some(seed)
+        raxmlBoot.b = Some(math.abs(r.nextInt()))
+        raxmlBoot.w = dirSufixRaxml
+        raxmlBoot.N = Some(1)
+        raxmlBoot.n = outputName + "_boot_" + t
+        add(raxmlBoot)
+        raxmlBoot.getBootstrapFile.get
+      }
+
+      val cat = Cat(this, bootList.toList, new File(outputDir, "/boot_list"))
+      add(cat)
+
+      val raxmlBi = new Raxml(this)
+      raxmlBi.input = concensusVariants
+      raxmlBi.t = raxmlMl.getBestTreeFile
+      raxmlBi.z = Some(cat.output)
+      raxmlBi.m = config("raxml_ml_model", default = "GTRGAMMAX")
+      raxmlBi.p = Some(seed)
+      raxmlBi.f = "b"
+      raxmlBi.n = outputName + "_bi"
+      raxmlBi.w = dirSufixRaxml
+      add(raxmlBi)
+
+      val gubbins = new RunGubbins(this)
+      gubbins.fastafile = concensusVariants
+      gubbins.startingTree = raxmlBi.getBipartitionsFile
+      gubbins.outputDirectory = dirSufixGubbins
+      add(gubbins)
+    }
+
+    addTreeJobs(catVariantsSnps.output, catConsensusVariantsSnps.output,
+      new File(outputDir, "trees" + File.separator + "snps_only"), "snps_only")
+    addTreeJobs(catVariants.output, catConsensusVariants.output,
+      new File(outputDir, "trees" + File.separator + "snps_indels"), "snps_indels")
+
+  }
+
+  def addGenerateFasta(sampleName: String, outputDir: File, outputName: String = null,
+                       snpsOnly: Boolean = false): FastaOutput = {
+    val bastyGenerateFasta = new BastyGenerateFasta(this)
+    bastyGenerateFasta.outputName = if (outputName != null) outputName else sampleName
+    bastyGenerateFasta.inputVcf = shiva.multisampleVariantCalling.get.finalFile
+    if (shiva.samples.contains(sampleName)) {
+      bastyGenerateFasta.bamFile = shiva.samples(sampleName).preProcessBam.get
+    }
+    bastyGenerateFasta.outputVariants = new File(outputDir, bastyGenerateFasta.outputName + ".variants" + (if (snpsOnly) ".snps_only" else "") + ".fasta")
+    bastyGenerateFasta.outputConsensus = new File(outputDir, bastyGenerateFasta.outputName + ".consensus" + (if (snpsOnly) ".snps_only" else "") + ".fasta")
+    bastyGenerateFasta.outputConsensusVariants = new File(outputDir, bastyGenerateFasta.outputName + ".consensus_variants" + (if (snpsOnly) ".snps_only" else "") + ".fasta")
+    bastyGenerateFasta.sampleName = sampleName
+    bastyGenerateFasta.snpsOnly = snpsOnly
+    qscript.add(bastyGenerateFasta)
+    FastaOutput(bastyGenerateFasta.outputVariants, bastyGenerateFasta.outputConsensus, bastyGenerateFasta.outputConsensusVariants)
+  }
 }
 
-object Basty extends PipelineCommand
\ No newline at end of file
+object Basty extends PipelineCommand

