Merge remote-tracking branch 'remotes/origin/develop' into feature-qiime

biopet-aggregate/copy-src.sh

-#!/bin/bash
-
-DIR=`readlink -f \`dirname $0\``
-
-cp -r $DIR/../*/*/src/* $DIR/src
-

biopet-aggregate/pom.xml

@@ -2,45 +2,42 @@
 <project xmlns="http://maven.apache.org/POM/4.0.0"
          xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
          xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
-    <parent>
-        <artifactId>BiopetRoot</artifactId>
-        <groupId>nl.lumc.sasc</groupId>
-        <version>0.6.0-SNAPSHOT</version>
-    </parent>
+
     <modelVersion>4.0.0</modelVersion>
 
     <artifactId>BiopetAggregate</artifactId>
+    <packaging>pom</packaging>
 
-    <dependencies>
-        <dependency>
-            <groupId>org.testng</groupId>
-            <artifactId>testng</artifactId>
-            <version>6.8</version>
-            <scope>test</scope>
-        </dependency>
-        <dependency>
-            <groupId>org.mockito</groupId>
-            <artifactId>mockito-all</artifactId>
-            <version>1.9.5</version>
-            <scope>test</scope>
-        </dependency>
-        <dependency>
-            <groupId>org.scalatest</groupId>
-            <artifactId>scalatest_2.10</artifactId>
-            <version>2.2.1</version>
-            <scope>test</scope>
-        </dependency>
-        <dependency>
-            <groupId>nl.lumc.sasc</groupId>
-            <artifactId>BiopetProtectedPackage</artifactId>
-            <version>0.6.0-SNAPSHOT</version>
-        </dependency>
-        <dependency>
-            <groupId>com.google.guava</groupId>
-            <artifactId>guava</artifactId>
-            <version>18.0</version>
-        </dependency>
+    <parent>
+        <groupId>nl.lumc.sasc</groupId>
+        <artifactId>Biopet</artifactId>
+        <version>0.6.0-SNAPSHOT</version>
+        <relativePath>../public</relativePath>
+    </parent>
 
-    </dependencies>
+    <modules>
+        <module>../public/biopet-core</module>
+        <module>../public/biopet-public-package</module>
+        <module>../public/bammetrics</module>
+        <module>../public/flexiprep</module>
+        <module>../public/gentrap</module>
+        <module>../public/mapping</module>
+        <module>../public/sage</module>
+        <module>../public/kopisu</module>
+        <module>../public/gears</module>
+        <module>../public/bam2wig</module>
+        <module>../public/carp</module>
+        <module>../public/toucan</module>
+        <module>../public/shiva</module>
+        <module>../public/basty</module>
+        <module>../public/biopet-utils</module>
+        <module>../public/biopet-tools</module>
+        <module>../public/biopet-tools-extensions</module>
+        <module>../public/biopet-extensions</module>
+        <module>../public/biopet-tools-package</module>
+        <module>../protected/biopet-gatk-extensions</module>
+        <module>../protected/biopet-gatk-pipelines</module>
+        <module>../protected/biopet-protected-package</module>
+    </modules>
 
 </project>
\ No newline at end of file

biopet-aggregate/rm-src.sh

-#!/bin/bash
-
-DIR=`readlink -f \`dirname $0\``
-
-rm -r $DIR/src/main $DIR/src/test
-

biopet-aggregate/src/.gitignore

-main
-test

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala

@@ -8,10 +8,11 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
 import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.Output
+import org.broadinstitute.gatk.utils.commandline.{ Gather, Output }
 
 class GenotypeGVCFs(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.GenotypeGVCFs with GatkGeneral {
 
+  @Gather(enabled = false)
   @Output(required = false)
   protected var vcfIndex: File = _
 

protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/IndelRealigner.scala

@@ -8,9 +8,11 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
 import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.Output
+import org.broadinstitute.gatk.utils.commandline.{ Gather, Output }
 
 class IndelRealigner(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.IndelRealigner with GatkGeneral {
+
+  @Gather(enabled = false)
   @Output
   protected var bamIndex: File = _
 

