Split variantcalllers in separated files

external-example/src/main/scala/org/example/group/pipelines/BiopetPipeline.scala

@@ -31,6 +31,8 @@ class BiopetPipeline(val root: Configurable) extends QScript with SummaryQScript
 
     // Executing a biopet pipeline inside
     val shiva = new Shiva(this)
+    add(shiva)
+
     shiva.init()
     shiva.biopetScript()
     addAll(shiva.functions)

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

@@ -8,7 +8,7 @@ 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.extensions.gatk.broad._
-import nl.lumc.sasc.biopet.pipelines.shiva.{ ShivaTrait, ShivaVariantcallingTrait }
+import nl.lumc.sasc.biopet.pipelines.shiva.{ ShivaVariantcallingTrait, ShivaTrait }
 import org.broadinstitute.gatk.queue.QScript
 
 /**

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

@@ -6,9 +6,9 @@
 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.extensions.gatk.broad.GenotypeGVCFs
+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
 
 /**
@@ -22,99 +22,13 @@ class ShivaVariantcalling(val root: Configurable) extends QScript with ShivaVari
 
   /** Will generate all available variantcallers */
   override def callersList = {
-    new HaplotypeCallerGvcf ::
-      new HaplotypeCallerAllele ::
-      new UnifiedGenotyperAllele ::
-      new UnifiedGenotyper ::
-      new HaplotypeCaller ::
+    new HaplotypeCallerGvcf(this) ::
+      new HaplotypeCallerAllele(this) ::
+      new UnifiedGenotyperAllele(this) ::
+      new UnifiedGenotyper(this) ::
+      new HaplotypeCaller(this) ::
       super.callersList
   }
-
-  /** Default mode for the haplotypecaller */
-  class HaplotypeCaller extends Variantcaller {
-    val name = "haplotypecaller"
-    protected val defaultPrio = 1
-
-    def outputFile = new File(outputDir, namePrefix + ".haplotypecaller.vcf.gz")
-
-    def addJobs() {
-      val hc = new nl.lumc.sasc.biopet.extensions.gatk.broad.HaplotypeCaller(qscript)
-      hc.input_file = inputBams
-      hc.out = outputFile
-      add(hc)
-    }
-  }
-
-  /** Default mode for UnifiedGenotyper */
-  class UnifiedGenotyper extends Variantcaller {
-    val name = "unifiedgenotyper"
-    protected val defaultPrio = 20
-
-    def outputFile = new File(outputDir, namePrefix + ".unifiedgenotyper.vcf.gz")
-
-    def addJobs() {
-      val ug = new nl.lumc.sasc.biopet.extensions.gatk.broad.UnifiedGenotyper(qscript)
-      ug.input_file = inputBams
-      ug.out = outputFile
-      add(ug)
-    }
-  }
-
-  /** Allele mode for Haplotypecaller */
-  class HaplotypeCallerAllele extends Variantcaller {
-    val name = "haplotypecaller_allele"
-    protected val defaultPrio = 5
-
-    def outputFile = new File(outputDir, namePrefix + ".haplotypecaller_allele.vcf.gz")
-
-    def addJobs() {
-      val hc = new nl.lumc.sasc.biopet.extensions.gatk.broad.HaplotypeCaller(qscript)
-      hc.input_file = inputBams
-      hc.out = outputFile
-      hc.alleles = config("input_alleles")
-      hc.genotyping_mode = org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingOutputMode.GENOTYPE_GIVEN_ALLELES
-      add(hc)
-    }
-  }
-
-  /** Allele mode for GenotyperAllele */
-  class UnifiedGenotyperAllele extends Variantcaller {
-    val name = "unifiedgenotyper_allele"
-    protected val defaultPrio = 9
-
-    def outputFile = new File(outputDir, namePrefix + ".unifiedgenotyper_allele.vcf.gz")
-
-    def addJobs() {
-      val ug = new nl.lumc.sasc.biopet.extensions.gatk.broad.UnifiedGenotyper(qscript)
-      ug.input_file = inputBams
-      ug.out = outputFile
-      ug.alleles = config("input_alleles")
-      ug.genotyping_mode = org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingOutputMode.GENOTYPE_GIVEN_ALLELES
-      add(ug)
-    }
-  }
-
-  /** Gvcf mode for haplotypecaller */
-  class HaplotypeCallerGvcf extends Variantcaller {
-    val name = "haplotypecaller_gvcf"
-    protected val defaultPrio = 5
-
-    def outputFile = new File(outputDir, namePrefix + ".haplotypecaller_gvcf.vcf.gz")
-
-    def addJobs() {
-      val gvcfFiles = for (inputBam <- inputBams) yield {
-        val hc = new nl.lumc.sasc.biopet.extensions.gatk.broad.HaplotypeCaller(qscript)
-        hc.input_file = List(inputBam)
-        hc.out = new File(outputDir, inputBam.getName.stripSuffix(".bam") + ".gvcf.vcf.gz")
-        hc.useGvcf()
-        add(hc)
-        hc.out
-      }
-
-      val genotypeGVCFs = GenotypeGVCFs(qscript, gvcfFiles, outputFile)
-      add(genotypeGVCFs)
-    }
-  }
 }
 
