Merge branch 'feature-reference' into 'develop'

Feature reference

Part of issue #81

This is only checking and not auto generating anything. Adding auto generate is now not a lot of work anymore.

See merge request !147

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala

@@ -5,10 +5,10 @@
  */
 package nl.lumc.sasc.biopet.extensions.gatk.broad
 
-import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
+import nl.lumc.sasc.biopet.core.{ Reference, BiopetJavaCommandLineFunction }
 import org.broadinstitute.gatk.queue.extensions.gatk.CommandLineGATK
 
-trait GatkGeneral extends CommandLineGATK with BiopetJavaCommandLineFunction {
+trait GatkGeneral extends CommandLineGATK with BiopetJavaCommandLineFunction with Reference {
   memoryLimit = Option(3)
 
   override def subPath = "gatk" :: super.subPath
@@ -19,7 +19,11 @@ trait GatkGeneral extends CommandLineGATK with BiopetJavaCommandLineFunction {
 
   if (config.contains("intervals")) intervals = config("intervals").asFileList
   if (config.contains("exclude_intervals")) excludeIntervals = config("exclude_intervals").asFileList
-  reference_sequence = config("reference")
   if (config.contains("gatk_key")) gatk_key = config("gatk_key")
   if (config.contains("pedigree")) pedigree = config("pedigree")
+
+  override def beforeGraph: Unit = {
+    super.beforeGraph
+    if (reference_sequence == null) reference_sequence = referenceFasta()
+  }
 }

protected/biopet-gatk-pipelines/src/test/resources/ref.dict

+@HD	VN:1.4	SO:unsorted
+@SQ	SN:chr1	LN:9	UR:file:/home/pjvan_thof/pipelines/biopet/public/mapping/src/test/resources/ref.fa	M5:fe15dbbd0900310caf32827f6da57550

protected/biopet-gatk-pipelines/src/test/resources/ref.fa

+>chr1
+AGTAGTAGT

protected/biopet-gatk-pipelines/src/test/resources/ref.fa.fai

+chr1	9	6	9	10

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

@@ -5,6 +5,8 @@
  */
 package nl.lumc.sasc.biopet.pipelines.gatk
 
+import java.io.{ FileOutputStream, File }
+
 import com.google.common.io.Files
 import nl.lumc.sasc.biopet.core.config.Config
 import nl.lumc.sasc.biopet.extensions.bwa.BwaMem
@@ -90,10 +92,22 @@ class ShivaTest extends TestNGSuite with Matchers {
 object ShivaTest {
   val outputDir = Files.createTempDir()
 
+  private def copyFile(name: String): Unit = {
+    val is = getClass.getResourceAsStream("/" + name)
+    val os = new FileOutputStream(new File(outputDir, name))
+    org.apache.commons.io.IOUtils.copy(is, os)
+    os.close()
+  }
+
+  copyFile("ref.fa")
+  copyFile("ref.dict")
+  copyFile("ref.fa.fai")
+
   val config = Map(
     "name_prefix" -> "test",
     "output_dir" -> outputDir,
-    "reference" -> "test",
+    "reference" -> (outputDir + File.separator + "ref.fa"),
+    "reference_fasta" -> (outputDir + File.separator + "ref.fa"),
     "gatk_jar" -> "test",
     "samtools" -> Map("exe" -> "test"),
     "bcftools" -> Map("exe" -> "test"),

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

@@ -5,7 +5,7 @@
  */
 package nl.lumc.sasc.biopet.pipelines.gatk
 
-import java.io.File
+import java.io.{ FileOutputStream, File }
 
 import com.google.common.io.Files
 import nl.lumc.sasc.biopet.core.config.Config
@@ -106,10 +106,22 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
 object ShivaVariantcallingTest {
   val outputDir = Files.createTempDir()
 