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala

@@ -21,7 +21,7 @@ class Shiva(val root: Configurable) extends QScript with ShivaTrait {
   def this() = this(null)
 
   /** Make variantcalling submodule, this with the gatk modes in there */
-  override def makeVariantcalling(multisample: Boolean = false): ShivaVariantcallingTrait = {
+  override def makeVariantcalling(multisample: Boolean = false) = {
     if (multisample) new ShivaVariantcalling(qscript) {
       override def namePrefix = "multisample"
       override def configName = "shivavariantcalling"
@@ -56,36 +56,40 @@ class Shiva(val root: Configurable) extends QScript with ShivaTrait {
         ("use_indel_realigner" -> useIndelRealigner) +
         ("use_base_recalibration" -> useBaseRecalibration)
 
-      /** This will adds preprocess steps, gatk indel realignment and base recalibration is included here */
-      override def preProcess(input: File): Option[File] = {
-        if (!useIndelRealigner && !useBaseRecalibration) None
-        else {
-          val indelRealignFile = useIndelRealigner match {
-            case true  => addIndelRealign(input, libDir, useBaseRecalibration || libraries.size > 1)
-            case false => input
-          }
-
-          useBaseRecalibration match {
-            case true  => Some(addBaseRecalibrator(indelRealignFile, libDir, libraries.size > 1))
-            case false => Some(indelRealignFile)
-          }
+      override def preProcessBam = if (useIndelRealigner && useBaseRecalibration)
+        bamFile.map(swapExt(libDir, _, ".bam", ".realign.baserecal.bam"))
+      else if (useIndelRealigner) bamFile.map(swapExt(libDir, _, ".bam", ".realign.bam"))
+      else if (useBaseRecalibration) bamFile.map(swapExt(libDir, _, ".bam", ".baserecal.bam"))
+      else bamFile
+
+      override def addJobs(): Unit = {
+        super.addJobs()
+        if (useIndelRealigner && useBaseRecalibration) {
+          val file = addIndelRealign(bamFile.get, libDir, isIntermediate = true)
+          addBaseRecalibrator(file, libDir, libraries.size > 1)
+        } else if (useIndelRealigner) {
+          addIndelRealign(bamFile.get, libDir, libraries.size > 1)
+        } else if (useBaseRecalibration) {
+          addBaseRecalibrator(bamFile.get, libDir, libraries.size > 1)
         }
       }
     }
 
+    override def keepMergedFiles: Boolean = config("keep_merged_files", default = false)
+
     override def summarySettings = super.summarySettings + ("use_indel_realigner" -> useIndelRealigner)
 
     lazy val useIndelRealigner: Boolean = config("use_indel_realigner", default = true)
 
-    /** This methods will add double preprocess steps, with GATK indel realignment */
-    override protected def addDoublePreProcess(input: List[File], isIntermediate: Boolean = false): Option[File] = {
-      if (input.size <= 1) super.addDoublePreProcess(input)
-      else super.addDoublePreProcess(input, isIntermediate = useIndelRealigner).collect {
-        case file =>
-          useIndelRealigner match {
-            case true  => addIndelRealign(file, sampleDir, isIntermediate = false)
-            case false => file
-          }
+    override def preProcessBam = if (useIndelRealigner && libraries.values.flatMap(_.preProcessBam).size > 1) {
+      bamFile.map(swapExt(sampleDir, _, ".bam", ".realign.bam"))
+    } else bamFile
+
+    override def addJobs(): Unit = {
+      super.addJobs()
+
+      if (useIndelRealigner && libraries.values.flatMap(_.preProcessBam).size > 1) {
+        addIndelRealign(bamFile.get, sampleDir, false)
       }
     }
   }