 /** object to add default main method to pipeline */

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

+package nl.lumc.sasc.biopet.pipelines.gatk.variantcallers
+
+import nl.lumc.sasc.biopet.pipelines.shiva.variantcallers.Variantcaller
+import nl.lumc.sasc.biopet.utils.config.Configurable
+
+/** Default mode for the haplotypecaller */
+class HaplotypeCaller(val root: Configurable) extends Variantcaller {
+  val name = "haplotypecaller"
+  protected def defaultPrio = 1
+
+  def biopetScript() {
+    val hc = new nl.lumc.sasc.biopet.extensions.gatk.broad.HaplotypeCaller(this)
+    hc.input_file = inputBams.values.toList
+    hc.out = outputFile
+    add(hc)
+  }
+}
+

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

+package nl.lumc.sasc.biopet.pipelines.gatk.variantcallers
+
+import nl.lumc.sasc.biopet.pipelines.shiva.variantcallers.Variantcaller
+import nl.lumc.sasc.biopet.utils.config.Configurable
+
+/** Allele mode for Haplotypecaller */
+class HaplotypeCallerAllele(val root: Configurable) extends Variantcaller {
+  val name = "haplotypecaller_allele"
+  protected def defaultPrio = 5
+
+  def biopetScript() {
+    val hc = new nl.lumc.sasc.biopet.extensions.gatk.broad.HaplotypeCaller(this)
+    hc.input_file = inputBams.values.toList
+    hc.out = outputFile
+    hc.alleles = config("input_alleles")
+    hc.genotyping_mode = org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingOutputMode.GENOTYPE_GIVEN_ALLELES
+    add(hc)
+  }
+}

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

+package nl.lumc.sasc.biopet.pipelines.gatk.variantcallers
+
+import nl.lumc.sasc.biopet.extensions.gatk.broad.GenotypeGVCFs
+import nl.lumc.sasc.biopet.pipelines.shiva.variantcallers.Variantcaller
+import nl.lumc.sasc.biopet.utils.config.Configurable
+
+/** Gvcf mode for haplotypecaller */
+class HaplotypeCallerGvcf(val root: Configurable) extends Variantcaller {
+  val name = "haplotypecaller_gvcf"
+  protected def defaultPrio = 5
+
+  def biopetScript() {
+    val gvcfFiles = for ((sample, inputBam) <- inputBams) yield {
+      val hc = new nl.lumc.sasc.biopet.extensions.gatk.broad.HaplotypeCaller(this)
+      hc.input_file = List(inputBam)
+      hc.out = new File(outputDir, sample + ".gvcf.vcf.gz")
+      hc.useGvcf()
+      add(hc)
+      hc.out
+    }
+
+    val genotypeGVCFs = GenotypeGVCFs(this, gvcfFiles.toList, outputFile)
+    add(genotypeGVCFs)
+  }
+}

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

+package nl.lumc.sasc.biopet.pipelines.gatk.variantcallers
+
+import nl.lumc.sasc.biopet.pipelines.shiva.variantcallers.Variantcaller
+import nl.lumc.sasc.biopet.utils.config.Configurable
+
+/** Default mode for UnifiedGenotyper */
+class UnifiedGenotyper(val root: Configurable) extends Variantcaller {
+  val name = "unifiedgenotyper"
+  protected def defaultPrio = 20
+
+  def biopetScript() {
+    val ug = new nl.lumc.sasc.biopet.extensions.gatk.broad.UnifiedGenotyper(this)
+    ug.input_file = inputBams.values.toList
+    ug.out = outputFile
+    add(ug)
+  }
+}