+  private def copyFile(name: String): Unit = {
+    val is = getClass.getResourceAsStream("/" + name)
+    val os = new FileOutputStream(new File(outputDir, name))
+    org.apache.commons.io.IOUtils.copy(is, os)
+    os.close()
+  }
+
+  copyFile("ref.fa")
+  copyFile("ref.dict")
+  copyFile("ref.fa.fai")
+
   val config = Map(
     "name_prefix" -> "test",
     "output_dir" -> outputDir,
-    "reference" -> "test",
+    "reference" -> (outputDir + File.separator + "ref.fa"),
+    "reference_fasta" -> (outputDir + File.separator + "ref.fa"),
     "gatk_jar" -> "test",
     "samtools" -> Map("exe" -> "test"),
     "bcftools" -> Map("exe" -> "test"),

public/bammetrics/src/test/resources/ref.dict

+@HD	VN:1.4	SO:unsorted
+@SQ	SN:chr1	LN:9	UR:file:/home/pjvan_thof/pipelines/biopet/public/mapping/src/test/resources/ref.fa	M5:fe15dbbd0900310caf32827f6da57550

public/bammetrics/src/test/resources/ref.fa

+>chr1
+AGTAGTAGT

public/bammetrics/src/test/resources/ref.fa.fai

+chr1	9	6	9	10

public/bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala

 package nl.lumc.sasc.biopet.pipelines.bammetrics
 
-import java.io.File
+import java.io.{ FileOutputStream, File }
 
 import com.google.common.io.Files
 import nl.lumc.sasc.biopet.core.config.Config
@@ -81,9 +81,20 @@ class BamMetricsTest extends TestNGSuite with Matchers {
 object BamMetricsTest {
   val outputDir = Files.createTempDir()
 
+  private def copyFile(name: String): Unit = {
+    val is = getClass.getResourceAsStream("/" + name)
+    val os = new FileOutputStream(new File(outputDir, name))
+    org.apache.commons.io.IOUtils.copy(is, os)
+    os.close()
+  }
+
+  copyFile("ref.fa")
+  copyFile("ref.dict")
+  copyFile("ref.fa.fai")
+
   val executables = Map(
     "refFlat" -> "bla.refFlat",
-    "reference" -> "reference.fa",
+    "reference_fasta" -> (outputDir + File.separator + "ref.fa"),
     "samtools" -> Map("exe" -> "test"),
     "bedtools" -> Map("exe" -> "test")
   )

