diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala
index 224d6208d16f3d1756dfa480f6c9684e18041f8c..8bd2d588d704b668f76d8c502b66c209854cf54f 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala
@@ -22,6 +22,12 @@ trait GatkGeneral extends CommandLineGATK with BiopetJavaCommandLineFunction wit
if (config.contains("gatk_key")) gatk_key = config("gatk_key")
if (config.contains("pedigree")) pedigree = config("pedigree")
+ override val versionRegex = """(.*)""".r
+ override val versionExitcode = List(0, 1)
+ override def versionCommand = executable + " -jar " + jarFile + " -version"
+
+ override def getVersion = super.getVersion.collect { case version => "Gatk " + version }
+
override def beforeGraph: Unit = {
super.beforeGraph
if (reference_sequence == null) reference_sequence = referenceFasta()
diff --git a/protected/biopet-gatk-pipelines/pom.xml b/protected/biopet-gatk-pipelines/pom.xml
index cc1e68d7a949a8ed924979ace6f13584308e11f7..a7803602f670b18f38e561f0632f680c3dd35fad 100644
--- a/protected/biopet-gatk-pipelines/pom.xml
+++ b/protected/biopet-gatk-pipelines/pom.xml
@@ -57,7 +57,7 @@
</dependency>
<dependency>
<groupId>org.scalatest</groupId>
- <artifactId>scalatest_2.11</artifactId>
+ <artifactId>scalatest_2.10</artifactId>
<version>2.2.1</version>
<scope>test</scope>
</dependency>
diff --git a/public/bammetrics/pom.xml b/public/bammetrics/pom.xml
index b8dc8707c14cddb19ad0554292c9e6df088a39a2..b876611c2e9205749405ee54b82498c65a792d42 100644
--- a/public/bammetrics/pom.xml
+++ b/public/bammetrics/pom.xml
@@ -47,7 +47,7 @@
</dependency>
<dependency>
<groupId>org.scalatest</groupId>
- <artifactId>scalatest_2.11</artifactId>
+ <artifactId>scalatest_2.10</artifactId>
<version>2.2.1</version>
<scope>test</scope>
</dependency>
diff --git a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp
new file mode 100644
index 0000000000000000000000000000000000000000..d5931c4b81b1c3e80e261d88adcc52316d1fe29a
--- /dev/null
+++ b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp
@@ -0,0 +1,90 @@
+#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.core.report.ReportPage)
+#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
+#import(java.io.File)
+<%@ var summary: Summary %>
+<%@ var sampleId: Option[String] = None %>
+<%@ var libId: Option[String] = None %>
+<%@ var sampleLevel: Boolean = false %>
+<%@ var rootPath: String %>
+<%@ var outputDir: File %>
+<%@ 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>
+ Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nunc risus est, volutpat quis enim sit amet, lacinia posuere ante. Mauris eget massa efficitur, luctus nisl ut, placerat nibh. Pellentesque id nulla maximus, rutrum dui nec, lobortis odio. Fusce eu enim ac sem auctor congue. Ut ac ullamcorper quam, eget sollicitudin felis. Maecenas posuere sagittis blandit. Proin mollis magna lectus, id gravida est consectetur vitae. Nulla id risus at tellus laoreet finibus in id lacus. Duis lobortis commodo nisl viverra tempor. Curabitur sit amet pretium dui, sit amet tincidunt mauris. Duis volutpat eu purus ut molestie.
