Merge branch 'feature-report' into 'develop'

Feature report

second phase for reporting

Adding report to all general pipelines

See merge request !184

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

-#{ //TODO: Need content }#
+#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.core.report.ReportPage)
+<%@ var summary: Summary %>
+<%@ var rootPath: String %>
+<%@ var sampleId: Option[String] %>
+<%@ var libId: Option[String] = None %>
 
-Todo
\ No newline at end of file
+<table class="table">
+<tbody>
+    <tr><th>Pipeline</th><td>BamMetrics</td></tr>
+    <tr><th>Version</th><td>${summary.getValue("meta", "pipeline_version")}</td></tr>
+    <tr><th>Last commit hash</th><td>${summary.getValue("meta", "last_commit_hash")}</td></tr>
+    <tr><th>Output directory</th><td>${summary.getValue("meta", "output_dir")}</td></tr>
+    <tr><th>Sample ID</th><td>${sampleId}</td></tr>
+    #if (libId.isDefined) <tr><th>Library ID</th><td>${libId}</td></tr> #end
+</tbody>
+</table>
+<br/>
+<div class="row">
+<div class="col-md-1"></div>
+<div class="col-md-6">
+    <p>
+        In this web document you can find your <em>BamMetrics</em> pipeline report.
+        Different categories of data can be found in the left-side menu.
+        Statistics per sample and library can be accessed through the top-level menu.
+        Futhermore, you can view all versions of software tools used by selecting <em>Versions</em> from the top menu.
+    </p>
+
+    <p>
+        <small>Brought to you by <a href="https://sasc.lumc.nl">SASC</a> and <a href="https://www.lumc.nl/org/klinische-genetica/">KG</a>, LUMC. </small>
+    </p>
+</div>
+</div>
\ No newline at end of file

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

+#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.core.report.ReportPage)
+#import(java.io.File)
+<%@ var summary: Summary %>
+<%@ var sampleId: Option[String] %>
+<%@ var libId: Option[String] = None %>
+<%@ var metricsTag: String = "bammetrics" %>
+
+<table class="table sortable-theme-bootstrap">
+<thead><tr>
+    <th>Path</th>
+    <th>MD5</th>
+</tr></thead>
+<tbody>
+<tr>
+<td>${summary.getValue(sampleId, libId, metricsTag, "files", "pipeline", "bamfile", "path")}</td>
+<td>${summary.getValue(sampleId, libId, metricsTag, "files", "pipeline", "bamfile", "md5")}</td>
+</tr>
+</tbody>
+</table>
\ No newline at end of file

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

@@ -10,17 +10,17 @@
 <%@ var metricsTag: String = "bammetrics" %>
 <%@ var target: String %>
 #{
-    val originalPlot = new File(summary.getLibraryValue(sampleId, libId, metricsTag, "files", target + "_cov_stats", "plot", "path")
+    val originalPlot = new File(summary.getValue(sampleId, libId, metricsTag, "files", target + "_cov_stats", "plot", "path")
         .getOrElse(throw new IllegalArgumentException("No plot found in summary")).toString)
     val plot = new File(outputDir, target + "_cov_stats.png")
 
-    val values = summary.getLibraryValue(sampleId, libId, metricsTag, "stats", target + "_cov_stats", "coverage", "_all")
+    val values = summary.getValue(sampleId, libId, metricsTag, "stats", target + "_cov_stats", "coverage", "_all")
         .getOrElse(throw new IllegalArgumentException("No plot found in summary")).asInstanceOf[Map[String, Any]]
 
     if (originalPlot.exists()) IoUtils.copyFile(originalPlot, plot)
 }#
 
-<img src="${plot}">
+<img src="${plot.getName}">
 
 <table class="table">
 <thead><tr>

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

@@ -58,6 +58,17 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
   def summarySettings = Map("amplicon_name" -> ampliconBedFile.collect { case x => x.getName.stripSuffix(".bed") },
     "roi_name" -> roiBedFiles.map(_.getName.stripSuffix(".bed")))
 
+  override def reportClass = {
+    val bammetricsReport = new BammetricsReport(this)
+    bammetricsReport.outputDir = new File(outputDir, "report")
+    bammetricsReport.summaryFile = summaryFile
+    bammetricsReport.args = if (libId.isDefined) Map(
+      "sampleId" -> sampleId.getOrElse("."),
+      "libId" -> libId.getOrElse("."))
+    else Map("sampleId" -> sampleId.getOrElse("."))
+    Some(bammetricsReport)
+  }
+
   /** executed before script */
   def init() {
   }