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

+package nl.lumc.sasc.biopet.pipelines.gatk.variantcallers
+
+import nl.lumc.sasc.biopet.pipelines.shiva.variantcallers.Variantcaller
+import nl.lumc.sasc.biopet.utils.config.Configurable
+
+/** Allele mode for GenotyperAllele */
+class UnifiedGenotyperAllele(val root: Configurable) extends Variantcaller {
+  val name = "unifiedgenotyper_allele"
+  protected def defaultPrio = 9
+
+  def biopetScript() {
+    val ug = new nl.lumc.sasc.biopet.extensions.gatk.broad.UnifiedGenotyper(this)
+    ug.input_file = inputBams.values.toList
+    ug.out = outputFile
+    ug.alleles = config("input_alleles")
+    ug.genotyping_mode = org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingOutputMode.GENOTYPE_GIVEN_ALLELES
+    add(ug)
+  }
+}

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

@@ -76,7 +76,7 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
     val map = Map("variantcallers" -> callers.toList)
     val pipeline = initPipeline(map)
 
-    pipeline.inputBams = (for (n <- 1 to bams) yield ShivaVariantcallingTest.inputTouch("bam_" + n + ".bam")).toList
+    pipeline.inputBams = (for (n <- 1 to bams) yield n.toString -> ShivaVariantcallingTest.inputTouch("bam_" + n + ".bam")).toMap
 
     val illegalArgumentException = pipeline.inputBams.isEmpty ||
       (!raw && !bcftools &&

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

@@ -27,9 +27,10 @@ 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: QScript =>
 
   case class FastaOutput(variants: File, consensus: File, consensusVariants: File)
 

public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala

@@ -17,17 +17,18 @@ package nl.lumc.sasc.biopet.core
 
 import java.io.File
 
+import nl.lumc.sasc.biopet.core.summary.SummaryQScript
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
 import nl.lumc.sasc.biopet.utils.Logging
-import org.broadinstitute.gatk.queue.QSettings
+import org.broadinstitute.gatk.queue.{ QScript, QSettings }
 import org.broadinstitute.gatk.queue.function.QFunction
 import org.broadinstitute.gatk.queue.function.scattergather.ScatterGatherableFunction
 import org.broadinstitute.gatk.queue.util.{ Logging => GatkLogging }
 import org.broadinstitute.gatk.utils.commandline.Argument
 
 /** Base for biopet pipeline */
-trait BiopetQScript extends Configurable with GatkLogging {
+trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
 
   @Argument(doc = "JSON / YAML config file(s)", fullName = "config_file", shortName = "config", required = false)
   val configfiles: List[File] = Nil
@@ -125,6 +126,25 @@ trait BiopetQScript extends Configurable with GatkLogging {
     function.isIntermediate = isIntermediate
     add(function)
   }
+
+  def add(subPipeline: QScript): Unit = {
+    subPipeline.qSettings = this.qSettings
+    subPipeline match {
+      case that: SummaryQScript =>
+        that.init()
+        that.biopetScript()
+        that.addSummaryJobs()
+        this match {
+          case s: SummaryQScript => s.addSummaryQScript(that)
+          case _ =>
+        }
+      case that:BiopetQScript =>
+        that.init()
+        that.biopetScript()
+      case _ => subPipeline.script
+    }
+    addAll(subPipeline.functions)
+  }
 }
 
 object BiopetQScript {

public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala

@@ -19,11 +19,11 @@ import java.io.File
 
 import nl.lumc.sasc.biopet.core.summary.{ Summarizable, SummaryQScript }
 import nl.lumc.sasc.biopet.utils.{ Logging, ConfigUtils }
+import org.broadinstitute.gatk.queue.QScript
 import org.broadinstitute.gatk.utils.commandline.Argument
 
 /** This trait creates a structured way of use multisample pipelines */
-trait MultiSampleQScript extends SummaryQScript {
-  qscript =>
+trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
 
