Remove "reference" from testing

(cherry picked from commit 8bf162ad)

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

@@ -109,7 +109,6 @@ object ShivaTest {
     "dir" -> "test",
     "vep_script" -> "test",
     "output_dir" -> outputDir,
-    "reference" -> (outputDir + File.separator + "ref.fa"),
     "reference_fasta" -> (outputDir + File.separator + "ref.fa"),
     "gatk_jar" -> "test",
     "samtools" -> Map("exe" -> "test"),

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

@@ -131,7 +131,6 @@ object ShivaVariantcallingTest {
     "cache" -> true,
     "dir" -> "test",
     "vep_script" -> "test",
-    "reference" -> (outputDir + File.separator + "ref.fa"),
     "reference_fasta" -> (outputDir + File.separator + "ref.fa"),
     "gatk_jar" -> "test",
     "samtools" -> Map("exe" -> "test"),

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

@@ -17,12 +17,13 @@ package nl.lumc.sasc.biopet.extensions.picard
 
 import java.io.File
 
+import nl.lumc.sasc.biopet.core.Reference
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.core.summary.Summarizable
 import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
 
 /** Extension for picard CollectAlignmentSummaryMetrics */
-class CollectAlignmentSummaryMetrics(val root: Configurable) extends Picard with Summarizable {
+class CollectAlignmentSummaryMetrics(val root: Configurable) extends Picard with Summarizable with Reference {
   javaMainClass = new picard.analysis.CollectAlignmentSummaryMetrics().getClass.getName
 
   @Input(doc = "The input SAM or BAM files to analyze.  Must be coordinate sorted.", required = true)
@@ -41,7 +42,7 @@ class CollectAlignmentSummaryMetrics(val root: Configurable) extends Picard with
   var output: File = _
 
   @Argument(doc = "Reference file", required = false)
-  var reference: File = config("reference")
+  var reference: File = _
 
   @Argument(doc = "ASSUME_SORTED", required = false)
   var assumeSorted: Boolean = config("assumeSorted", default = true)
@@ -52,6 +53,11 @@ class CollectAlignmentSummaryMetrics(val root: Configurable) extends Picard with
   @Argument(doc = "STOP_AFTER", required = false)
   var stopAfter: Option[Long] = config("stopAfter")
 
+  override def beforeGraph(): Unit = {
+    super.beforeGraph()
+    if (reference == null) reference = referenceFasta()
+  }
+
   /** Returns command to execute */
   override def cmdLine = super.cmdLine +
     required("INPUT=", input, spaceSeparated = false) +

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

@@ -17,6 +17,7 @@ package nl.lumc.sasc.biopet.extensions.picard
 
 import java.io.File
 
+import nl.lumc.sasc.biopet.core.Reference
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.core.summary.Summarizable
 import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
@@ -24,7 +25,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
 import scala.collection.immutable.Nil
 
 /** Extension for picard CollectInsertSizeMetrics */
-class CollectInsertSizeMetrics(val root: Configurable) extends Picard with Summarizable {
+class CollectInsertSizeMetrics(val root: Configurable) extends Picard with Summarizable with Reference {
   javaMainClass = new picard.analysis.CollectInsertSizeMetrics().getClass.getName
 
   @Input(doc = "The input SAM or BAM files to analyze.  Must be coordinate sorted.", required = true)
@@ -37,7 +38,7 @@ class CollectInsertSizeMetrics(val root: Configurable) extends Picard with Summa
   protected var outputHistogram: File = null
 
   @Argument(doc = "Reference file", required = false)
-  var reference: File = config("reference")
+  var reference: File = _
 
   @Argument(doc = "DEVIATIONS", required = false)
   var deviations: Option[Double] = config("deviations")
@@ -59,6 +60,7 @@ class CollectInsertSizeMetrics(val root: Configurable) extends Picard with Summa
 
   override def beforeGraph() {
     outputHistogram = new File(output + ".pdf")
+    if (reference == null) reference = referenceFasta()
   }
 
   /** Returns command to execute */

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

@@ -116,7 +116,6 @@ object CarpTest {
   copyFile("ref.fa.fai")
 
   val executables = Map(
-    "reference" -> (outputDir + File.separator + "ref.fa"),
     "reference_fasta" -> (outputDir + File.separator + "ref.fa"),
     "fastqc" -> Map("exe" -> "test"),
     "seqtk" -> Map("exe" -> "test"),

public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala

@@ -198,7 +198,6 @@ object GentrapTest {
   copyFile("ref.fa.fai")
 
   val executables = Map(
-    "reference" -> (outputDir + File.separator + "ref.fa"),
     "reference_fasta" -> (outputDir + File.separator + "ref.fa"),
     "refFlat" -> "test",
     "annotation_gtf" -> "test",

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

@@ -109,7 +109,6 @@ object ShivaTest {
     "cache" -> true,
     "dir" -> "test",
     "vep_script" -> "test",
-    "reference" -> (outputDir + File.separator + "ref.fa"),
     "reference_fasta" -> (outputDir + File.separator + "ref.fa"),
     "gatk_jar" -> "test",
     "samtools" -> Map("exe" -> "test"),

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

@@ -112,7 +112,6 @@ object ShivaVariantcallingTest {
     "cache" -> true,
     "dir" -> "test",
     "vep_script" -> "test",
-    "reference" -> (outputDir + File.separator + "ref.fa"),
     "reference_fasta" -> (outputDir + File.separator + "ref.fa"),
     "gatk_jar" -> "test",
     "samtools" -> Map("exe" -> "test"),