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

+package nl.lumc.sasc.biopet.core
+
+import java.io.File
+
+import htsjdk.samtools.reference.IndexedFastaSequenceFile
+import nl.lumc.sasc.biopet.core.config.Configurable
+import scala.collection.JavaConversions._
+
+/**
+ * Created by pjvan_thof on 4/6/15.
+ */
+trait Reference extends Configurable {
+
+  def referenceSpecies: String = {
+    root match {
+      case r: Reference if r.referenceSpecies != "unknown_species" => r.referenceSpecies
+      case _ => config("species", default = "unknown_species", path = super.configPath)
+    }
+  }
+
+  def referenceName: String = {
+    root match {
+      case r: Reference if r.referenceName != "unknown_ref" => r.referenceName
+      case _ => {
+        val default: String = config("default", default = "unknown_ref", path = List("references", referenceSpecies))
+        config("reference_name", default = default, path = super.configPath)
+      }
+    }
+  }
+
+  override def subPath = {
+    referenceConfigPath ::: super.subPath
+  }
+
+  /** Returns the reference config path */
+  def referenceConfigPath = {
+    List("references", referenceSpecies, referenceName)
+  }
+
+  protected def faiRequired = false
+
+  protected def dictRequired = false
+
+  /** Returns the fasta file */
+  def referenceFasta(): File = {
+    val file: File = config("reference_fasta")
+    checkFasta(file)
+
+    val dict = new File(file.getAbsolutePath.stripSuffix(".fa").stripSuffix(".fasta") + ".dict")
+    val fai = new File(file.getAbsolutePath + ".fai")
+
+    this match {
+      case c: BiopetCommandLineFunctionTrait => c.deps :::= dict :: fai :: Nil
+      case _                                 =>
+    }
+
+    file
+  }
+
+  /** Create summary part for reference */
+  def referenceSummary: Map[String, Any] = {
+    val file = new IndexedFastaSequenceFile(referenceFasta())
+    Map("contigs" ->
+      (for (seq <- file.getSequenceDictionary.getSequences) yield seq.getSequenceName -> {
+        val md5 = Option(seq.getAttribute("M5"))
+        Map("md5" -> md5, "length" -> seq.getSequenceLength)
+      }).toMap,
+      "species" -> referenceSpecies,
+      "name" -> referenceName
+    )
+  }
+
+  //TODO: this become obsolete when index get autogenerated
+
+  /** Check fasta file if file exist and index file are there */
+  def checkFasta(file: File): Unit = {
+    if (!Reference.checked.contains(file)) {
+      require(file.exists(), "Reference not found: " + file)
+
+      if (dictRequired) {
+        val dict = new File(file.getAbsolutePath.stripSuffix(".fa").stripSuffix(".fasta") + ".dict")
+        require(dict.exists(), "Reference is missing a dict file")
+      }
+
+      if (faiRequired) {
+        val fai = new File(file.getAbsolutePath + ".fai")
+        require(fai.exists(), "Reference is missing a fai file")
+        require(IndexedFastaSequenceFile.canCreateIndexedFastaReader(file), "Index of reference cannot be loaded, reference: " + file)
+      }
+
+      Reference.checked += file
+    }
+  }
+}
+
+object Reference {
+
+  /** Used as cache to avoid double checking */
+  private var checked: Set[File] = Set()
+}

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala

@@ -22,11 +22,11 @@ trait Configurable extends ImplicitConversions {
   val root: Configurable
   def globalConfig: Config = if (root != null) root.globalConfig else Config.global
 
-  /** subfix to the path */
+  /** suffix to the path */
   def subPath: List[String] = Nil
 
   /** Get default path to search config values for current object */
-  def configPath: List[String] = if (root != null) root.configFullPath ::: subPath else subPath
+  def configPath: List[String] = if (root != null) root.configFullPath else Nil
 
   /** Gets name of module for config */
   protected[core] def configName = getClass.getSimpleName.toLowerCase
@@ -92,7 +92,7 @@ trait Configurable extends ImplicitConversions {
       val s = if (sample != null || defaultSample.isEmpty) sample else defaultSample.get
       val l = if (library != null || defaultLibrary.isEmpty) library else defaultLibrary.get
       val m = if (submodule != null) submodule else configName
-      val p = if (path == null) getConfigPath(s, l, submodule) else path
+      val p = (if (path == null) getConfigPath(s, l, submodule) ::: subPath else path)
       val d = {
         val value = Config.getValueFromMap(defaults.toMap, ConfigValueIndex(m, p, key, freeVar))
         if (value.isDefined) value.get.value else default
@@ -119,7 +119,7 @@ trait Configurable extends ImplicitConversions {
       val s = if (sample != null || defaultSample.isEmpty) sample else defaultSample.get
       val l = if (library != null || defaultLibrary.isEmpty) library else defaultLibrary.get
       val m = if (submodule != null) submodule else configName
-      val p = if (path == null) getConfigPath(s, l, submodule) else path
+      val p = (if (path == null) getConfigPath(s, l, submodule) ::: subPath else path)
 
       globalConfig.contains(m, p, key, freeVar) || !(Config.getValueFromMap(defaults.toMap, ConfigValueIndex(m, p, key, freeVar)) == None)
     }

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala

@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.core.{ Reference, BiopetCommandLineFunction }
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
@@ -26,7 +26,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
  *
  * Based on version 1.1.1
  */
-class Bowtie(val root: Configurable) extends BiopetCommandLineFunction {
+class Bowtie(val root: Configurable) extends BiopetCommandLineFunction with Reference {
   @Input(doc = "Fastq file R1", shortName = "R1")
   var R1: File = null
 
