Merge branch 'toucan-groups' into 'develop'

Toucan groups

Fixes #315 and adds some for #324 

See merge request !385

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

@@ -156,9 +156,9 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
   override def beforeGraph(): Unit = {
     super.beforeGraph()
     if (!cache && !database) {
-      Logging.addError("Must supply either cache or database for VariantEffectPredictor")
+      Logging.addError("Must either set 'cache' or 'database' to true for VariantEffectPredictor")
     } else if (cache && dir.isEmpty) {
-      Logging.addError("Must supply dir to cache for VariantEffectPredictor")
+      Logging.addError("Must supply 'dir_cache' to cache for VariantEffectPredictor")
     }
     if (statsText) _summary = new File(output.getAbsolutePath + "_summary.txt")
   }

docs/pipelines/toucan.md

@@ -83,6 +83,25 @@ The following config values are optional:
 Annotation queries can be set by the `annotation_queries` config value in the `manwe` config namespace. 
 By default, a global query is returned. 
 
+
+###Groups
+In case you want to add your samples to a specific group in your varda database, you can use the tagging system in your sample config.
+Specifically, the `varda_group` tag should be a list of strings pointing to group. 
+
+E.g. :
+
+```json
+{
+    "samples": {
+        "sample1": {
+            "tags": {
+                "varda_group": ["group1", "group2"]
+            }
+        }
+    }
+}
+```
+
 Running the pipeline
 ---------------
 The command to run the pipeline is:

toucan/pom.xml

@@ -43,5 +43,17 @@
             <artifactId>BiopetToolsExtensions</artifactId>
             <version>${project.version}</version>
         </dependency>
+        <dependency>
+            <groupId>org.testng</groupId>
+            <artifactId>testng</artifactId>
+            <version>6.8</version>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.scalatest</groupId>
+            <artifactId>scalatest_2.10</artifactId>
+            <version>2.2.1</version>
+            <scope>test</scope>
+        </dependency>
     </dependencies>
 </project>

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

@@ -40,15 +40,17 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
   @Input(doc = "Input GVCF file", shortName = "gvcf", required = false)
   var inputGvcf: Option[File] = None
 
-  var sampleIds: List[String] = Nil
+  var outputVcf: Option[File] = None
+
+  def sampleInfo: Map[String, Map[String, Any]] = root match {
+    case m: MultiSampleQScript => m.samples.map { case (sampleId, sample) => sampleId -> sample.sampleTags }
+    case null                  => VcfUtils.getSampleIds(inputVCF).map(x => x -> Map[String, Any]()).toMap
+    case s: SampleLibraryTag   => s.sampleId.map(x => x -> Map[String, Any]()).toMap
+    case _                     => throw new IllegalArgumentException("")
+  }
+
   def init(): Unit = {
     inputFiles :+= new InputFile(inputVCF)
-    sampleIds = root match {
-      case m: MultiSampleQScript => m.samples.keys.toList
-      case null                  => VcfUtils.getSampleIds(inputVCF)
-      case s: SampleLibraryTag   => s.sampleId.toList
-      case _                     => throw new IllegalArgumentException("You don't have any samples")
-    }
   }
 
   override def defaults = Map(
@@ -79,29 +81,29 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
     val gonlVcfFile: Option[File] = config("gonl_vcf")
     val exacVcfFile: Option[File] = config("exac_vcf")
 
-    var outputFile = normalizer.outputVcf
+    outputVcf = Some(normalizer.outputVcf)
 
     gonlVcfFile match {
       case Some(gonlFile) =>
         val vcfWithVcf = new VcfWithVcf(this)
-        vcfWithVcf.input = outputFile
+        vcfWithVcf.input = outputVcf.getOrElse(new File(""))
         vcfWithVcf.secondaryVcf = gonlFile
         vcfWithVcf.output = swapExt(outputDir, normalizer.outputVcf, ".vcf.gz", ".gonl.vcf.gz")
         vcfWithVcf.fields ::= ("AF", "AF_gonl", None)
         add(vcfWithVcf)
-        outputFile = vcfWithVcf.output
+        outputVcf = Some(vcfWithVcf.output)
       case _ =>
     }
 
     exacVcfFile match {
       case Some(exacFile) =>
         val vcfWithVcf = new VcfWithVcf(this)
-        vcfWithVcf.input = outputFile
+        vcfWithVcf.input = outputVcf.getOrElse(new File(""))
         vcfWithVcf.secondaryVcf = exacFile
-        vcfWithVcf.output = swapExt(outputDir, outputFile, ".vcf.gz", ".exac.vcf.gz")
+        vcfWithVcf.output = swapExt(outputDir, outputVcf.getOrElse(new File("")), ".vcf.gz", ".exac.vcf.gz")
         vcfWithVcf.fields ::= ("AF", "AF_exac", None)
         add(vcfWithVcf)
-        outputFile = vcfWithVcf.output
+        outputVcf = Some(vcfWithVcf.output)
       case _ =>
     }
 
@@ -116,7 +118,7 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
    * @param annotation: ManweDownloadAnnotateVcf object of annotated vcf
    * @return
    */
-  def importAndActivateSample(sampleID: String, inputVcf: File,
+  def importAndActivateSample(sampleID: String, sampleGroups: List[String], inputVcf: File,
                               gVCF: File, annotation: ManweAnnotateVcf): ManweActivateAfterAnnotImport = {
 
     val minGQ: Int = config("minimum_genome_quality", default = 20, namespace = "manwe")
@@ -165,6 +167,7 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
     imported.beds = List(bgzippedBed.output)
     imported.name = Some(sampleID)
     imported.public = isPublic
+    imported.group = sampleGroups
     imported.waitToComplete = false
     imported.isIntermediate = true
     imported.output = swapExt(outputDir, intersected.output, ".vcf.gz", ".manwe.import")
@@ -186,7 +189,6 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
   def varda(vcf: File, gVcf: File): File = {
 
     val annotationQueries: List[String] = config("annotation_queries", default = List("GLOBAL *"), namespace = "manwe")
-    //TODO: add groups!!! Need sample-specific group tags for this
 
     val annotate = new ManweAnnotateVcf(this)
     annotate.vcf = vcf
@@ -202,7 +204,14 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
     annotatedVcf.output = swapExt(outputDir, annotate.output, ".manwe.annot", "manwe.annot.vcf.gz")
     add(annotatedVcf)
 
-    val activates = sampleIds map { x => importAndActivateSample(x, vcf, gVcf, annotate) }
+    val activates = sampleInfo map { x =>
+      val sampleGroup = x._2.getOrElse("varda_group", Nil) match {
+        case x: List[String] => x
+        case Nil             => Nil
+        case _               => throw new IllegalArgumentException("Sample tag 'varda_group' is not a list of strings")
+      }
+      importAndActivateSample(x._1, sampleGroup, vcf, gVcf, annotate)
+    }
 
     val finalLn = new Ln(this)
     activates.foreach(x => finalLn.deps :+= x.output)