+ </p>
+ </div>
+ </div>
+#end
+#if (showPlot)
+#{ BammetricsReport.alignmentSummaryPlot(outputDir, "alignmentSummary", summary, !sampleLevel, sampleId = sampleId) }#
+
+ <div class="panel-body">
+ <img src="alignmentSummary.png" class="img-responsive" />
+ </div>
+ <div class="panel-footer">
+ #if (showTable)
+ <button type="button" class="btn btn-info" data-toggle="collapse" data-target="#alignmentSummaryTable">Hide table</button>
+ #else
+ <button type="button" class="btn btn-info" data-toggle="collapse" data-target="#alignmentSummaryTable">Show table</button>
+ #end
+ <i class="glyphicon glyphicon-file"></i> <a href="alignmentSummary.tsv">tsv file</a>
+ </div>
+#end
+<div class="panel-body collapse #if (showTable)in#end" id="alignmentSummaryTable">
+<!-- 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
+ <th>Total</th>
+ <th>Mapped</th>
+ <th>(%)</th>
+ <th>Duplicates</th>
+ <th>(%)</th>
+ </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 total = summary.getValue((prefixPath ::: List("biopet_flagstat", "All")):_*).getOrElse(0L).asInstanceOf[Long]
+ val mapped = summary.getValue((prefixPath ::: List("biopet_flagstat", "Mapped")):_*).getOrElse(0L).asInstanceOf[Long]
+ val duplicates = summary.getValue((prefixPath ::: List("biopet_flagstat", "Duplicates")):_*).getOrElse(0L).asInstanceOf[Long]
+ }#
+ <td>${total}</td>
+ <td>${mapped}</td>
+ <td>${mapped.toDouble / total * 100}%</td>
+ <td>${duplicates}</td>
+ <td>${duplicates.toDouble / total * 100}%</td>
+ </tr>
+ #end
+ #end
+ </tbody>
+</table>
+
+</div>
\ No newline at end of file
diff --git a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bamMetricsFront.ssp b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bamMetricsFront.ssp
new file mode 100644
index 0000000000000000000000000000000000000000..8701c981a774cf44daf0bd39ccf837a7d69afe1b
--- /dev/null
+++ b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bamMetricsFront.ssp
@@ -0,0 +1,3 @@
+#{ //TODO: Need content }#
+
+Todo
\ No newline at end of file
diff --git a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bamStats.ssp b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bamStats.ssp
new file mode 100644
index 0000000000000000000000000000000000000000..c6ea6f5db5084bc3644cd6dacd22728821b024be
--- /dev/null
+++ b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bamStats.ssp
@@ -0,0 +1,22 @@
+#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.core.report.ReportPage)
+<%@ var summary: Summary %>
+<%@ var sampleId: Option[String] %>
+<%@ var libId: Option[String] = None %>
+<%@ var rootPath: String %>
+<%@ var metricsTag: String = "bammetrics" %>
+<%@ var fields: List[String] = List("All", "Mapped", "Duplicates", "MAPQ>30", "MateUnmapped", "Mate on other chr")%>
+
+<table>
+<tbody>
+#for (field <- fields)
+ <tr><th>${field}</th><td>
+ #if (libId.isDefined)
+ ${summary.getLibraryValue(sampleId.get, libId.get, metricsTag, "stats", "biopet_flagstat", field)}
+ #else
+ ${summary.getSampleValue(sampleId.get, metricsTag, "stats", "biopet_flagstat", field)}
+ #end
+ </td></tr>
+#end
+</tbody>
+</table>
diff --git a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp
new file mode 100644
index 0000000000000000000000000000000000000000..294b7ba010b36d9673848d91f13d46b376fdefaa
--- /dev/null
+++ b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp
@@ -0,0 +1,67 @@
+#import(nl.lumc.sasc.biopet.utils.IoUtils)
+#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.core.report.ReportPage)
+#import(org.apache.commons.io.FileUtils)
+#import(java.io.File)
+<%@ var summary: Summary %>
+<%@ var sampleId: Option[String] = None %>
+<%@ var libId: Option[String] = None %>
+<%@ var sampleLevel: Boolean = true %>
+<%@ var rootPath: String %>
+<%@ var outputDir: File %>
+<%@ var metricsTag: String = "bammetrics" %>
+<%@ var target: String %>
+#{
+ val samples = sampleId match {
+ case Some(sample) => List(sample.toString)
+ case _ => summary.samples.toList
+ }
+}#
+
+
+<table class="table">
+<thead><tr>
+ <th>sample</th>
+ <th>mean</th>
+ <th>median</th>
+ <th>max</th>
+ <th>horizontal</th>
+ <th>frac min 10x</th>
+ <th>frac min 20x</th>
+ <th>frac min 30x</th>
+ <th>frac min 40x</th>
+ <th>frac min 50x</th>
+</tr></thead>
+<tbody>
+ #for (sample <- samples.toList.sorted)
+ #{
+ val libs = (libId, sampleLevel) match {
+ case (_, true) => List("")
+ case (Some(libId), _) => List(libId.toString)
+ case _ => summary.libraries(sample).toList
+ }
+ }#
+ <tr><td rowspan="${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">${libId}</a></td> #end
+ #{
+ val prefixPath = List("samples", sample) ::: (if (libId.isEmpty) Nil else List("libraries", libId)) ::: List(metricsTag, "stats", target + "_cov_stats", "coverage", "_all")