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

@@ -2,24 +2,48 @@ package nl.lumc.sasc.biopet.pipelines.bammetrics
 
 import java.io.{ PrintWriter, File }
 
-import nl.lumc.sasc.biopet.core.report.{ ReportBuilder, ReportPage, ReportSection }
+import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.core.report.{ ReportBuilderExtension, ReportBuilder, ReportPage, ReportSection }
 import nl.lumc.sasc.biopet.core.summary.{ SummaryValue, Summary }
 import nl.lumc.sasc.biopet.extensions.rscript.{ XYPlot, StackedBarPlot }
 
+class BammetricsReport(val root: Configurable) extends ReportBuilderExtension {
+  val builder = BammetricsReport
+}
+
 /**
  * Created by pjvan_thof on 3/30/15.
  */
 object BammetricsReport extends ReportBuilder {
-  // FIXME: Not yet finished
 
+  /** Name of report */
   val reportName = "Bam Metrics"
 
-  def indexPage = ReportPage(List(), List(), Map())
+  /** Root page for single BamMetrcis report */
+  def indexPage = {
+    val bamMetricsPage = this.bamMetricsPage(summary, sampleId, libId)
+    ReportPage(bamMetricsPage.subPages ::: List(
+      "Versions" -> ReportPage(List(), List((
+        "Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp"
+        ))), Map()),
+      "Files" -> ReportPage(List(), List(
+        "Input fastq files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/bammetricsInputFile.ssp")
+      ), Map())
+    ), List(
+      "Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/bamMetricsFront.ssp")
+    ) ::: bamMetricsPage.sections,
+      Map()
+    )
+  }
 
-  def bamMetricsPage(summary: Summary, sampleId: Option[String], libId: Option[String]) = {
+  /** Generates a page with alignment stats */
+  def bamMetricsPage(summary: Summary,
+                     sampleId: Option[String],
+                     libId: Option[String],
+                     metricsTag: String = "bammetrics") = {
     val targets = (
-      summary.getLibraryValue(sampleId, libId, "bammetrics", "settings", "amplicon_name"),
-      summary.getLibraryValue(sampleId, libId, "bammetrics", "settings", "roi_name")
+      summary.getValue(sampleId, libId, "bammetrics", "settings", "amplicon_name"),
+      summary.getValue(sampleId, libId, "bammetrics", "settings", "roi_name")
     ) match {
         case (Some(amplicon: String), Some(roi: List[_])) => amplicon :: roi.map(_.toString)
         case (_, Some(roi: List[_])) => roi.map(_.toString)
@@ -33,12 +57,21 @@ 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))
+        "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))
       ),
-      Map()
+      Map("metricsTag" -> metricsTag)
     )
   }
 
+  /**
+   * Generate a stackbar plot for alignment stats
+   * @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 alignmentSummaryPlot(outputDir: File,
                            prefix: String,
                            summary: Summary,
@@ -94,6 +127,14 @@ object BammetricsReport extends ReportBuilder {
     plot.runLocal()
   }
 
+  /**
+   * Generate a line plot for insertsize
+   * @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 insertSizePlot(outputDir: File,
                      prefix: String,
                      summary: Summary,
@@ -174,6 +215,14 @@ object BammetricsReport extends ReportBuilder {
     plot.runLocal()
   }
 
+  /**
+   * Generate a line plot for wgs 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 wgsHistogramPlot(outputDir: File,
                        prefix: String,
                        summary: Summary,

public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/executables.ssp

@@ -4,9 +4,9 @@
 <%@ var rootPath: String %>
 <%@ var sampleId: Option[String] = None %>
 <%@ var libId: Option[String] = None %>
+<%@ var pipeline: String = summary.getValue("meta", "pipeline_name").getOrElse("").toString %>
 #{
-    val pipeline = summary.getValue("meta", "pipeline_name").getOrElse("").toString
-    val executables = summary.getLibraryValue(sampleId, libId, pipeline, "executables").getOrElse(Map()).asInstanceOf[Map[String, Map[String, Any]]]
+    val executables = summary.getValue(sampleId, libId, pipeline, "executables").getOrElse(Map()).asInstanceOf[Map[String, Map[String, Any]]]
 }#
 
