make varda annotation optional (on by default).

toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/ManweActivateAfterAnnotImport.scala → toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/ManweActivateAfterImport.scala

@@ -25,15 +25,12 @@ import scala.io.Source
  * Created by ahbbollen on 9-10-15.
  * Wrapper for manwe activate after importing and annotating
  */
-class ManweActivateAfterAnnotImport(root: Configurable,
-                                    annotate: ManweAnnotateVcf,
+class ManweActivateAfterImport(root: Configurable,
                                imported: ManweSamplesImport) extends ManweSamplesActivate(root) {
 
   override def beforeGraph: Unit = {
     super.beforeGraph
-    require(annotate != null, "Annotate should be defined")
     require(imported != null, "Imported should be defined")
-    this.deps :+= annotate.jobOutputFile
     this.deps :+= imported.jobOutputFile
   }
 

toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala

@@ -170,11 +170,11 @@ class Toucan(val parent: Configurable) extends QScript with BiopetQScript with S
    * @param sampleID the sampleID to be used
    * @param inputVcf the input VCF
    * @param gVCF the gVCF for coverage
-   * @param annotation: ManweDownloadAnnotateVcf object of annotated vcf
+   * @param annotation: Optional ManweDownloadAnnotateVcf object of annotated vcf
    * @return
    */
   def importAndActivateSample(sampleID: String, sampleGroups: List[String], inputVcf: File,
-                              gVCF: File, annotation: ManweAnnotateVcf): ManweActivateAfterAnnotImport = {
+                              gVCF: File, annotation: Option[ManweAnnotateVcf]): ManweActivateAfterImport = {
 
     val minGQ: Int = config("minimum_genome_quality", default = 20, namespace = "manwe")
     val isPublic: Boolean = config("varda_is_public", default = true, namespace = "manwe")
@@ -228,7 +228,8 @@ class Toucan(val parent: Configurable) extends QScript with BiopetQScript with S
     imported.output = swapExt(outputDir, intersected.output, ".vcf.gz", ".manwe.import")
     add(imported)
 
-    val active = new ManweActivateAfterAnnotImport(this, annotation, imported)
+    val active = new ManweActivateAfterImport(this, imported)
+    annotation.foreach(a => active.deps :+= a.jobOutputFile)
     active.output = swapExt(outputDir, imported.output, ".import", ".activated")
     add(active)
     active
@@ -236,7 +237,7 @@ class Toucan(val parent: Configurable) extends QScript with BiopetQScript with S
   }
 
   /**
-   * Perform varda analysis
+   * Import to and optionally annotate with varda
    *
    * @param vcf input vcf
    * @param gVcf The gVCF to be used for coverage calculations
@@ -245,7 +246,23 @@ class Toucan(val parent: Configurable) extends QScript with BiopetQScript with S
   def varda(vcf: File, gVcf: File): File = {
 
     val annotationQueries: List[String] = config("annotation_queries", default = List("GLOBAL *"), namespace = "manwe")
+    val doAnnotate: Boolean = config("annotate", namespace = "varda", default = true)
 
+    val sampleGroups = sampleInfo map { x =>
+      val maybeSampleGroup = x._2.get("varda_group") match {
+        case None => Some(Nil)
+        case Some(vals) => vals match {
+          case xs: List[_] => xs
+            .traverse[Option, String] { x => Option(x.toString).filter(_ == x) }
+          case otherwise => None
+        }
+      }
+      val sampleGroup = maybeSampleGroup
+        .getOrElse(throw new IllegalArgumentException("Sample tag 'varda_group' is not a list of strings"))
+      x._1 -> sampleGroup
+    }
+
+    if (doAnnotate) {
       val annotate = new ManweAnnotateVcf(this)
       annotate.vcf = vcf
       if (annotationQueries.nonEmpty) {
@@ -260,18 +277,8 @@ class Toucan(val parent: Configurable) extends QScript with BiopetQScript with S
       annotatedVcf.output = swapExt(outputDir, annotate.output, ".manwe.annot", "manwe.annot.vcf.gz")
       add(annotatedVcf)
 
-    val activates = sampleInfo map { x =>
-      val maybeSampleGroup = x._2.get("varda_group") match {
-        case None => Some(Nil)
-        case Some(vals) => vals match {
-          case xs: List[_] => xs
-            .traverse[Option, String] { x => Option(x.toString).filter(_ == x) }
-          case otherwise => None
-        }
-      }
-      val sampleGroup = maybeSampleGroup
-        .getOrElse(throw new IllegalArgumentException("Sample tag 'varda_group' is not a list of strings"))
-      importAndActivateSample(x._1, sampleGroup, vcf, gVcf, annotate)
+      val activates = sampleGroups map { x =>
+        importAndActivateSample(x._1, x._2, vcf, gVcf, Some(annotate))
       }
 
       val finalLn = new Ln(this)
@@ -282,6 +289,12 @@ class Toucan(val parent: Configurable) extends QScript with BiopetQScript with S
       add(finalLn)
 
       finalLn.output
+    } else {
+      sampleGroups.foreach { x =>
+        importAndActivateSample(x._1, x._2, vcf, gVcf, None)
+      }
+      vcf
+    }
   }
 
   def summaryFiles = Map("input_vcf" -> inputVcf, "outputVcf" -> outputVcf)