public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp

+#import(nl.lumc.sasc.biopet.utils.summary.Summary)
+#import(nl.lumc.sasc.biopet.core.report.ReportPage)
+#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
+#import(java.io.File)
+#import(org.apache.commons.io.FileUtils)
+<%@ var summary: Summary %>
+<%@ var sampleId: Option[String] = None %>
+<%@ var libId: Option[String] = None %>
+<%@ var rootPath: String %>
+<%@ var metricsTag: String = "bammetrics" %>
+<%@ var sampleLevel: Boolean = false %>
+<%@ var outputDir: File %>
+<%@ var fields: List[String] = List("PF_ALIGNED_BASES", "MEDIAN_5PRIME_BIAS", "MEDIAN_3PRIME_BIAS", "MEDIAN_5PRIME_TO_3PRIME_BIAS")%>
+<%@ var showPlot: Boolean = false %>
+<%@ var showTable: Boolean = true %>
+<%@ var showIntro: Boolean = true%>
+#{
+    val samples = sampleId match {
+    case Some(sample) => {
+    List(sample.toString)
+    }
+    case _ => summary.samples.toList
+    }
+}#
+
+#if (showIntro)
+    <br/>
+    <div class="row">
+    <div class="col-md-1"></div>
+    <div class="col-md-6">
+        <p>
+            This Show the relative coverage for all transcripts. De data here is generated by picard CollectRnaMetrics
+        </p>
+    </div>
+    </div>
+#end
+
+#if (showPlot)
+    #{ BammetricsReport.rnaHistogramPlot(outputDir, "rna", summary, !sampleLevel, sampleId = sampleId, libId = libId) }#
+
+    <div class="panel-body">
+    <img src="rna.png" class="img-responsive" />
+    </div>
+    <div class="panel-footer">
+        #if (showTable)
+            <button type="button" class="btn btn-info" data-toggle="collapse" data-target="#rnaTable">Hide table</button>
+        #else
+            <button type="button" class="btn btn-info" data-toggle="collapse" data-target="#rnaTable">Show table</button>
+        #end
+        <i class="glyphicon glyphicon-file"></i> <a href="rna.tsv">tsv file</a>
+    </div>
+#end
+
+<div class="panel-body collapse #if (showTable)in#end" id="rnaTable">
+<!-- Table -->
+<table class="table sortable-theme-bootstrap" data-sortable>
+    <thead><tr>
+        <th data-sorted="true" data-sorted-direction="ascending">Sample</th>
+        #if (!sampleLevel) <th>Library</th> #end
+        #for (field <- fields)
+            <th>${field.replaceAll("_", " ")}</th>
+        #end
+    </tr></thead>
+    <tbody>
+        #for (sample <- samples.toList.sorted)
+            #{
+                val libs = (libId, sampleLevel) match {
+                case (_, true) => List("")
+                case (Some(libId), _) => List(libId.toString)
+                case _ => summary.libraries(sample).toList
+                }
+            }#
+            <tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample}/index.html">${sample}</a></td>
+            #for (libId <- libs)
+                #if (libs.head != libId) <tr> #end
+                    #if (!sampleLevel) <td><a href="${rootPath}Samples/${sample}/Libraries/${libId}/index.html">${libId}</a></td> #end
+                    #{
+                        val prefixPath = List("samples", sample) ::: (if (libId.isEmpty) Nil else List("libraries", libId)) ::: List("bammetrics", "stats")
+
+                        val fieldValues = for (field <- fields) yield {
+                            summary.getValue((prefixPath ::: List("rna", "metrics", field.toUpperCase)):_*).getOrElse(prefixPath ::: metricsTag :: Nil)
+                        }
+                    }#
+                    #for (value <- fieldValues)
+                        <td>${value}</td>
+                    #end
+                </tr>
+            #end
+        #end
+    </tbody>
+</table>
+
+</div>

public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala

@@ -39,7 +39,6 @@ class BamMetrics(val root: Configurable) extends QScript
   var inputBam: File = _
 
   /** Settings for CollectRnaSeqMetrics */
-  var rnaMetricsSettings: Map[String, String] = Map()
   var transcriptRefFlatFile: Option[File] = config("transcript_refflat")
 