 <table class="table">

public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/reference.ssp

+#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.core.report.ReportPage)
+<%@ var summary: Summary %>
+<%@ var rootPath: String %>
+<%@ var pipeline: String %>
+
+#{
+    val contigs = summary.getValue(pipeline, "settings", "reference", "contigs").get.asInstanceOf[Map[String, Map[String, Any]]]
+}#
+
+<table class="table">
+    <tbody>
+        <tr><th>Species</th><td>${summary.getValue(pipeline, "settings", "reference", "species")}</td></tr>
+        <tr><th>Name</th><td>${summary.getValue(pipeline, "settings", "reference", "name")}</td></tr>
+        <tr><th>File</th><td>${summary.getValue(pipeline, "files", "pipeline", "referenceFasta", "path")}</td></tr>
+        <tr><th>MD5</th><td>${summary.getValue(pipeline, "files", "pipeline", "referenceFasta", "md5")}</td></tr>
+    </tbody>
+</table>
+
+<br/>
+
+<table class="table sortable-theme-bootstrap" data-sortable>
+    <thead>
+        <tr><th>Contig Name</th><th data-sorted="true" data-sorted-direction="descending">Length</th><th>MD5</th></tr>
+    </thead>
+    <tbody>
+        #for (c <- contigs.toList.sortBy(_._2("length").asInstanceOf[Long]).reverse)
+            <tr><th>${c._1}</th><td>${c._2.get("length")}</td><td>${c._2.get("md5")}</td></tr>
+        #end
+    </tbody>
+</table>
\ No newline at end of file

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/MultisampleReportBuilder.scala

@@ -4,22 +4,28 @@ package nl.lumc.sasc.biopet.core.report
  * Created by pjvan_thof on 3/30/15.
  */
 trait MultisampleReportBuilder extends ReportBuilder {
+
+  /** Method to generate a single sample page */
   def samplePage(sampleId: String, args: Map[String, Any]): ReportPage
 
+  /** Default list of samples, can be override */
   def samplesSections: List[(String, ReportSection)] = {
     List(
       ("Samples", ReportSection("/nl/lumc/sasc/biopet/core/report/samplesList.ssp"))
     )
   }
 
+  /** Method to generate a single library page */
   def libraryPage(sampleId: String, libraryId: String, args: Map[String, Any]): ReportPage
 
+  /** Default list of libraries, can be override */
   def libririesSections: List[(String, ReportSection)] = {
     List(
       ("Libraries", ReportSection("/nl/lumc/sasc/biopet/core/report/librariesList.ssp"))
     )
   }
 
+  /** Generate the samples page including a single sample page for each sample in the summary */
   def generateSamplesPage(args: Map[String, Any]): ReportPage = {
     val samplePages = summary.samples
       .map(sampleId => (sampleId -> samplePage(sampleId, args ++ Map("sampleId" -> Some(sampleId)))))
@@ -27,6 +33,7 @@ trait MultisampleReportBuilder extends ReportBuilder {
     ReportPage(samplePages, samplesSections, args)
   }
 
+  /** Generate the libraries page for a single sample with a subpage for eacht library */
   def generateLibraryPage(args: Map[String, Any]): ReportPage = {
     val sampleId = args("sampleId") match {
       case Some(x) => x.toString

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala

@@ -2,65 +2,81 @@ package nl.lumc.sasc.biopet.core.report
 
 import java.io._
 
-import nl.lumc.sasc.biopet.core.{ ToolCommandFuntion, BiopetJavaCommandLineFunction, ToolCommand }
+import nl.lumc.sasc.biopet.core.{ Logging, ToolCommandFuntion, ToolCommand }
 import nl.lumc.sasc.biopet.core.summary.Summary
 import org.broadinstitute.gatk.utils.commandline.Input
 import org.fusesource.scalate.{ TemplateSource, TemplateEngine }
 import nl.lumc.sasc.biopet.utils.IoUtils
+import scala.collection.mutable
 
 /**
  * Created by pjvan_thof on 3/27/15.
  */
 trait ReportBuilderExtension extends ToolCommandFuntion {
 
+  /** Report builder object */
   val builder: ReportBuilder
 
   @Input(required = true)
   var summaryFile: File = _
 
+  /** OutputDir for the report  */
   var outputDir: File = _
 
+  /** Arguments that are passed on the commandline */
   var args: Map[String, String] = Map()
 
+  override val defaultCoreMemory = 3.0
+
   override def beforeGraph: Unit = {
     super.beforeGraph
     jobOutputFile = new File(outputDir, ".report.log.out")
     javaMainClass = builder.getClass.getName.takeWhile(_ != '$')
   }
 