public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.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.
- */
-/**
- * Due to the license issue with GATK, this part of Biopet can only be used inside the
- * LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
- * on how to use this protected part of biopet or contact us at sasc@lumc.nl
- */
-package nl.lumc.sasc.biopet.pipelines.basty
-
-import java.io.File
-
-import nl.lumc.sasc.biopet.core.MultiSampleQScript
-import nl.lumc.sasc.biopet.extensions.{ Cat, Raxml, RunGubbins }
-import nl.lumc.sasc.biopet.pipelines.shiva.{ Shiva, ShivaTrait }
-import nl.lumc.sasc.biopet.extensions.tools.BastyGenerateFasta
-import nl.lumc.sasc.biopet.utils.ConfigUtils
-import org.broadinstitute.gatk.queue.QScript
-
-trait BastyTrait extends MultiSampleQScript {
-  qscript: QScript =>
-
-  case class FastaOutput(variants: File, consensus: File, consensusVariants: File)
-
-  def variantcallers = List("freebayes")
-
-  override def defaults = Map(
-    "ploidy" -> 1,
-    "variantcallers" -> variantcallers
-  )
-
-  lazy val shiva: ShivaTrait = new Shiva(qscript)
-
-  def summaryFile: File = new File(outputDir, "Basty.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) {
-    //TODO: Add summary
-    def summaryFiles: Map[String, File] = Map()
-
-    //TODO: Add summary
-    def summaryStats: Map[String, Any] = Map()
-
-    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()
-
-      protected def addJobs(): Unit = {}
-    }
-
-    var output: FastaOutput = _
-    var outputSnps: FastaOutput = _
-
-    protected def addJobs(): Unit = {
-      addPerLibJobs()
-      output = addGenerateFasta(sampleId, sampleDir)
-      outputSnps = addGenerateFasta(sampleId, sampleDir, snpsOnly = true)
-    }
-  }
-
-  def init() {
-    shiva.outputDir = outputDir
-    shiva.init()
-  }
-
-  def biopetScript() {
-    shiva.biopetScript()
-    addAll(shiva.functions)
-    addSummaryQScript(shiva)
-
-    inputFiles :::= shiva.inputFiles
-
-    addSamplesJobs()
-  }
-
-  def addMultiSampleJobs(): Unit = {
-    val refVariants = addGenerateFasta(null, new File(outputDir, "fastas" + File.separator + "reference"), outputName = "reference")
-    val refVariantSnps = addGenerateFasta(null, new File(outputDir, "fastas" + File.separator + "reference"), outputName = "reference", snpsOnly = true)
-
-    val catVariants = Cat(this, refVariants.variants :: samples.map(_._2.output.variants).toList,
-      new File(outputDir, "fastas" + File.separator + "variant.fasta"))
-    add(catVariants)
-    val catVariantsSnps = Cat(this, refVariantSnps.variants :: samples.map(_._2.outputSnps.variants).toList,
-      new File(outputDir, "fastas" + File.separator + "variant.snps_only.fasta"))
-    add(catVariantsSnps)
-
-    val catConsensus = Cat(this, refVariants.consensus :: samples.map(_._2.output.consensus).toList,
-      new File(outputDir, "fastas" + File.separator + "consensus.fasta"))
-    add(catConsensus)
-    val catConsensusSnps = Cat(this, refVariantSnps.consensus :: samples.map(_._2.outputSnps.consensus).toList,
-      new File(outputDir, "fastas" + File.separator + "consensus.snps_only.fasta"))
-    add(catConsensusSnps)
-
-    val catConsensusVariants = Cat(this, refVariants.consensusVariants :: samples.map(_._2.output.consensusVariants).toList,
-      new File(outputDir, "fastas" + File.separator + "consensus.variant.fasta"))
-    add(catConsensusVariants)
-    val catConsensusVariantsSnps = Cat(this, refVariantSnps.consensusVariants :: samples.map(_._2.outputSnps.consensusVariants).toList,
-      new File(outputDir, "fastas" + File.separator + "consensus.variant.snps_only.fasta"))
-    add(catConsensusVariantsSnps)
-
-    val seed: Int = config("seed", default = 12345)
-    def addTreeJobs(variants: File, concensusVariants: File, outputDir: File, outputName: String) {
-      val dirSufixRaxml = new File(outputDir, "raxml")
-      val dirSufixGubbins = new File(outputDir, "gubbins")
-
-      val raxmlMl = new Raxml(this)
-      raxmlMl.input = variants
-      raxmlMl.m = config("raxml_ml_model", default = "GTRGAMMAX")
-      raxmlMl.p = Some(seed)
-      raxmlMl.n = outputName + "_ml"
-      raxmlMl.w = dirSufixRaxml
-      raxmlMl.N = config("ml_runs", default = 20, namespace = "raxml")
-      add(raxmlMl)
-
-      val r = new scala.util.Random(seed)
-      val numBoot = config("boot_runs", default = 100, namespace = "raxml").asInt
-      val bootList = for (t <- 0 until numBoot) yield {
-        val raxmlBoot = new Raxml(this)
-        raxmlBoot.input = variants
-        raxmlBoot.m = config("raxml_ml_model", default = "GTRGAMMAX")
-        raxmlBoot.p = Some(seed)
-        raxmlBoot.b = Some(math.abs(r.nextInt()))
-        raxmlBoot.w = dirSufixRaxml
-        raxmlBoot.N = Some(1)
-        raxmlBoot.n = outputName + "_boot_" + t
-        add(raxmlBoot)
-        raxmlBoot.getBootstrapFile.get
-      }
-
-      val cat = Cat(this, bootList.toList, new File(outputDir, "/boot_list"))
-      add(cat)
-
-      val raxmlBi = new Raxml(this)
-      raxmlBi.input = concensusVariants
-      raxmlBi.t = raxmlMl.getBestTreeFile
-      raxmlBi.z = Some(cat.output)
-      raxmlBi.m = config("raxml_ml_model", default = "GTRGAMMAX")
-      raxmlBi.p = Some(seed)
-      raxmlBi.f = "b"
-      raxmlBi.n = outputName + "_bi"
-      raxmlBi.w = dirSufixRaxml
-      add(raxmlBi)
-
-      val gubbins = new RunGubbins(this)
-      gubbins.fastafile = concensusVariants
-      gubbins.startingTree = raxmlBi.getBipartitionsFile
-      gubbins.outputDirectory = dirSufixGubbins
-      add(gubbins)
-    }
-
-    addTreeJobs(catVariantsSnps.output, catConsensusVariantsSnps.output,
-      new File(outputDir, "trees" + File.separator + "snps_only"), "snps_only")
-    addTreeJobs(catVariants.output, catConsensusVariants.output,
-      new File(outputDir, "trees" + File.separator + "snps_indels"), "snps_indels")
-
-  }
-
-  def addGenerateFasta(sampleName: String, outputDir: File, outputName: String = null,
-                       snpsOnly: Boolean = false): FastaOutput = {
-    val bastyGenerateFasta = new BastyGenerateFasta(this)
-    bastyGenerateFasta.outputName = if (outputName != null) outputName else sampleName
-    bastyGenerateFasta.inputVcf = shiva.multisampleVariantCalling.get.finalFile
-    if (shiva.samples.contains(sampleName)) {
-      bastyGenerateFasta.bamFile = shiva.samples(sampleName).preProcessBam.get
-    }
-    bastyGenerateFasta.outputVariants = new File(outputDir, bastyGenerateFasta.outputName + ".variants" + (if (snpsOnly) ".snps_only" else "") + ".fasta")
-    bastyGenerateFasta.outputConsensus = new File(outputDir, bastyGenerateFasta.outputName + ".consensus" + (if (snpsOnly) ".snps_only" else "") + ".fasta")
-    bastyGenerateFasta.outputConsensusVariants = new File(outputDir, bastyGenerateFasta.outputName + ".consensus_variants" + (if (snpsOnly) ".snps_only" else "") + ".fasta")
-    bastyGenerateFasta.sampleName = sampleName
-    bastyGenerateFasta.snpsOnly = snpsOnly
-    qscript.add(bastyGenerateFasta)
-    FastaOutput(bastyGenerateFasta.outputVariants, bastyGenerateFasta.outputConsensus, bastyGenerateFasta.outputConsensusVariants)
-  }
-}