   /** return location of summary file */
@@ -77,7 +76,7 @@ class BamMetrics(val root: Configurable) extends QScript
 
   /** Script to add jobs */
   def biopetScript() {
-    add(SamtoolsFlagstat(this, inputBam, swapExt(outputDir, inputBam, ".bam", ".flagstat")))
+    add(SamtoolsFlagstat(this, inputBam, outputDir))
 
     val biopetFlagstat = BiopetFlagstat(this, inputBam, outputDir)
     add(biopetFlagstat)
@@ -107,8 +106,6 @@ class BamMetrics(val root: Configurable) extends QScript
       rnaMetrics.output = swapExt(outputDir, inputBam, ".bam", ".rna.metrics")
       rnaMetrics.chartOutput = Some(swapExt(outputDir, inputBam, ".bam", ".rna.metrics.pdf"))
       rnaMetrics.refFlat = transcriptRefFlatFile.get
-      rnaMetrics.ribosomalIntervals = rnaMetricsSettings.get("ribosomal_intervals").collect { case n => new File(n) }
-      rnaMetrics.strandSpecificity = rnaMetricsSettings.get("strand_specificity")
       add(rnaMetrics)
       addSummarizable(rnaMetrics, "rna")
     }

public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala

@@ -57,9 +57,13 @@ object BammetricsReport extends ReportBuilder {
                      sampleId: Option[String],
                      libId: Option[String],
                      metricsTag: String = "bammetrics") = {
+
+    val wgsExecuted = summary.getValue(sampleId, libId, metricsTag, "stats", "wgs").isDefined
+    val rnaExecuted = summary.getValue(sampleId, libId, metricsTag, "stats", "rna").isDefined
+
     val targets = (
-      summary.getValue(sampleId, libId, "bammetrics", "settings", "amplicon_name"),
-      summary.getValue(sampleId, libId, "bammetrics", "settings", "roi_name")
+      summary.getValue(sampleId, libId, metricsTag, "settings", "amplicon_name"),
+      summary.getValue(sampleId, libId, metricsTag, "settings", "roi_name")
     ) match {
         case (Some(amplicon: String), Some(roi: List[_])) => amplicon :: roi.map(_.toString)
         case (_, Some(roi: List[_])) => roi.map(_.toString)
@@ -74,9 +78,13 @@ object BammetricsReport extends ReportBuilder {
         Map())),
       List(
         "Summary" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"),
-        "Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp", Map("showPlot" -> true)),
-        "Whole genome coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp", Map("showPlot" -> true))
-      ),
+        "Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp", Map("showPlot" -> true))
+      ) ++ (if (wgsExecuted) List("Whole genome coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp",
+          Map("showPlot" -> true)))
+        else Nil) ++
+        (if (rnaExecuted) List("Rna coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp",
+          Map("showPlot" -> true)))
+        else Nil),
       Map("metricsTag" -> metricsTag)
     )
   }
@@ -321,4 +329,94 @@ object BammetricsReport extends ReportBuilder {
     plot.title = Some("Whole genome coverage")
     plot.runLocal()
   }
+
+  /**
+   * Generate a line plot for rna coverage
+   * @param outputDir OutputDir for the tsv and png file
+   * @param prefix Prefix of the tsv and png file
+   * @param summary Summary class
+   * @param libraryLevel Default false, when set true plot will be based on library stats instead of sample stats
+   * @param sampleId Default it selects all sampples, when sample is giving it limits to selected sample
+   */
+  def rnaHistogramPlot(outputDir: File,
+                       prefix: String,
+                       summary: Summary,
+                       libraryLevel: Boolean = false,
+                       sampleId: Option[String] = None,
+                       libId: Option[String] = None): Unit = {
+    val tsvFile = new File(outputDir, prefix + ".tsv")
+    val pngFile = new File(outputDir, prefix + ".png")
+    val tsvWriter = new PrintWriter(tsvFile)