@@ -34,7 +34,7 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction {
   var R2: Option[File] = None
 
   @Input(doc = "The reference file for the bam files.", shortName = "R", required = true)
-  var reference: File = config("reference")
+  var reference: File = null
 
   @Output(doc = "Output file SAM", shortName = "output", required = true)
   var output: File = null
@@ -59,6 +59,11 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction {
   var maqerr: Option[Int] = config("maqerr")
   var maxins: Option[Int] = config("maxins")
 
+  override def beforeGraph {
+    super.beforeGraph
+    if (reference == null) reference = referenceFasta()
+  }
+
   /** return commandline to execute */
   def cmdLine = {
     required(executable) +

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala

@@ -19,14 +19,14 @@ import java.io.File
 
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
 
-import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.core.{ Reference, BiopetCommandLineFunction }
 import nl.lumc.sasc.biopet.core.config.Configurable
 
 /**
  * Wrapper for the gsnap command line tool
  * Written based on gsnap version 2014-05-15
  */
-class Gsnap(val root: Configurable) extends BiopetCommandLineFunction {
+class Gsnap(val root: Configurable) extends BiopetCommandLineFunction with Reference {
 
   /** default executable */
   executable = config("exe", default = "gsnap", freeVar = false)

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala

@@ -17,12 +17,12 @@ package nl.lumc.sasc.biopet.extensions
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.core.{ Reference, BiopetCommandLineFunction }
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /** Extension for stampy */
-class Stampy(val root: Configurable) extends BiopetCommandLineFunction {
+class Stampy(val root: Configurable) extends BiopetCommandLineFunction with Reference {
   @Input(doc = "FastQ file R1", shortName = "R1")
   var R1: File = _
 
@@ -30,7 +30,7 @@ class Stampy(val root: Configurable) extends BiopetCommandLineFunction {
   var R2: File = _
 
   @Input(doc = "The reference file for the bam files.", shortName = "ref")
-  var reference: File = config("reference")
+  var reference: File = null
 
   @Input(doc = "The genome prefix.")
   var genome: File = config("genome")
@@ -73,6 +73,7 @@ class Stampy(val root: Configurable) extends BiopetCommandLineFunction {
   override def beforeGraph: Unit = {
     super.beforeGraph
     require(readgroup != null)
+    if (reference == null) reference = referenceFasta()
   }
 
   /** Returns command to execute */

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala

@@ -17,16 +17,16 @@ package nl.lumc.sasc.biopet.extensions
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.core.{ Reference, BiopetCommandLineFunction }
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
 
 /**
  * Extension for STAR
  */
-class Star(val root: Configurable) extends BiopetCommandLineFunction {
+class Star(val root: Configurable) extends BiopetCommandLineFunction with Reference {
   @Input(doc = "The reference file for the bam files.", required = false)
-  var reference: File = new File(config("reference"))
+  var reference: File = null
 
   @Input(doc = "Fastq file R1", required = false)
   var R1: File = _
@@ -57,7 +57,7 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction {
   @Argument(doc = "Output Directory")
   var outputDir: File = _
 
-  var genomeDir: File = config("genomeDir", new File(reference.getAbsoluteFile.getParent, "star"))
+  var genomeDir: File = null
   var runmode: String = _
   var sjdbOverhang: Int = _
   var outFileNamePrefix: String = _
@@ -68,6 +68,9 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction {
 
   /** Sets output files for the graph */
   override def beforeGraph() {
+    super.beforeGraph
+    if (reference == null) reference = referenceFasta()
+    genomeDir = config("genomeDir", new File(reference.getAbsoluteFile.getParent, "star"))
     if (outFileNamePrefix != null && !outFileNamePrefix.endsWith(".")) outFileNamePrefix += "."
     val prefix = if (outFileNamePrefix != null) outputDir + outFileNamePrefix else outputDir
     if (runmode == null) {