   @Argument(doc = "Only Sample", shortName = "s", required = false, fullName = "sample")
   private[core] val onlySamples: List[String] = Nil

public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala

@@ -19,6 +19,7 @@ import java.io.File
 
 import nl.lumc.sasc.biopet.core._
 import nl.lumc.sasc.biopet.core.extensions.{ CheckChecksum, Md5sum }
+import org.broadinstitute.gatk.queue.QScript
 
 import scala.collection.mutable
 
@@ -27,7 +28,7 @@ import scala.collection.mutable
  *
  * Created by pjvan_thof on 2/14/15.
  */
-trait SummaryQScript extends BiopetQScript { qscript =>
+trait SummaryQScript extends BiopetQScript { qscript: QScript =>
 
   /** Key is sample/library, None is sample or library is not applicable */
   private[summary] var summarizables: Map[(String, Option[String], Option[String]), List[Summarizable]] = Map()

public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/PipelineCommandTest.scala

@@ -5,6 +5,8 @@ import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
 import org.testng.annotations.Test
 
+import scala.language.reflectiveCalls
+
 /**
  * Created by pjvanthof on 17/11/15.
  */

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/Delly.scala

@@ -34,6 +34,8 @@ class Delly(val root: Configurable) extends QScript with BiopetQScript with Refe
   @Output(doc = "Delly result VCF")
   var outputVcf: File = _
 
+  this.inputFiles
+
   var outputName: String = _
 
   // select the analysis types DEL,DUP,INV,TRA

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

@@ -15,6 +15,7 @@
  */
 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 {
@@ -33,7 +34,7 @@ object BiopetExecutablePublic extends BiopetExecutable {
 
   def pipelines: List[MainCommand] = List(
     nl.lumc.sasc.biopet.pipelines.shiva.Shiva,
-    nl.lumc.sasc.biopet.pipelines.shiva.ShivaVariantcalling,
+    ShivaVariantcalling,
     nl.lumc.sasc.biopet.pipelines.basty.Basty
   ) ::: publicPipelines
 

public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/BamUtils.scala

+package nl.lumc.sasc.biopet.utils
+
+import java.io.File
+
+import htsjdk.samtools.SamReaderFactory
+
+import scala.collection.JavaConversions._
+
+/**
+ * Created by pjvan_thof on 11/19/15.
+ */
+object BamUtils {
+
+  /**
+   * This method will convert a list of bam files to a Map[<sampleName>, <bamFile>]
+   *
+   * Each sample may only be once in the list
+   *
+   * @throws IllegalArgumentException
+   * @param bamFiles input bam files
+   * @return
+   */
+  def sampleBamMap(bamFiles: List[File]): Map[String, File] = {
+    val temp = bamFiles.map { file =>
+      val inputSam = SamReaderFactory.makeDefault.open(file)
+      val samples = inputSam.getFileHeader.getReadGroups.map(_.getSample).distinct
+      if (samples.size == 1) samples.head -> file
+      else throw new IllegalArgumentException("Bam contains multiple sample IDs: " + file)
+    }
+    if (temp.map(_._1).distinct.size != temp.size) throw new IllegalArgumentException("Samples has been found twice")
+    temp.toMap
+  }
+}

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

@@ -15,18 +15,15 @@
  */
 package nl.lumc.sasc.biopet.pipelines.shiva
 
-import htsjdk.samtools.SamReaderFactory
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
 import nl.lumc.sasc.biopet.core.{ PipelineCommand, Reference, SampleLibraryTag }
 import nl.lumc.sasc.biopet.extensions.breakdancer.Breakdancer
 import nl.lumc.sasc.biopet.extensions.clever.CleverCaller
 import nl.lumc.sasc.biopet.extensions.delly.Delly
-import nl.lumc.sasc.biopet.utils.Logging
+import nl.lumc.sasc.biopet.utils.{ BamUtils, Logging }
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.QScript
 
-import scala.collection.JavaConversions._
-
 /**
  * Common trait for ShivaVariantcalling
  *
@@ -40,25 +37,11 @@ class ShivaSvCalling(val root: Configurable) extends QScript with SummaryQScript
   @Input(doc = "Bam files (should be deduped bams)", shortName = "BAM", required = true)
   protected var inputBamsArg: List[File] = Nil
 
