Merge branch 'develop' into fix-BIOPET-637

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

+#import(nl.lumc.sasc.biopet.utils.summary.db.Schema._)
 #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
 #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._)
 #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._)
@@ -16,8 +17,13 @@
 <%@ var showTable: Boolean = true %>
 <%@ var showIntro: Boolean = true%>
 <%@ var runId: Int %>
+<%@ var allSamples: Seq[Sample] %>
+<%@ var allLibraries: Seq[Library] %>
 #{
-    val samples = Await.result(summary.getSamples(runId = Some(runId)), Duration.Inf)
+    val samples = sampleId match {
+    case Some(id) => allSamples.filter(_.id == id).toList
+    case _ => allSamples.toList
+    }
 }#
 #if (showIntro)
     <br/>
@@ -74,12 +80,12 @@
                 val libs: List[Option[Int]] = (libId, sampleLevel) match {
                 case (_, true) => List(None)
                 case (Some(_), _) => List(libId)
-                case _ => Await.result(summary.getLibraries(sampleId = Some(sample.id), runId = Some(runId)), Duration.Inf).map(x => Some(x.id)).toList
+                case _ => allLibraries.filter(_.sampleId == sample.id).map(x => Some(x.id)).toList
                 }
             }#
             <tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample.name}/index.html">${sample.name}</a></td>
             #for (libId <- libs)
-                #{ val libName = libId.map(l => Await.result(summary.getLibraryName(l), Duration.Inf)) }#
+                #{ val libName = libId.map(l => allLibraries.find(_.id == l).get.name) }#
                 #if (libs.head != libId) <tr> #end
                     #if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end
                     #{

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

@@ -2,9 +2,8 @@
 #import(nl.lumc.sasc.biopet.core.report.ReportPage)
 <%@ var summary: Summary %>
 <%@ var rootPath: String %>
-<%@ var sampleId: Option[String] %>
-<%@ var libId: Option[String] = None %>
-
+<%@ var sampleId: Option[Int] %>
+<%@ var libId: Option[Int] = None %>
 <table class="table">
 <tbody>
     <tr><th>Pipeline</th><td>BamMetrics</td></tr>

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

-#import(nl.lumc.sasc.biopet.utils.summary.Summary)
-#import(nl.lumc.sasc.biopet.core.report.ReportPage)
-<%@ var summary: Summary %>
-<%@ var sampleId: Option[String] %>
-<%@ var libId: Option[String] = None %>
-<%@ var rootPath: String %>
-<%@ var metricsTag: String = "bammetrics" %>
-<%@ var fields: List[String] = List("All", "Mapped", "Duplicates", "MAPQ>30", "MateUnmapped", "Mate on other chr")%>
-
-<table>
-<tbody>
-#for (field <- fields)
-    <tr><th>${field}</th><td>
-    #if (libId.isDefined)
-        ${summary.getLibraryValue(sampleId.get, libId.get, metricsTag, "stats", "bamstats", "flagstats", field)}
-    #else
-        ${summary.getSampleValue(sampleId.get, metricsTag, "stats", "bamstats", "flagstats", field)}
-    #end
-    </td></tr>
-#end
-</tbody>
-</table>

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

-#import(nl.lumc.sasc.biopet.utils.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