public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutablePublic.scala

@@ -15,7 +15,6 @@
  */
 package nl.lumc.sasc.biopet
 
-import nl.lumc.sasc.biopet.pipelines.shiva.ShivaVariantcalling
 import nl.lumc.sasc.biopet.utils.{ BiopetExecutable, MainCommand }
 
 object BiopetExecutablePublic extends BiopetExecutable {
@@ -33,13 +32,13 @@ object BiopetExecutablePublic extends BiopetExecutable {
     nl.lumc.sasc.biopet.pipelines.shiva.ShivaSvCalling,
     nl.lumc.sasc.biopet.pipelines.gears.GearsSingle,
     nl.lumc.sasc.biopet.pipelines.gears.Gears,
-    nl.lumc.sasc.biopet.pipelines.gwastest.GwasTest
+    nl.lumc.sasc.biopet.pipelines.gwastest.GwasTest,
+    nl.lumc.sasc.biopet.pipelines.shiva.ShivaVariantcalling,
+    nl.lumc.sasc.biopet.pipelines.basty.Basty
   )
 
   def pipelines: List[MainCommand] = List(
-    nl.lumc.sasc.biopet.pipelines.shiva.Shiva,
-    ShivaVariantcalling,
-    nl.lumc.sasc.biopet.pipelines.basty.Basty
+    nl.lumc.sasc.biopet.pipelines.shiva.Shiva
   ) ::: publicPipelines
 
   def tools: List[MainCommand] = BiopetToolsExecutable.tools

public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala

@@ -43,7 +43,7 @@ trait ShivaTrait extends MultisampleMappingTrait with Reference with TargetRegio
   )
 