+  /** Command to generate the report */
   override def commandLine: String = {
     super.commandLine +
       required("--summary", summaryFile) +
       required("--outputDir", outputDir) +
-      args.map(x => required(x._1, x._2)).mkString
+      args.map(x => required("-a", x._1 + "=" + x._2)).mkString
   }
 }
 
 trait ReportBuilder extends ToolCommand {
 
-  case class Args(summary: File = null, outputDir: File = null, pageArgs: Map[String, String] = Map()) extends AbstractArgs
+  case class Args(summary: File = null, outputDir: File = null, pageArgs: mutable.Map[String, Any] = mutable.Map()) extends AbstractArgs
 
   class OptParser extends AbstractOptParser {
-    opt[File]('s', "summary") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
+    opt[File]('s', "summary") unbounded () required () maxOccurs 1 valueName "<file>" action { (x, c) =>
       c.copy(summary = x)
     }
-    opt[File]('o', "outputDir") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
+    opt[File]('o', "outputDir") unbounded () required () maxOccurs 1 valueName "<file>" action { (x, c) =>
       c.copy(outputDir = x)
     }
-    opt[Map[String, String]]('a', "args") action { (x, c) =>
+    opt[Map[String, String]]('a', "args") unbounded () action { (x, c) =>
       c.copy(pageArgs = c.pageArgs ++ x)
     }
   }
 
+  /** summary object internaly */
   private var setSummary: Summary = _
 
+  /** Retrival of summary, read only */
   final def summary = setSummary
 
+  /** default args that are passed to all page withing the report */
   def pageArgs: Map[String, Any] = Map()
 
   private var done = 0
   private var total = 0
 
+  private var _sampleId: Option[String] = None
+  protected def sampleId = _sampleId
+  private var _libId: Option[String] = None
+  protected def libId = _libId
+
+  /** Main function to for building the report */
   def main(args: Array[String]): Unit = {
     logger.info("Start")
 
@@ -70,6 +86,22 @@ trait ReportBuilder extends ToolCommand {
     require(cmdArgs.outputDir.exists(), "Output dir does not exist")
     require(cmdArgs.outputDir.isDirectory, "Output dir is not a directory")
 
+    cmdArgs.pageArgs.get("sampleId") match {
+      case Some(s: String) => {
+        cmdArgs.pageArgs += "sampleId" -> Some(s)
+        _sampleId = Some(s)
+      }
+      case _ =>
+    }
+
+    cmdArgs.pageArgs.get("libId") match {
+      case Some(l: String) => {
+        cmdArgs.pageArgs += "libId" -> Some(l)
+        _libId = Some(l)
+      }
+      case _ =>
+    }
+
     logger.info("Copy Base files")
 
     // Static files that will be copied to the output folder, then file is added to [resourceDir] it's need to be added here also
@@ -95,25 +127,32 @@ trait ReportBuilder extends ToolCommand {
     logger.info("Parsing summary")
     setSummary = new Summary(cmdArgs.summary)
 
-    total = countPages(indexPage)
+    total = ReportBuilder.countPages(indexPage)
     logger.info(total + " pages to be generated")
 
     logger.info("Generate pages")
     val jobs = generatePage(summary, indexPage, cmdArgs.outputDir,
-      args = pageArgs ++ cmdArgs.pageArgs ++
+      args = pageArgs ++ cmdArgs.pageArgs.toMap ++
         Map("summary" -> summary, "reportName" -> reportName, "indexPage" -> indexPage))
 
     logger.info(jobs + " Done")
   }
 
+  /** This must be implemented, this will be the root page of the report */
   def indexPage: ReportPage
 
+  /** This must be implemented, this will because the title of the report */
   def reportName: String
 
-  def countPages(page: ReportPage): Int = {
-    page.subPages.map(x => countPages(x._2)).fold(1)(_ + _)
-  }
-
+  /**
+   * This method will render the page and the subpages recursivly
+   * @param summary The summary object
+   * @param page Page to render
+   * @param outputDir Root output dir of the report
+   * @param path Path from root to current page
+   * @param args Args to add to this sub page, are args from current page are passed automaticly
+   * @return Number of pages including all subpages that are rendered
+   */
   def generatePage(summary: Summary,
                    page: ReportPage,
                    outputDir: File,
@@ -151,10 +190,17 @@ trait ReportBuilder extends ToolCommand {
 
 object ReportBuilder {
 
+  /** Single template render engine, this will have a cache for all compile templates */
   protected val engine = new TemplateEngine()
 
+  /** Cache of temp file for templates from the classpath / jar */
   private var templateCache: Map[String, File] = Map()
 