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

+#import(nl.lumc.sasc.biopet.utils.summary.db.Schema._)
 #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
 #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._)
 #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._)
 #import(nl.lumc.sasc.biopet.core.report.ReportPage)
-#import(scala.concurrent.Await)
-#import(scala.concurrent.duration.Duration)
 #import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
 #import(java.io.File)
 <%@ var summary: SummaryDb %>
@@ -17,10 +16,14 @@
 <%@ var showIntro: Boolean = true%>
 <%@ var runId: Int %>
 <%@ var fields: List[String] = List("min", "max", "mean", "median", "modal")%>
+<%@ var allSamples: Seq[Sample] %>
+<%@ var allLibraries: Seq[Library] %>
 #{
-    val samples = Await.result(summary.getSamples(runId = Some(runId)), Duration.Inf)
+    val samples = sampleId match {
+    case Some(id) => allSamples.filter(_.id == id).toList
+    case _ => allSamples.toList
+    }
 }#
-
 #if (showIntro)
     <br/>
     <div class="row">
@@ -74,12 +77,12 @@
                 val libs: List[Option[Int]] = (libId, sampleLevel) match {
                 case (_, true) => List(None)
                 case (Some(_), _) => List(libId)
-                case _ => Await.result(summary.getLibraries(sampleId = Some(sample.id), runId = Some(runId)), Duration.Inf).map(x => Some(x.id)).toList
+                case _ => allLibraries.filter(_.sampleId == sample.id).map(x => Some(x.id)).toList
                 }
             }#
             <tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample.name}/index.html">${sample.name}</a></td>
             #for (libId <- libs)
-                #{ val libName = libId.map(l => Await.result(summary.getLibraryName(l), Duration.Inf)) }#
+                #{ val libName = libId.map(l => allLibraries.find(_.id == l).get.name) }#
                 #if (libs.head != libId) <tr> #end
                     #if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end
                     #{

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

 #import(nl.lumc.sasc.biopet.utils.IoUtils)
 #import(org.apache.commons.io.FileUtils)
+#import(nl.lumc.sasc.biopet.utils.summary.db.Schema._)
 #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
 #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._)
 #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._)
@@ -18,11 +19,14 @@
 <%@ var target: Option[String] %>
 <%@ var runId: Int %>
 <%@ var fields: List[String] = List("mean", "median", "max", "horizontal", "frac_min_10x", "frac_min_20x", "frac_min_30x", "frac_min_40x", "frac_min_50x") %>
+<%@ var allSamples: Seq[Sample] %>
+<%@ var allLibraries: Seq[Library] %>
 #{
-    val samples = Await.result(summary.getSamples(runId = Some(runId)), Duration.Inf)
+    val samples = sampleId match {
+    case Some(id) => allSamples.filter(_.id == id).toList
+    case _ => allSamples.toList
+    }
 }#
-
-
 <table class="table">
 <thead><tr>
     <th>sample</th>
@@ -36,7 +40,7 @@
             val libs: List[Option[Int]] = (libId, sampleLevel) match {
                 case (_, true) => List(None)
                 case (Some(_), _) => List(libId)
-                case _ => Await.result(summary.getLibraries(sampleId = Some(sample.id), runId = Some(runId)), Duration.Inf).map(x => Some(x.id)).toList
+                case _ => allLibraries.filter(_.sampleId == sample.id).map(x => Some(x.id)).toList
             }
         }#
         <tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample.name}/index.html">${sample.name}</a></td>

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

-#{ //TODO: Need content }#
-
-Todo
\ No newline at end of file

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

 #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
 #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._)
 #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._)
+#import(nl.lumc.sasc.biopet.utils.summary.db.Schema._)
 #import(nl.lumc.sasc.biopet.core.report.ReportPage)
-#import(scala.concurrent.Await)
-#import(scala.concurrent.duration.Duration)
 #import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
 #import(java.io.File)
 <%@ var summary: SummaryDb %>
@@ -18,10 +17,14 @@
 <%@ var showTable: Boolean = true %>
 <%@ var showIntro: Boolean = true%>
 <%@ var runId: Int %>
+<%@ var allSamples: Seq[Sample] %>
+<%@ var allLibraries: Seq[Library] %>
 #{
-    val samples = Await.result(summary.getSamples(runId = Some(runId)), Duration.Inf)
+    val samples = sampleId match {
+    case Some(id) => allSamples.filter(_.id == id).toList
+    case _ => allSamples.toList
+    }
 }#
-
 #if (showIntro)
     <br/>
     <div class="row">
@@ -76,12 +79,12 @@
                 val libs: List[Option[Int]] = (libId, sampleLevel) match {
                 case (_, true) => List(None)
                 case (Some(_), _) => List(libId)
-                case _ => Await.result(summary.getLibraries(sampleId = Some(sample.id), runId = Some(runId)), Duration.Inf).map(x => Some(x.id)).toList
+                case _ => allLibraries.filter(_.sampleId == sample.id).map(x => Some(x.id)).toList
                 }
             }#
             <tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample.name}/index.html">${sample.name}</a></td>
             #for (libId <- libs)
-                #{ val libName = libId.map(l => Await.result(summary.getLibraryName(l), Duration.Inf)) }#
+                #{ val libName = libId.map(l => allLibraries.find(_.id == l).get.name) }#
                 #if (libs.head != libId) <tr> #end
                         #if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end
                         #{