+    if (libraryLevel) {
+      tsvWriter.println((for (
+        sample <- summary.samples if sampleId.isEmpty || sampleId.get == sample;
+        lib <- summary.libraries(sample) if libId.isEmpty || libId.get == lib
+      ) yield s"$sample-$lib")
+        .mkString("library\t", "\t", ""))
+    } else {
+      sampleId match {
+        case Some(sample) => tsvWriter.println("\t" + sample)
+        case _            => tsvWriter.println(summary.samples.mkString("Sample\t", "\t", ""))
+      }
+    }
+
+    var map: Map[Int, Map[String, Double]] = Map()
+
+    def fill(sample: String, lib: Option[String]): Unit = {
+
+      val insertSize = new SummaryValue(List("bammetrics", "stats", "rna", "histogram", "normalized_position"),
+        summary, Some(sample), lib).value.getOrElse(List())
+      val counts = new SummaryValue(List("bammetrics", "stats", "rna", "histogram", "All_Reads.normalized_coverage"),
+        summary, Some(sample), lib).value.getOrElse(List())
+
+      (insertSize, counts) match {
+        case (l: List[_], l2: List[_]) =>
+          l.zip(l2).foreach(i => {
+            val insertSize = i._1.toString.toInt
+            val count = i._2.toString.toDouble
+            val old = map.getOrElse(insertSize, Map())
+            if (libraryLevel) map += insertSize -> (old + ((s"$sample-" + lib.get) -> count))
+            else map += insertSize -> (old + (sample -> count))
+          })
+        case _ => throw new IllegalStateException("Must be a list")
+      }
+    }
+
+    if (libraryLevel) {
+      for (
+        sample <- summary.samples if sampleId.isEmpty || sampleId.get == sample;
+        lib <- summary.libraries(sample) if libId.isEmpty || libId.get == lib
+      ) fill(sample, Some(lib))
+    } else if (sampleId.isDefined) fill(sampleId.get, None)
+    else summary.samples.foreach(fill(_, None))
+
+    for ((insertSize, counts) <- map) {
+      tsvWriter.print(insertSize)
+      if (libraryLevel) {
+        for (
+          sample <- summary.samples if sampleId.isEmpty || sampleId.get == sample;
+          lib <- summary.libraries(sample) if libId.isEmpty || libId.get == lib
+        ) {
+          tsvWriter.print("\t" + counts.getOrElse(s"$sample-$lib", "0"))
+        }
+      } else {
+        for (sample <- summary.samples if sampleId.isEmpty || sampleId.get == sample) {
+          tsvWriter.print("\t" + counts.getOrElse(sample, "0"))
+        }
+      }
+      tsvWriter.println()
+    }
+
+    tsvWriter.close()
+
+    val plot = new LinePlot(null)
+    plot.input = tsvFile
+    plot.output = pngFile
+    plot.xlabel = Some("Reletive position")
+    plot.ylabel = Some("Coverage")
+    plot.width = Some(1200)
+    plot.removeZero = true
+    plot.title = Some("Rna coverage")
+    plot.runLocal()
+  }
 }

public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala

@@ -17,10 +17,10 @@ package nl.lumc.sasc.biopet.core
 
 import java.io.File
 
+import nl.lumc.sasc.biopet.core.MultiSampleQScript.Gender
 import nl.lumc.sasc.biopet.core.summary.{ Summarizable, SummaryQScript }
 import nl.lumc.sasc.biopet.utils.{ Logging, ConfigUtils }
 import org.broadinstitute.gatk.queue.QScript
-import org.broadinstitute.gatk.utils.commandline.Argument
 
 /** This trait creates a structured way of use multisample pipelines */
 trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
@@ -31,7 +31,7 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
   require(globalConfig.map.contains("samples"), "No Samples found in config")
 
   /** Sample class with basic functions build in */
-  abstract class AbstractSample(val sampleId: String) extends Summarizable {
+  abstract class AbstractSample(val sampleId: String) extends Summarizable { sample =>
     /** Overrules config of qscript with default sample */
     val config = new ConfigFunctions(defaultSample = sampleId)
 