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala

@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.core.{ Reference, BiopetCommandLineFunction }
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
 
@@ -25,7 +25,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
  * Extension for VariantEffectPredictor
  * Created by ahbbollen on 15-1-15.
  */
-class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFunction {
+class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFunction with Reference {
 
   executable = config("exe", submodule = "perl", default = "perl")
   var vep_script: String = config("vep_script")

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala

@@ -17,6 +17,7 @@ package nl.lumc.sasc.biopet.extensions.bwa
 
 import java.io.File
 
+import nl.lumc.sasc.biopet.core.Reference
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
 
@@ -27,12 +28,12 @@ import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
  *
  * Created by pjvan_thof on 1/16/15.
  */
-class BwaAln(val root: Configurable) extends Bwa {
+class BwaAln(val root: Configurable) extends Bwa with Reference {
   @Input(doc = "Fastq file", required = true)
   var fastq: File = _
 
   @Input(doc = "The reference file for the bam files.", required = true)
-  var reference: File = config("reference")
+  var reference: File = null
 
   @Output(doc = "Output file SAM", required = false)
   var output: File = _
@@ -63,6 +64,11 @@ class BwaAln(val root: Configurable) extends Bwa {
   override val defaultCoreMemory = 4.0
   override val defaultThreads = 8
 
+  override def beforeGraph {
+    super.beforeGraph
+    if (reference == null) reference = referenceFasta()
+  }
+
   /** Returns command to execute */
   def cmdLine = required(executable) +
     required("aln") +

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala

@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions.bwa
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.core.{ Reference, BiopetCommandLineFunction }
 import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.core.summary.Summarizable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
@@ -27,7 +27,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
  *
  * Based on version 0.7.12-r1039
  */
-class BwaMem(val root: Configurable) extends Bwa {
+class BwaMem(val root: Configurable) extends Bwa with Reference {
   @Input(doc = "Fastq file R1", shortName = "R1")
   var R1: File = _
 
@@ -35,7 +35,7 @@ class BwaMem(val root: Configurable) extends Bwa {
   var R2: File = _
 
   @Input(doc = "The reference file for the bam files.", shortName = "R")
-  var reference: File = config("reference")
+  var reference: File = null
 
   @Output(doc = "Output file SAM", shortName = "output")
   var output: File = _
@@ -72,6 +72,11 @@ class BwaMem(val root: Configurable) extends Bwa {
   override val defaultCoreMemory = 4.0
   override val defaultThreads = 8
 
+  override def beforeGraph {
+    super.beforeGraph
+    if (reference == null) reference = referenceFasta()
+  }
+
   def cmdLine = {
     required(executable) +
       required("mem") +

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala

@@ -17,6 +17,7 @@ package nl.lumc.sasc.biopet.extensions.bwa
 
 import java.io.File
 
+import nl.lumc.sasc.biopet.core.Reference
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
 
@@ -26,7 +27,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
  * based on executable version 0.7.10-r789
  *
  */
-class BwaSampe(val root: Configurable) extends Bwa {
+class BwaSampe(val root: Configurable) extends Bwa with Reference {
   @Input(doc = "Fastq file R1", required = true)
   var fastqR1: File = _
 
@@ -40,7 +41,7 @@ class BwaSampe(val root: Configurable) extends Bwa {
   var saiR2: File = _
 
   @Input(doc = "The reference file for the bam files.", required = true)
-  var reference: File = config("reference")
+  var reference: File = null
 
   @Output(doc = "Output file SAM", required = false)
   var output: File = _
@@ -56,6 +57,11 @@ class BwaSampe(val root: Configurable) extends Bwa {
 
   var r: String = _
 
+  override def beforeGraph {
+    super.beforeGraph
+    if (reference == null) reference = referenceFasta()
+  }
+
   def cmdLine = required(executable) +
     required("sampe") +
     optional("-a", a) +