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

 #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
+#import(nl.lumc.sasc.biopet.utils.summary.db.Schema._)
 #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._)
 #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._)
 #import(nl.lumc.sasc.biopet.core.report.ReportPage)
-#import(scala.concurrent.Await)
-#import(scala.concurrent.duration.Duration)
 #import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
 #import(java.io.File)
 <%@ var summary: SummaryDb %>
@@ -17,11 +16,14 @@
 <%@ var showIntro: Boolean = true%>
 <%@ var runId: Int %>
 <%@ var fields: List[String] = List("min", "max", "mean", "median", "modal")%>
-
+<%@ var allSamples: Seq[Sample] %>
+<%@ var allLibraries: Seq[Library] %>
 #{
-    val samples = Await.result(summary.getSamples(runId = Some(runId)), Duration.Inf)
+    val samples = sampleId match {
+    case Some(id) => allSamples.filter(_.id == id).toList
+    case _ => allSamples.toList
+    }
 }#
-
 #if (showIntro)
     <br/>
     <div class="row">
@@ -75,12 +77,12 @@
                 val libs: List[Option[Int]] = (libId, sampleLevel) match {
                 case (_, true) => List(None)
                 case (Some(_), _) => List(libId)
-                case _ => Await.result(summary.getLibraries(sampleId = Some(sample.id), runId = Some(runId)), Duration.Inf).map(x => Some(x.id)).toList
+                case _ => allLibraries.filter(_.sampleId == sample.id).map(x => Some(x.id)).toList
                 }
             }#
             <tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample.name}/index.html">${sample.name}</a></td>
             #for (libId <- libs)
-                #{ val libName = libId.map(l => Await.result(summary.getLibraryName(l), Duration.Inf)) }#
+                #{ val libName = libId.map(l => allLibraries.find(_.id == l).get.name) }#
                 #if (libs.head != libId) <tr> #end
                     #if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end
                     #{

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

-#{ //TODO: Need content }#
-
-Todo
\ No newline at end of file

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

+#import(nl.lumc.sasc.biopet.utils.summary.db.Schema._)
 #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
 #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._)
 #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._)
 #import(nl.lumc.sasc.biopet.core.report.ReportPage)
-#import(scala.concurrent.Await)
-#import(scala.concurrent.duration.Duration)
 #import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
 #import(java.io.File)
 <%@ var summary: SummaryDb %>
@@ -18,10 +17,14 @@
 <%@ var showTable: Boolean = true %>
 <%@ var showIntro: Boolean = true%>
 <%@ var runId: Int %>
+<%@ var allSamples: Seq[Sample] %>
+<%@ var allLibraries: Seq[Library] %>
 #{
-    val samples = Await.result(summary.getSamples(runId = Some(runId)), Duration.Inf)
+    val samples = sampleId match {
+    case Some(id) => allSamples.filter(_.id == id).toList
+    case _ => allSamples.toList
+    }
 }#
-
 #if (showIntro)
     <br/>
     <div class="row">
@@ -66,12 +69,12 @@
                 val libs: List[Option[Int]] = (libId, sampleLevel) match {
                 case (_, true) => List(None)
                 case (Some(_), _) => List(libId)
-                case _ => Await.result(summary.getLibraries(sampleId = Some(sample.id), runId = Some(runId)), Duration.Inf).map(x => Some(x.id)).toList
+                case _ => allLibraries.filter(_.sampleId == sample.id).map(x => Some(x.id)).toList
                 }
             }#
             <tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample}/index.html">${sample}</a></td>
             #for (libId <- libs)
-                #{ val libName = libId.map(l => Await.result(summary.getLibraryName(l), Duration.Inf)) }#
+                #{ val libName = libId.map(l => allLibraries.find(_.id == l).get.name) }#
                 #if (libs.head != libId) <tr> #end
                     #if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end
                     #{

