Switch pipeline to reference module

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"),
+    "referenceFasta" -> (outputDir + File.separator + "ref.fa"),
     "gatk_jar" -> "test",
     "samtools" -> Map("exe" -> "test"),
     "bcftools" -> Map("exe" -> "test"),

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 = referenceFasta()
 
   @Output(doc = "Output file SAM", shortName = "output")
   var output: File = _

public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala

@@ -35,7 +35,7 @@ import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
  * Chip-Seq analysis pipeline
  * This pipeline performs QC,mapping and peak calling
  */
-class Carp(val root: Configurable) extends QScript with MultiSampleQScript with SummaryQScript {
+class Carp(val root: Configurable) extends QScript with MultiSampleQScript with SummaryQScript with Reference {
   qscript =>
   def this() = this(null)
 

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

+>chr1
+AGTAGTAGT

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

+chr1	9	6	9	10

public/carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala

@@ -15,7 +15,7 @@
  */
 package nl.lumc.sasc.biopet.pipelines.carp
 
-import java.io.File
+import java.io.{ FileOutputStream, File }
 
 import com.google.common.io.Files
 import org.apache.commons.io.FileUtils
@@ -97,8 +97,20 @@ class CarpTest extends TestNGSuite with Matchers {
 object CarpTest {
   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(
-    "reference" -> "test",
+    "reference" -> (outputDir + File.separator + "ref.fa"),
+    "referenceFasta" -> (outputDir + File.separator + "ref.fa"),
     "fastqc" -> Map("exe" -> "test"),
     "seqtk" -> Map("exe" -> "test"),
     "sickle" -> Map("exe" -> "test"),

public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala

@@ -21,10 +21,9 @@ import scala.math._
 
 import org.broadinstitute.gatk.queue.QScript
 
-import nl.lumc.sasc.biopet.core.{ SampleLibraryTag, PipelineCommand }
+import nl.lumc.sasc.biopet.core._
 import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
-import nl.lumc.sasc.biopet.core.{ SampleLibraryTag, BiopetQScript, PipelineCommand }
 import nl.lumc.sasc.biopet.extensions._
 import nl.lumc.sasc.biopet.extensions.bwa.{ BwaSamse, BwaSampe, BwaAln, BwaMem }
 import nl.lumc.sasc.biopet.extensions.{ Gsnap, Tophat }
@@ -35,7 +34,7 @@ import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
 import nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
 
 // TODO: documentation
-class Mapping(val root: Configurable) extends QScript with SummaryQScript with SampleLibraryTag {
+class Mapping(val root: Configurable) extends QScript with SummaryQScript with SampleLibraryTag with Reference {
 
   def this() = this(null)
 
@@ -112,7 +111,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
     "aligner" -> aligner,
     "chunking" -> chunking,
     "numberChunks" -> numberChunks.getOrElse(1)
-  )
+  ) ++ (if (root == null) Map() else Map("reference" -> referenceSummary))
 
   /** Will be executed before script */
   def init() {

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

+>chr1
+AGTAGTAGT

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

+chr1	9	6	9	10

public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala

@@ -15,7 +15,7 @@
  */
 package nl.lumc.sasc.biopet.pipelines.mapping
 
-import java.io.File
+import java.io.{ FileOutputStream, File }
 
 import com.google.common.io.Files
 import nl.lumc.sasc.biopet.extensions._
@@ -130,8 +130,20 @@ class MappingTest extends TestNGSuite with Matchers {
 object MappingTest {
   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(
-    "reference" -> "test",
+    "reference" -> (outputDir + File.separator + "ref.fa"),
+    "referenceFasta" -> (outputDir + File.separator + "ref.fa"),
     "fastqc" -> Map("exe" -> "test"),
     "seqtk" -> Map("exe" -> "test"),
     "sickle" -> Map("exe" -> "test"),

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

@@ -19,7 +19,7 @@ import java.io.File
 
 import htsjdk.samtools.SamReaderFactory
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
-import nl.lumc.sasc.biopet.core.MultiSampleQScript
+import nl.lumc.sasc.biopet.core.{ Reference, MultiSampleQScript }
 import nl.lumc.sasc.biopet.extensions.Ln
 import nl.lumc.sasc.biopet.extensions.picard.{ AddOrReplaceReadGroups, SamToFastq, MarkDuplicates }
 import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
@@ -31,7 +31,7 @@ import scala.collection.JavaConversions._
  *
  * Created by pjvan_thof on 2/26/15.
  */
-trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
+trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
   qscript =>
 
   /** Executed before running the script */
@@ -286,8 +286,8 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
   def summaryFile = new File(outputDir, "Shiva.summary.json")
 
   /** Settings of pipeline for summary */
-  def summarySettings = Map()
+  def summarySettings = Map("reference" -> referenceSummary)
 
   /** Files for the summary */
-  def summaryFiles = Map()
+  def summaryFiles = Map("referenceFasta" -> referenceFasta())
 }

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

+>chr1
+AGTAGTAGT

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

+chr1	9	6	9	10

public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala

@@ -15,6 +15,8 @@
  */
 package nl.lumc.sasc.biopet.pipelines.shiva
 
+import java.io.{ File, FileOutputStream }
+
 import com.google.common.io.Files
 import nl.lumc.sasc.biopet.core.config.Config
 import nl.lumc.sasc.biopet.extensions.bwa.BwaMem
@@ -85,10 +87,22 @@ 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"),
+    "referenceFasta" -> (outputDir + File.separator + "ref.fa"),
     "gatk_jar" -> "test",
     "samtools" -> Map("exe" -> "test"),
     "bcftools" -> Map("exe" -> "test"),