+  /** This will give the total number of pages including all nested pages */
+  def countPages(page: ReportPage): Int = {
+    page.subPages.map(x => countPages(x._2)).fold(1)(_ + _)
+  }
+
   /**
    * This method will render a template that is located in the classpath / jar
    * @param location location in the classpath / jar
@@ -162,6 +208,12 @@ object ReportBuilder {
    * @return Rendered result of template
    */
   def renderTemplate(location: String, args: Map[String, Any] = Map()): String = {
+    Logging.logger.info("Rendering: " + location)
+
+    if (location == "/nl/lumc/sasc/biopet/pipelines/carp/carpFront.ssp") {
+      println("hier dus")
+    }
+
     val templateFile: File = templateCache.get(location) match {
       case Some(template) => template
       case _ => {

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportPage.scala

@@ -2,6 +2,10 @@ package nl.lumc.sasc.biopet.core.report
 
 /**
  * Created by pjvan_thof on 3/27/15.
+ *
+ * @param subPages Subpages for this page
+ * @param sections Sections for this page
+ * @param args Arguments for this page, this arguments get passed to all section and subpages
  */
 case class ReportPage(subPages: List[(String, ReportPage)],
                       sections: List[(String, ReportSection)],

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportSection.scala

@@ -2,15 +2,18 @@ package nl.lumc.sasc.biopet.core.report
 
 /**
  * Created by pjvan_thof on 4/8/15.
+ *
+ * @param location Location inside the classpath / jar
+ * @param args arguments only for current section, this is not passed to other sub pages
  */
 case class ReportSection(location: String,
-                         args: Map[String, Any] = Map(),
-                         intro: Option[String] = None) {
-
-  def render(args: Map[String, Any]): String = {
-    (intro match {
-      case Some(template) => ReportBuilder.renderTemplate(location, args ++ this.args)
-      case _              => ""
-    }) + ReportBuilder.renderTemplate(location, args ++ this.args)
+                         args: Map[String, Any] = Map()) {
+  /**
+   * This method will render this section
+   * @param args Possible to give more arguments
+   * @return Rendered result for this section
+   */
+  def render(args: Map[String, Any] = Map()): String = {
+    ReportBuilder.renderTemplate(location, args ++ this.args)
   }
 }

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summary.scala

@@ -10,6 +10,7 @@ import nl.lumc.sasc.biopet.utils.ConfigUtils
 class Summary(file: File) {
   val map = ConfigUtils.fileToConfigMap(file)
 
+  /** List of all samples in the summary */
   lazy val samples: Set[String] = {
     ConfigUtils.getValueFromPath(map, List("samples")) match {
       case Some(samples) => ConfigUtils.any2map(samples).keySet
@@ -17,6 +18,7 @@ class Summary(file: File) {
     }
   }
 
+  /** List of all libraries for each sample */
   lazy val libraries: Map[String, Set[String]] = {
     (for (sample <- samples) yield sample -> {
       ConfigUtils.getValueFromPath(map, List("samples", sample, "libraries")) match {
@@ -26,27 +28,33 @@ class Summary(file: File) {
     }).toMap
   }
 
+  /** getValue from on given nested path */
   def getValue(path: String*): Option[Any] = {
     ConfigUtils.getValueFromPath(map, path.toList)
   }
 
+  /** getValue from on given nested path with prefix "samples" -> [sampleId] */
   def getSampleValue(sampleId: String, path: String*): Option[Any] = {
     ConfigUtils.getValueFromPath(map, "samples" :: sampleId :: path.toList)
   }
 
+  /** Get values for all samples on given path with prefix "samples" -> [sampleId] */
   def getSampleValues(path: String*): Map[String, Option[Any]] = {
     (for (sample <- samples) yield sample -> getSampleValue(sample, path: _*)).toMap
   }
 
+  /** Executes given function for each sample */
   def getSampleValues(function: (Summary, String) => Option[Any]): Map[String, Option[Any]] = {
     (for (sample <- samples) yield sample -> function(this, sample)).toMap
   }
 
+  /** Get value on nested path with prefix "samples" -> [sampleId] -> "libraries" -> [libId] */
   def getLibraryValue(sampleId: String, libId: String, path: String*): Option[Any] = {
     ConfigUtils.getValueFromPath(map, "samples" :: sampleId :: "libraries" :: libId :: path.toList)
   }
 
-  def getLibraryValue(sampleId: Option[String], libId: Option[String], path: String*): Option[Any] = {
+  /** Get value on nested path with prefix depending is sampleId and/or libId is None or not */
+  def getValue(sampleId: Option[String], libId: Option[String], path: String*): Option[Any] = {
     (sampleId, libId) match {
       case (Some(sample), Some(lib)) => getLibraryValue(sample, lib, path: _*)
       case (Some(sample), _)         => getSampleValue(sample, path: _*)
@@ -54,12 +62,22 @@ class Summary(file: File) {
     }
   }
 
+  /**