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala

@@ -17,6 +17,7 @@ package nl.lumc.sasc.biopet.extensions.bwa
 
 import java.io.File
 
+import nl.lumc.sasc.biopet.core.Reference
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
 
@@ -26,7 +27,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
  * based on executable version 0.7.10-r789
  *
  */
-class BwaSamse(val root: Configurable) extends Bwa {
+class BwaSamse(val root: Configurable) extends Bwa with Reference {
   @Input(doc = "Fastq file", required = true)
   var fastq: File = _
 
@@ -34,7 +35,7 @@ class BwaSamse(val root: Configurable) extends Bwa {
   var sai: File = _
 
   @Input(doc = "The reference file for the bam files.", required = true)
-  var reference: File = config("reference")
+  var reference: File = null
 
   @Output(doc = "Output file SAM", required = false)
   var output: File = _
@@ -42,6 +43,11 @@ class BwaSamse(val root: Configurable) extends Bwa {
   var n: Option[Int] = config("n")
   var r: String = _
 
+  override def beforeGraph {
+    super.beforeGraph
+    if (reference == null) reference = referenceFasta()
+  }
+
   /** Returns command to execute */
   def cmdLine = required(executable) +
     required("samse") +

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/Gatk.scala

@@ -17,14 +17,14 @@ package nl.lumc.sasc.biopet.extensions.gatk
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
+import nl.lumc.sasc.biopet.core.{ Reference, BiopetJavaCommandLineFunction }
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.Input
 
 /**
  * Created by pjvan_thof on 2/26/15.
  */
-abstract class Gatk extends BiopetJavaCommandLineFunction {
+abstract class Gatk extends BiopetJavaCommandLineFunction with Reference {
   override def subPath = "gatk" :: super.subPath
 
   jarFile = config("gatk_jar")
@@ -34,7 +34,7 @@ abstract class Gatk extends BiopetJavaCommandLineFunction {
   override val defaultCoreMemory = 3.0
 
   @Input(required = true)
-  var reference: File = config("reference")
+  var reference: File = null
 
   @Input(required = false)
   var gatkKey: Option[File] = config("gatk_key")
@@ -48,6 +48,13 @@ abstract class Gatk extends BiopetJavaCommandLineFunction {
   @Input(required = false)
   var pedigree: List[File] = config("pedigree", default = Nil)
 
+  override def dictRequired = true
+
+  override def beforeGraph: Unit = {
+    super.beforeGraph
+    if (reference == null) reference = referenceFasta()
+  }
+
   override def commandLine = super.commandLine +
     required("-T", analysisType) +
     required("-R", reference) +

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BedToIntervalList.scala

@@ -2,20 +2,21 @@ package nl.lumc.sasc.biopet.extensions.picard
 
 import java.io.File
 
+import nl.lumc.sasc.biopet.core.Reference
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
 
 /**
  * Created by pjvan_thof on 4/15/15.
  */
-class BedToIntervalList(val root: Configurable) extends Picard {
+class BedToIntervalList(val root: Configurable) extends Picard with Reference {
   javaMainClass = new picard.util.BedToIntervalList().getClass.getName
 
   @Input(doc = "Input bed file", required = true)
   var input: File = null
 
   @Input(doc = "Reference dict file", required = true)
-  var dict: File = new File(config("reference").asString.stripSuffix(".fa").stripSuffix(".fasta") + ".dict")
+  var dict: File = new File(referenceFasta().toString.stripSuffix(".fa").stripSuffix(".fasta") + ".dict")
 
   @Output(doc = "Output interval list", required = true)
   var output: File = null

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CalculateHsMetrics.scala

@@ -16,12 +16,13 @@
 package nl.lumc.sasc.biopet.extensions.picard
 
 import java.io.File
+import nl.lumc.sasc.biopet.core.Reference
 import nl.lumc.sasc.biopet.core.config.Configurable