Added more summary testing

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

@@ -33,10 +33,18 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
 
   def this() = this(null)
 
-  case class FastaOutput(variants: File, consensus: File, consensusVariants: File)
+  case class FastaOutput(variants: File, consensus: File, consensusVariants: File) {
+    def summaryFiles(prefix: Option[String] = None) = Map(
+      s"${prefix.map(_ + "_").getOrElse("")}variants_fasta" -> variants,
+      s"${prefix.map(_ + "_").getOrElse("")}consensus_fasta" -> consensus,
+      s"${prefix.map(_ + "_").getOrElse("")}consensus_variants_fasta" -> consensusVariants
+    )
+  }
 
   def variantcallers = List("unifiedgenotyper")
 
+  val numBoot = config("boot_runs", default = 100, namespace = "raxml").asInt
+
   override def defaults = Map(
     "ploidy" -> 1,
     "variantcallers" -> variantcallers
@@ -46,25 +54,25 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
 
   def summaryFile: File = new File(outputDir, "Basty.summary.json")
 
-  def summaryFiles: Map[String, File] = shiva.summaryFiles
+  def summaryFiles: Map[String, File] = Map()
 
-  def summarySettings: Map[String, Any] = shiva.summarySettings
+  def summarySettings: Map[String, Any] = Map("boot_runs" -> numBoot)
 
   def makeSample(id: String) = new Sample(id)
   class Sample(sampleId: String) extends AbstractSample(sampleId) {
-    def summaryFiles: Map[String, File] = shiva.samples(sampleId).summaryFiles
+    def summaryFiles: Map[String, File] = output.summaryFiles() ++ outputSnps.summaryFiles(Some("snps_only"))
 
-    def summaryStats: Map[String, Any] = shiva.samples(sampleId).summaryStats
+    def summaryStats: Map[String, Any] = Map()
 
-    override def summarySettings: Map[String, Any] = shiva.samples(sampleId).summarySettings
+    override def summarySettings: Map[String, Any] = Map()
 
     def makeLibrary(id: String) = new Library(id)
     class Library(libId: String) extends AbstractLibrary(libId) {
-      def summaryFiles: Map[String, File] = shiva.samples(sampleId).libraries(libId).summaryFiles
+      def summaryFiles: Map[String, File] = Map()
 
-      def summaryStats: Map[String, Any] = shiva.samples(sampleId).libraries(libId).summaryStats
+      def summaryStats: Map[String, Any] = Map()
 
-      override def summarySettings: Map[String, Any] = shiva.samples(sampleId).libraries(libId).summarySettings
+      override def summarySettings: Map[String, Any] = Map()
 
       protected def addJobs(): Unit = {}
     }
@@ -134,7 +142,6 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
       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

basty/src/test/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTest.scala

@@ -88,19 +88,23 @@ class BastyTest extends TestNGSuite with Matchers {
       pipeline.functions.count(_.isInstanceOf[BaseRecalibrator]) shouldBe (if (dbsnp && baseRecalibration) (numberLibs * 2) else 0)
       pipeline.functions.count(_.isInstanceOf[PrintReads]) shouldBe (if (dbsnp && baseRecalibration) numberLibs else 0)
 
-      pipeline.summarySettings.get("annotation") shouldBe Some(annotation)
-      pipeline.summarySettings.get("sv_calling") shouldBe Some(svCalling)
-      pipeline.summarySettings.get("cnv_calling") shouldBe Some(cnvCalling)
+      pipeline.summarySettings.get("boot_runs") shouldBe Some(bootRuns.getOrElse(100))
 
       pipeline.samples foreach {
         case (sampleId, sample) =>
-          sample.summarySettings.get("single_sample_variantcalling") shouldBe Some(sampleCalling)
-          sample.summarySettings.get("use_indel_realigner") shouldBe Some(realign)
+          sample.summarySettings shouldBe Map()
+          sample.summaryFiles.get("variants_fasta") should not be None
+          sample.summaryFiles.get("consensus_fasta") should not be None
+          sample.summaryFiles.get("consensus_variants_fasta") should not be None
+          sample.summaryFiles.get("snps_only_variants_fasta") should not be None
+          sample.summaryFiles.get("snps_only_consensus_fasta") should not be None
+          sample.summaryFiles.get("snps_only_consensus_variants_fasta") should not be None
+          sample.summaryStats shouldBe Map()
           sample.libraries.foreach {
             case (libId, lib) =>
-              lib.summarySettings.get("library_variantcalling") shouldBe Some(libraryCalling)
-              lib.summarySettings.get("use_indel_realigner") shouldBe Some(realign)
-              lib.summarySettings.get("use_base_recalibration") shouldBe Some(baseRecalibration && dbsnp)
+              lib.summarySettings shouldBe Map()
+              lib.summaryFiles shouldBe Map()
+              lib.summaryStats shouldBe Map()
           }
       }