-  protected var inputBams: Map[String, File] = Map()
-
-  def addBamFile(file: File, sampleId: Option[String] = None): Unit = {
-    sampleId match {
-      case Some(sample)        => inputBams += sample -> file
-      case _ if !file.exists() => throw new IllegalArgumentException("Bam file does not exits: " + file)
-      case _ => {
-        val inputSam = SamReaderFactory.makeDefault.open(file)
-        val samples = inputSam.getFileHeader.getReadGroups.map(_.getSample).distinct
-        if (samples.size == 1) {
-          inputBams += samples.head -> file
-        } else throw new IllegalArgumentException("Bam contains multiple sample IDs: " + file)
-      }
-    }
-  }
+  var inputBams: Map[String, File] = Map()
 
   /** Executed before script */
   def init(): Unit = {
-    inputBamsArg.foreach(addBamFile(_))
+    if (inputBamsArg.nonEmpty) inputBams = BamUtils.sampleBamMap(inputBamsArg)
   }
 
   /** Variantcallers requested by the config */

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

@@ -15,8 +15,6 @@
  */
 package nl.lumc.sasc.biopet.pipelines.shiva
 
-import java.io.File
-
 import htsjdk.samtools.SamReaderFactory
 import nl.lumc.sasc.biopet.core.{ MultiSampleQScript, Reference }
 import nl.lumc.sasc.biopet.extensions.Ln
@@ -25,6 +23,7 @@ import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
 import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
 import nl.lumc.sasc.biopet.pipelines.toucan.Toucan
 import nl.lumc.sasc.biopet.utils.Logging
+import org.broadinstitute.gatk.queue.QScript
 
 import scala.collection.JavaConversions._
 
@@ -33,8 +32,7 @@ import scala.collection.JavaConversions._
  *
  * Created by pjvan_thof on 2/26/15.
  */
-trait ShivaTrait extends MultiSampleQScript with Reference {
-  qscript =>
+trait ShivaTrait extends MultiSampleQScript with Reference { qscript: QScript =>
 
   /** Executed before running the script */
   def init(): Unit = {
@@ -233,8 +231,8 @@ trait ShivaTrait extends MultiSampleQScript with Reference {
           vc.sampleId = Some(sampleId)
           vc.libId = Some(libId)
           vc.outputDir = new File(libDir, "variantcalling")
-          if (preProcessBam.isDefined) vc.inputBams = preProcessBam.get :: Nil
-          else vc.inputBams = bamFile.get :: Nil
+          if (preProcessBam.isDefined) vc.inputBams = Map(sampleId -> preProcessBam.get)
+          else vc.inputBams = Map(sampleId -> bamFile.get)
           vc.init()
           vc.biopetScript()
           addAll(vc.functions)
@@ -299,7 +297,7 @@ trait ShivaTrait extends MultiSampleQScript with Reference {
         variantcalling.foreach(vc => {
           vc.sampleId = Some(sampleId)
           vc.outputDir = new File(sampleDir, "variantcalling")
-          vc.inputBams = bam :: Nil
+          vc.inputBams = Map(sampleId -> bam)
           vc.init()
           vc.biopetScript()
           addAll(vc.functions)
@@ -326,7 +324,7 @@ trait ShivaTrait extends MultiSampleQScript with Reference {
   def addMultiSampleJobs(): Unit = {
     multisampleVariantCalling.foreach(vc => {
       vc.outputDir = new File(outputDir, "variantcalling")
-      vc.inputBams = samples.flatMap(_._2.preProcessBam).toList
+      vc.inputBams = samples.flatMap { case (sampleId, sample) => sample.preProcessBam.map(sampleId -> _) }
       vc.init()
       vc.biopetScript()
       addAll(vc.functions)
@@ -344,7 +342,7 @@ trait ShivaTrait extends MultiSampleQScript with Reference {
 
     svCalling.foreach(sv => {
       sv.outputDir = new File(outputDir, "sv_calling")
-      samples.foreach(x => x._2.preProcessBam.foreach(bam => sv.addBamFile(bam, Some(x._1))))
+      sv.inputBams = samples.flatMap { case (sampleId, sample) => sample.preProcessBam.map(sampleId -> _) }
       sv.init()
       sv.biopetScript()
       addAll(sv.functions)