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

-#{ //TODO: Need content }#
-
-Todo
\ No newline at end of file

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

+#import(nl.lumc.sasc.biopet.utils.summary.db.Schema._)
 #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
 #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._)
 #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._)
 #import(nl.lumc.sasc.biopet.core.report.ReportPage)
-#import(scala.concurrent.Await)
-#import(scala.concurrent.duration.Duration)
 #import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
 #import(java.io.File)
 <%@ var summary: SummaryDb %>
@@ -17,10 +16,14 @@
 <%@ var showIntro: Boolean = true%>
 <%@ var runId: Int %>
 <%@ var fields: List[String] = List("mean_coverage", "pct_5x", "pct_10x", "pct_15x", "pct_20x", "pct_25x", "pct_30x", "pct_40x", "pct_50x", "pct_60x", "pct_70x", "pct_80x", "pct_90x", "pct_100x")%>
+<%@ var allSamples: Seq[Sample] %>
+<%@ var allLibraries: Seq[Library] %>
 #{
-    val samples = Await.result(summary.getSamples(runId = Some(runId)), Duration.Inf)
+    val samples = sampleId match {
+    case Some(id) => allSamples.filter(_.id == id).toList
+    case _ => allSamples.toList
+    }
 }#
-
 #if (showIntro)
     <br/>
     <div class="row">
@@ -65,12 +68,12 @@
                 val libs: List[Option[Int]] = (libId, sampleLevel) match {
                 case (_, true) => List(None)
                 case (Some(_), _) => List(libId)
-                case _ => Await.result(summary.getLibraries(sampleId = Some(sample.id), runId = Some(runId)), Duration.Inf).map(x => Some(x.id)).toList
+                case _ => allLibraries.filter(_.sampleId == sample.id).map(x => Some(x.id)).toList
                 }
             }#
             <tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample.name}/index.html">${sample.name}</a></td>
             #for (libId <- libs)
-                #{ val libName = libId.map(l => Await.result(summary.getLibraryName(l), Duration.Inf)) }#
+                #{ val libName = libId.map(l => allLibraries.find(_.id == l).get.name) }#
                 #if (libs.head != libId) <tr> #end
                     #if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end
                     #{

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

@@ -48,9 +48,7 @@ object BammetricsReport extends ReportBuilder {
     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())
+      "Files" -> ReportPage(List(), List(), Map())
     ), List(
       "Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/bamMetricsFront.ssp")
     ) ::: bamMetricsPage.sections,

biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/librariesList.ssp

-#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
-#import(nl.lumc.sasc.biopet.core.report.ReportPage)
-#import(scala.concurrent.Await)
-#import(scala.concurrent.duration.Duration)
-<%@ var summary: SummaryDb %>
+#import(nl.lumc.sasc.biopet.utils.summary.db.Schema._)
 <%@ var rootPath: String %>
 <%@ var sampleId: Option[Int] = None %>
-<%@ var runId: Int %>
+<%@ var allLibraries: Seq[Library] %>
+<%@ var allSamples: Seq[Sample] %>
 <table class="table">
 <thead><tr><th>Libraries</th></tr></thead>
 <tbody>
-#for (lib <- Await.result(summary.getLibraries(runId = Some(runId)), Duration.Inf))
-    <tr><td><a href="${rootPath}Samples/${Await.result(summary.getSampleName(lib.sampleId), Duration.Inf)}/Libraries/${lib.name}/index.html">${lib}</a></td></tr>
+#{ val libs = sampleId match {
+    case Some(id) => allLibraries.filter(_.sampleId == id)
+    case _ => allLibraries
+} }#
+#for (lib <- libs)
+    #{ val sampleName: String = allSamples.find(_.id == lib.sampleId).get.name }#
+    <tr><td><a href="${rootPath}Samples/${sampleName}/Libraries/${lib.name}/index.html">${lib}</a></td></tr>
 #end
 </tbody>
 </table>
\ No newline at end of file

biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/samplesList.ssp

-#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
-#import(nl.lumc.sasc.biopet.core.report.ReportPage)
-#import(scala.concurrent.Await)
-#import(scala.concurrent.duration.Duration)
-<%@ var summary: SummaryDb %>
+#import(nl.lumc.sasc.biopet.utils.summary.db.Schema._)
 <%@ var rootPath: String %>
-<%@ var runId: Int %>
+<%@ var allSamples: Seq[Sample] %>
 <table class="table sortable-theme-bootstrap" data-sortable>
     <thead><tr><th data-sorted="true" data-sorted-direction="ascending">Sample</th></tr></thead>
     <tbody>
-        #for (sample <- Await.result(summary.getSamples(runId = Some(runId)), Duration.Inf))
+        #for (sample <- allSamples)
             <tr><td><a href="${rootPath}Samples/${sample.name}/index.html">${sample.name}</a></td></tr>
         #end
     </tbody>

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala

@@ -54,7 +54,7 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
     }
     writer.println("set -eubf")
     writer.println("set -o pipefail")
-    lines.foreach(writer.println)
+    writer.println(this.commandLine)
     jobDelayTime.foreach(x => writer.println(s"sleep $x"))
     writer.close()
   }
@@ -99,6 +99,8 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
     beforeGraph()
     internalBeforeGraph()
 
+    this.commandDirectory = this.jobOutputFile.getParentFile
+
     super.freezeFieldValues()
   }
 

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala

@@ -38,17 +38,16 @@ class CleverCaller(val parent: Configurable) extends BiopetCommandLineFunction w
   @Input(doc = "Reference")
   var reference: File = _
 
-  protected def cleverOutputDir: File = new File(cleverWorkDir, "work")
   var cleverWorkDir: File = _
 
   @Output(doc = "Clever VCF output")
   lazy val outputvcf: File = {
-    new File(cleverOutputDir, "predictions.vcf")
+    new File(cleverWorkDir, "predictions.vcf")
   }
 
   @Output(doc = "Clever raw output")
   lazy val outputraw: File = {
-    new File(cleverOutputDir, "predictions.raw.txt")
+    new File(cleverWorkDir, "predictions.raw.txt")
   }
 
   //  var T: Option[Int] = config("T", default = defaultThreads)
@@ -60,13 +59,13 @@ class CleverCaller(val parent: Configurable) extends BiopetCommandLineFunction w
 
   override def beforeGraph() {
     super.beforeGraph()
-    if (cleverOutputDir == null) throw new Exception("Clever :: Workdirectory is not defined")
+    if (cleverWorkDir == null) throw new Exception("Clever :: Workdirectory is not defined")
     if (reference == null) reference = referenceFasta()
   }
 
   def cmdLine = required(executable) +
-    " --sorted " +
-    " --use_xa " +
+    required("--sorted") +
+    required("--use_xa") +
     optional("-T", threads) +
     conditional(f, "-f") +
     conditional(a, "-a") +
@@ -74,7 +73,7 @@ class CleverCaller(val parent: Configurable) extends BiopetCommandLineFunction w
     conditional(r, "-r") +
     required(input) +
     required(reference) +
-    required(cleverOutputDir)
+    required(cleverWorkDir)
 }
 
 object CleverCaller {

docs/general/config.md

@@ -70,9 +70,9 @@ In the `tags` key inside a sample or library users can supply tags that belong t
 The settings config enables a user to alter the settings for almost all settings available in the tools used for a given pipeline.
 This config file should be written in either JSON or YAML format. It can contain setup settings like:
 
- * references,
- * cut offs,
- * program modes and memory limits (program specific),
+ * references
+ * cut offs
+ * program modes and memory limits (program specific)
  * Whether chunking should be used
  * set program executables (if for some reason the user does not want to use the systems default tools)
  * One could set global variables containing settings for all tools used in the pipeline or set tool specific options one layer 
@@ -128,9 +128,13 @@ It is also possible to set the `"species"` flag. Again, we will default to `unkn
 # More advanced use of config files.
 ### 4 levels of configuring settings
 In biopet, a value of a ConfigNamespace (e.g., "reference_fasta") for a tool or a pipeline can be defined in 4 different levels.
+
  * Level-4: As a fixed value hardcoded in biopet source code
+ 
  * Level-3: As a user specified value in the user config file
+ 
  * Level-2: As a system specified value in the global config files. On the LUMC's SHARK cluster, these global config files are located at /usr/local/sasc/config.
+ 
  * Level-1: As a default value provided in biopet source code.
 