@@ -39,7 +39,7 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
     def summarySettings: Map[String, Any] = Map()
 
     /** Library class with basic functions build in */
-    abstract class AbstractLibrary(val libId: String) extends Summarizable {
+    abstract class AbstractLibrary(val libId: String) extends Summarizable { lib =>
       /** Overrules config of qscript with default sample and default library */
       val config = new ConfigFunctions(defaultSample = sampleId, defaultLibrary = libId)
 
@@ -64,11 +64,22 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
       }
 
       /** Creates a library file with given suffix */
-      def createFile(suffix: String): File = new File(libDir, sampleId + "-" + libId + suffix)
+      def createFile(suffix: String): File = new File(libDir, s"$sampleId-$libId.$suffix")
 
       /** Returns library directory */
       def libDir = new File(sampleDir, "lib_" + libId)
 
+      lazy val libTags: Map[String, Any] =
+        config("tags", default = Map(), freeVar = false, submodule = libId, path = List("samples", sampleId, "libraries"))
+
+      def sampleId = sample.sampleId
+
+      lazy val libGroups: List[String] = libTags.get("groups") match {
+        case Some(g: List[_]) => g.map(_.toString)
+        case Some(g: String)  => List(g)
+        case _                => Nil
+      }
+
       /** Function that add library jobs */
       protected def addJobs()
     }
@@ -79,6 +90,49 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
     /** Stores all libraries */
     val libraries: Map[String, Library] = libIds.map(id => id -> makeLibrary(id)).toMap
 
+    lazy val sampleTags: Map[String, Any] =
+      config("tags", default = Map(), freeVar = false, submodule = sampleId, path = List("samples"))
+
+    lazy val gender = {
+      val g: Option[String] = sampleTags.get("gender").map(_.toString)
+      g.map(_.toLowerCase) match {
+        case Some("male")   => Gender.Male
+        case Some("female") => Gender.Female
+        case Some(s) =>
+          logger.warn(s"Could not convert '$g' to a gender")
+          Gender.Unknown
+        case _ => Gender.Unknown
+      }
+    }
+
+    lazy val father = {
+      val g: Option[String] = sampleTags.get("father").map(_.toString)
+      g.foreach { father =>
+        if (sampleId != father) Logging.addError(s"Father for $sampleId can not be itself")
+        if (samples.contains(father)) if (samples(father).gender == Gender.Male)
+          Logging.addError(s"Father of $sampleId is not a female")
+        else logger.warn(s"For sample '$sampleId' is father '$father' not found in config")
+      }
+      g
+    }
+
+    lazy val mother = {
+      val g: Option[String] = sampleTags.get("mother").map(_.toString)
+      g.foreach { mother =>
+        if (sampleId != mother) Logging.addError(s"mother for $sampleId can not be itself")
+        if (samples.contains(mother)) if (samples(mother).gender == Gender.Female)
+          Logging.addError(s"Mother of $sampleId is not a female")
+        else logger.warn(s"For sample '$sampleId' is mother '$mother' not found in config")
+      }
+      g
+    }
+
+    lazy val sampleGroups: List[String] = sampleTags.get("groups") match {
+      case Some(g: List[_]) => g.map(_.toString)
+      case Some(g: String)  => List(g)
+      case _                => Nil
+    }
+
     /**
      * Factory method for Library class
      * @param id SampleId
@@ -117,7 +171,7 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
     }
 
     /** Creates a sample file with given suffix */
-    def createFile(suffix: String) = new File(sampleDir, sampleId + suffix)
+    def createFile(suffix: String) = new File(sampleDir, s"$sampleId.$suffix")
 
     /** Returns sample directory */
     def sampleDir = new File(outputDir, "samples" + File.separator + sampleId)
@@ -180,3 +234,10 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
     sample ::: lib ::: super.configFullPath
   }
 }
+
+object MultiSampleQScript {