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

@@ -19,12 +19,11 @@ import java.io.File
 
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
 import nl.lumc.sasc.biopet.core.{ Reference, SampleLibraryTag }
-import nl.lumc.sasc.biopet.extensions.bcftools.{ BcftoolsCall, BcftoolsMerge }
-import nl.lumc.sasc.biopet.extensions.gatk.{ GenotypeConcordance, CombineVariants }
-import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup
-import nl.lumc.sasc.biopet.extensions.tools.{ MpileupToVcf, VcfFilter, VcfStats }
-import nl.lumc.sasc.biopet.extensions.{ Ln, Bgzip, Tabix }
-import nl.lumc.sasc.biopet.utils.Logging
+import nl.lumc.sasc.biopet.extensions.gatk.{ CombineVariants, GenotypeConcordance }
+import nl.lumc.sasc.biopet.extensions.tools.VcfStats
+import nl.lumc.sasc.biopet.pipelines.shiva.variantcallers._
+import nl.lumc.sasc.biopet.utils.{ BamUtils, Logging }
+import org.broadinstitute.gatk.queue.QScript
 import org.broadinstitute.gatk.utils.commandline.Input
 
 /**
@@ -33,10 +32,17 @@ import org.broadinstitute.gatk.utils.commandline.Input
  * Created by pjvan_thof on 2/26/15.
  */
 trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag with Reference {
-  qscript =>
+  qscript: QScript =>
 
   @Input(doc = "Bam files (should be deduped bams)", shortName = "BAM", required = true)
-  var inputBams: List[File] = Nil
+  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")
 
@@ -53,10 +59,6 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag with
 
   override def defaults = Map("bcftoolscall" -> Map("f" -> List("GQ")))
 
-  /** Executed before script */
-  def init(): Unit = {
-  }
-
   /** Final merged output files of all variantcaller modes */
   def finalFile = new File(outputDir, namePrefix + ".final.vcf.gz")
 
@@ -81,7 +83,8 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag with
     cv.genotypeMergeOptions = Some("PRIORITIZE")
     cv.rodPriorityList = callers.map(_.name).mkString(",")
     for (caller <- callers) {
-      caller.addJobs()
+      caller.inputBams = inputBams
+      add(caller)
       cv.addInput(caller.outputFile, caller.name)
 
       val vcfStats = new VcfStats(qscript)
@@ -123,163 +126,7 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag with
   }
 
   /** Will generate all available variantcallers */
-  protected def callersList: List[Variantcaller] = List(new Freebayes, new RawVcf, new Bcftools, new BcftoolsSingleSample)
-
-  /** General trait for a variantcaller mode */
-  trait Variantcaller {
-    /** Name of mode, this should also be used in the config */
-    val name: String
-
-    /** Output dir for this mode */
-    def outputDir = new File(qscript.outputDir, name)
-
-    /** Prio in merging  in the final file */
-    protected val defaultPrio: Int
-
-    /** Prio from the config */
-    lazy val prio: Int = config("prio_" + name, default = defaultPrio)
-
-    /** This should add the variantcaller jobs */
-    def addJobs()
-
-    /** Final output file of this mode */
-    def outputFile: File
-  }
-
-  /** default mode of freebayes */
-  class Freebayes extends Variantcaller {
-    val name = "freebayes"
-    protected val defaultPrio = 7
-
-    /** Final output file of this mode */
-    def outputFile = new File(outputDir, namePrefix + ".freebayes.vcf.gz")
-
-    def addJobs() {
-      val fb = new nl.lumc.sasc.biopet.extensions.Freebayes(qscript)
-      fb.bamfiles = inputBams
-      fb.outputVcf = new File(outputDir, namePrefix + ".freebayes.vcf")
-      fb.isIntermediate = true
-      add(fb)
-
-      //TODO: need piping for this, see also issue #114
-      val bz = new Bgzip(qscript)
-      bz.input = List(fb.outputVcf)
-      bz.output = outputFile
-      add(bz)
-
-      val ti = new Tabix(qscript)
-      ti.input = bz.output
-      ti.p = Some("vcf")
-      add(ti)
-    }
-  }
-
-  /** default mode of bcftools */