   /** Method to make the variantcalling namespace of shiva */
-  def makeVariantcalling(multisample: Boolean = false): ShivaVariantcallingTrait with QScript = {
+  def makeVariantcalling(multisample: Boolean = false): ShivaVariantcalling with QScript = {
     if (multisample) new ShivaVariantcalling(qscript) {
       override def namePrefix = "multisample"
       override def configNamespace: String = "shivavariantcalling"

public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcalling.scala

@@ -15,17 +15,178 @@
  */
 package nl.lumc.sasc.biopet.pipelines.shiva
 
-import nl.lumc.sasc.biopet.core.PipelineCommand
+import nl.lumc.sasc.biopet.core.{ PipelineCommand, Reference, SampleLibraryTag }
+import nl.lumc.sasc.biopet.core.summary.SummaryQScript
+import nl.lumc.sasc.biopet.extensions.Tabix
+import nl.lumc.sasc.biopet.extensions.gatk.{ CombineVariants, GenotypeConcordance }
+import nl.lumc.sasc.biopet.extensions.tools.VcfStats
+import nl.lumc.sasc.biopet.extensions.vt.{ VtDecompose, VtNormalize }
+import nl.lumc.sasc.biopet.pipelines.bammetrics.TargetRegions
+import nl.lumc.sasc.biopet.pipelines.gatk.variantcallers._
+import nl.lumc.sasc.biopet.pipelines.shiva.variantcallers.{ VarscanCnsSingleSample, _ }
+import nl.lumc.sasc.biopet.utils.{ BamUtils, Logging }
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.QScript
 
 /**
- * Implementation of ShivaVariantcalling without GATK variantcallers
+ * Implementation of ShivaVariantcalling
  *
  * Created by pjvan_thof on 2/26/15.
  */
-class ShivaVariantcalling(val root: Configurable) extends QScript with ShivaVariantcallingTrait {
+class ShivaVariantcalling(val root: Configurable) extends QScript
+  with SummaryQScript
+  with SampleLibraryTag
+  with Reference
+  with TargetRegions {
+  qscript =>
+
   def this() = this(null)
+
+  @Input(doc = "Bam files (should be deduped bams)", shortName = "BAM", required = true)
+  protected var inputBamsArg: List[File] = Nil
+
+  var inputBams: Map[String, File] = Map()
+
+  /** Executed before script */
+  def init(): Unit = {
+    if (inputBamsArg.nonEmpty) inputBams = BamUtils.sampleBamMap(inputBamsArg)
+  }
+
+  var referenceVcf: Option[File] = config("reference_vcf")
+
+  var referenceVcfRegions: Option[File] = config("reference_vcf_regions")
+
+  /** Name prefix, can override this methods if neeeded */
+  def namePrefix: String = {
+    (sampleId, libId) match {
+      case (Some(s), Some(l)) => s + "-" + l
+      case (Some(s), _)       => s
+      case _                  => config("name_prefix")
+    }
+  }
+
+  override def defaults = Map("bcftoolscall" -> Map("f" -> List("GQ")))
+
+  /** Final merged output files of all variantcaller modes */
+  def finalFile = new File(outputDir, namePrefix + ".final.vcf.gz")
+
+  /** Variantcallers requested by the config */
+  protected val configCallers: Set[String] = config("variantcallers")
+
+  protected val callers: List[Variantcaller] = {
+    (for (name <- configCallers) yield {
+      if (!callersList.exists(_.name == name))
+        Logging.addError(s"variantcaller '$name' does not exist, possible to use: " + callersList.map(_.name).mkString(", "))
+      callersList.find(_.name == name)
+    }).flatten.toList.sortBy(_.prio)
+  }
+
+  /** This will add jobs for this pipeline */
+  def biopetScript(): Unit = {
+    require(inputBams.nonEmpty, "No input bams found")
+    require(callers.nonEmpty, "must select at least 1 variantcaller, choices are: " + callersList.map(_.name).mkString(", "))