 During execution, biopet framework will resolve the value for each ConfigNamespace following the order from level-4 to level-1. Hence, a value defined in the a higher level will overwrite a value define in a lower level for the same ConfigNamespace.
@@ -172,4 +176,4 @@ biopet template Gentrap -o gentrap_config.yml -s gentrap_run.sh
 | -o | --outputConfig | Path (**required**) | Name of the config file that gets generated.|
 | -s | --outputScript | Path (optional) | Biopet can also output a script that can be directly used for running the pipeline, the call of the pipeline is generated with the config file as input. This parameter sets the name for the script file.|
 | -t | --template | Path (optional) | A template file with 2 placeholders *%s* is required for generating the script. The first placeholder will be replaced with the name of the pipeline, the second with the paths to the sample and settings config files. When Biopet has been pre-configured to use the default template file, then setting this parameter is optional. |
-|    | --expert |  | This flag enables the user to configure a more extensive list of parameters for the pipeline. |
\ No newline at end of file
+|    | --expert |  | This flag enables the user to configure a more extensive list of parameters for the pipeline. |

docs/pipelines/mapping.md

@@ -49,7 +49,7 @@ All other values should be provided in the config. Specific config values toward
 | ---- | ---- | -------- |
 | output_dir | Path (**required**) | directory for output files |
 | reference_fasta | Path (**required**) | Path to indexed fasta file to be used as reference |
-| aligner | String (optional) | Which aligner to use. Defaults to `bwa`. Choose from [`bwa`, `bwa-aln`, `bowtie`, `gsnap`, `tophat`, `stampy`, `star`, `star-2pass`, `hisat2`] |
+| aligner | String (optional) | Which aligner to use. Defaults to `bwa`. Choose from [`bwa-mem`, `bwa-aln`, `bowtie`, `bowtie2`, `gsnap`, `tophat`, `stampy`, `star`, `star-2pass`, `hisat2`] |
 | skip_flexiprep | Boolean (optional) | Whether to skip the flexiprep QC step (default = False) |
 | skip_markduplicates | Boolean (optional) | Whether to skip the Picard Markduplicates step (default = False) |
 | skip_metrics | Boolean (optional) | Whether to skip the metrics gathering step (default = False) |

docs/pipelines/yamsvp.md

-# Introduction
-
-# Invocation
-
-# Example
-Note that one should first create the appropriate [configs](../general/config.md).
-
-# Testcase A
-
-# Testcase B
-
-# Examine results
-
-## Result files
-
-## Best practice
-
-# References

flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepInputfiles.ssp

-#import(nl.lumc.sasc.biopet.utils.summary.Summary)
-#import(nl.lumc.sasc.biopet.core.report.ReportPage)
-#import(nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport)
-#import(java.io.File)
-<%@ var summary: Summary %>
-<%@ var sampleId: Option[String] = None %>
-<%@ var libId: Option[String] = None %>
-<%@ var rootPath: String %>
-<%@ var outputDir: File %>
-<%@ var showPlot: Boolean = false %>
-<%@ var showTable: Boolean = true %>
-#{
-    val samples = sampleId match {
-        case Some(sample) => List(sample.toString)
-        case _ => summary.samples.toList
-    }
-    val pipelineOutputDir = summary.getValue("meta", "output_dir").getOrElse("").toString
-    def removeDir(value: Option[Any]): Option[Any] = {
-        value.collect { case a =>
-            if (a.toString.startsWith(pipelineOutputDir) && pipelineOutputDir.nonEmpty) "./" + a.toString.stripPrefix(pipelineOutputDir + File.separator)
-            else a
-        }
-    }
-}#
-
-<table class="table">
-
-<thead><tr>
-    <th>Sample</th>
-    <th colspan="2">Library</th>
-    <th>Path</th>
-    <th>MD5</th>
-</tr></thead>
-<tbody>
-    #for (sample <- samples.toList.sorted)
-        #{
-            val libs = libId match {
-            case Some(libId) => List(libId.toString).sorted
-            case _ => summary.libraries(sample).toList.sorted
-            }
-
-            val sampleRowspan = {
-            libs.size +
-            libs.count(summary.getLibraryValue(sample, _, "flexiprep", "settings", "paired").getOrElse(false) == true)
-            }
-        }#
-        <tr><td rowspan="${sampleRowspan}"><a href="${rootPath}Samples/${sample}/index.html">${sample}</a></td>
-        #for (libId <- libs)
-            #if (libs.head != libId) <tr> #end
-                #{ val paired = summary.getLibraryValue(sample, libId, "flexiprep", "settings", "paired").getOrElse(false) }#
-                <td #if (paired == true) rowspan="2" #end><a href="${rootPath}Samples/${sample}/Libraries/${libId}/index.html">${libId}</a></td>
-                #{ val reads = if (paired == true) List("R1", "R2") else List("R1") }#
-                #for (read <- reads)
-                    #if (read == "R2") </tr><tr> #end
-                    <td>${read}</td>
-                    <td>${removeDir(summary.getLibraryValue(sample, libId, "flexiprep", "files", "pipeline", "input_" + read, "path"))}</td>
-                    <td>${summary.getLibraryValue(sample, libId, "flexiprep", "files", "pipeline", "input_" + read, "md5")}</td>
-                #end
-            </tr>
-        #end
-    #end
-</tbody>
-</table>
\ No newline at end of file

flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepOutputfiles.ssp

-#import(nl.lumc.sasc.biopet.utils.summary.Summary)
-#import(nl.lumc.sasc.biopet.core.report.ReportPage)
-#import(nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport)
-#import(java.io.File)
-<%@ var summary: Summary %>
-<%@ var sampleId: Option[String] = None %>
-<%@ var libId: Option[String] = None %>
-<%@ var rootPath: String %>
-<%@ var outputDir: File %>
-<%@ var showPlot: Boolean = false %>
-<%@ var showTable: Boolean = true %>
-#{
-    val samples = sampleId match {
-        case Some(sample) => List(sample.toString)
-        case _ => summary.samples.toList
-    }
-    val pipelineOutputDir = summary.getValue("meta", "output_dir").getOrElse("").toString
-    def removeDir(value: Option[Any]): Option[Any] = {
-        value.collect { case a =>
-            if (a.toString.startsWith(pipelineOutputDir) && pipelineOutputDir.nonEmpty) "./" + a.toString.stripPrefix(pipelineOutputDir + File.separator)
-            else a
-        }
-    }
-}#
-
-<table class="table">
-
-<thead><tr>
-    <th>Sample</th>
-    <th colspan="2">Library</th>
-    <th>Path</th>
-    <th>MD5</th>
-</tr></thead>
-<tbody>
-    #for (sample <- samples.toList.sorted)
-        #{
-            val libs = libId match {
-            case Some(libId) => List(libId.toString).sorted
-            case _ => summary.libraries(sample).toList.sorted
-            }
-
-            val sampleRowspan = {
-            libs.size +
-            libs.count(summary.getLibraryValue(sample, _, "flexiprep", "settings", "paired").getOrElse(false) == true)
-            }
-        }#
-        <tr><td rowspan="${sampleRowspan}"><a href="${rootPath}Samples/${sample}/index.html">${sample}</a></td>
-        #for (libId <- libs)
-            #if (libs.head != libId) <tr> #end
-                #{ val paired = summary.getLibraryValue(sample, libId, "flexiprep", "settings", "paired").getOrElse(false) }#
-                <td #if (paired == true) rowspan="2" #end><a href="${rootPath}Samples/${sample}/Libraries/${libId}/index.html">${libId}</a></td>
-                #{ val reads = if (paired == true) List("R1", "R2") else List("R1") }#
-                #for (read <- reads)
-                    #if (read == "R2") </tr><tr> #end
-                    <td>${read}</td>
-                    <td>${removeDir(summary.getLibraryValue(sample, libId, "flexiprep", "files", "pipeline", "output_" + read, "path"))}</td>