+ val total = summary.getValue((prefixPath ::: List("biopet_flagstat", "All")):_*).getOrElse(0L).asInstanceOf[Long]
+ val mapped = summary.getValue((prefixPath ::: List("biopet_flagstat", "Mapped")):_*).getOrElse(0L).asInstanceOf[Long]
+ val duplicates = summary.getValue((prefixPath ::: List("biopet_flagstat", "Duplicates")):_*).getOrElse(0L).asInstanceOf[Long]
+ }#
+ <td>${summary.getValue((prefixPath ::: "mean" :: Nil):_*)}</td>
+ <td>${summary.getValue((prefixPath ::: "median" :: Nil):_*)}</td>
+ <td>${summary.getValue((prefixPath ::: "max" :: Nil):_*)}</td>
+ <td>${summary.getValue((prefixPath ::: "horizontal" :: Nil):_*)}</td>
+ <td>${summary.getValue((prefixPath ::: "frac_min_10x" :: Nil):_*)}</td>
+ <td>${summary.getValue((prefixPath ::: "frac_min_20x" :: Nil):_*)}</td>
+ <td>${summary.getValue((prefixPath ::: "frac_min_30x" :: Nil):_*)}</td>
+ <td>${summary.getValue((prefixPath ::: "frac_min_40x" :: Nil):_*)}</td>
+ <td>${summary.getValue((prefixPath ::: "frac_min_50x" :: Nil):_*)}</td>
+ </tr>
+ #end
+ #end
+</tbody>
+</table>
diff --git a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp
new file mode 100644
index 0000000000000000000000000000000000000000..6aa6ff46ade93f4e7fcfa65527c133fc0392c6b9
--- /dev/null
+++ b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp
@@ -0,0 +1,50 @@
+#import(nl.lumc.sasc.biopet.utils.IoUtils)
+#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.core.report.ReportPage)
+#import(org.apache.commons.io.FileUtils)
+#import(java.io.File)
+<%@ var summary: Summary %>
+<%@ var sampleId: Option[String] %>
+<%@ var libId: Option[String] = None %>
+<%@ var outputDir: File %>
+<%@ var metricsTag: String = "bammetrics" %>
+<%@ var target: String %>
+#{
+ val originalPlot = new File(summary.getLibraryValue(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")
+ .getOrElse(throw new IllegalArgumentException("No plot found in summary")).asInstanceOf[Map[String, Any]]
+
+ if (originalPlot.exists()) IoUtils.copyFile(originalPlot, plot)
+}#
+
+<img src="${plot}">
+
+<table class="table">
+<thead><tr>
+ <th>mean</th>
+ <th>median</th>
+ <th>max</th>
+ <th>horizontal</th>
+ <th>frac min 10x</th>
+ <th>frac min 20x</th>
+ <th>frac min 30x</th>
+ <th>frac min 40x</th>
+ <th>frac min 50x</th>
+</tr></thead>
+<tbody>
+<tr>
+ <td>${values.get("mean")}</td>
+ <td>${values.get("median")}</td>
+ <td>${values.get("max")}</td>
+ <td>${values.get("horizontal")}</td>
+ <td>${values.get("frac_min_10x")}</td>
+ <td>${values.get("frac_min_20x")}</td>
+ <td>${values.get("frac_min_30x")}</td>
+ <td>${values.get("frac_min_40x")}</td>
+ <td>${values.get("frac_min_50x")}</td>
+</tr>
+</tbody>
+</table>
diff --git a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/gcBias.ssp b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/gcBias.ssp
new file mode 100644
index 0000000000000000000000000000000000000000..8701c981a774cf44daf0bd39ccf837a7d69afe1b
--- /dev/null
+++ b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/gcBias.ssp
@@ -0,0 +1,3 @@
+#{ //TODO: Need content }#
+
+Todo
\ No newline at end of file
diff --git a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp
new file mode 100644
index 0000000000000000000000000000000000000000..47491d04201455760f66c30f36fde37cd8911fa4
--- /dev/null
+++ b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp
@@ -0,0 +1,93 @@
+#import(nl.lumc.sasc.biopet.core.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("mean_insert_size", "standard_deviation", "median_insert_size")%>
+<%@ 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>
+ Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nunc risus est, volutpat quis enim sit amet, lacinia posuere ante. Mauris eget massa efficitur, luctus nisl ut, placerat nibh. Pellentesque id nulla maximus, rutrum dui nec, lobortis odio. Fusce eu enim ac sem auctor congue. Ut ac ullamcorper quam, eget sollicitudin felis. Maecenas posuere sagittis blandit. Proin mollis magna lectus, id gravida est consectetur vitae. Nulla id risus at tellus laoreet finibus in id lacus. Duis lobortis commodo nisl viverra tempor. Curabitur sit amet pretium dui, sit amet tincidunt mauris. Duis volutpat eu purus ut molestie.
+ </p>
+ </div>
+ </div>
+#end
+
+#if (showPlot)
+ #{ BammetricsReport.insertSizePlot(outputDir, "insertsize", summary, !sampleLevel, sampleId = sampleId) }#
+
+ <div class="panel-body">
+ <img src="insertsize.png" class="img-responsive" />
+ </div>
+ <div class="panel-footer">
+ #if (showTable)
+ <button type="button" class="btn btn-info" data-toggle="collapse" data-target="#insertsizeTable">Hide table</button>
+ #else
+ <button type="button" class="btn btn-info" data-toggle="collapse" data-target="#insertsizeTable">Show table</button>
+ #end
+ <i class="glyphicon glyphicon-file"></i> <a href="insertsize.tsv">tsv file</a>
+ </div>
+#end
+
+<div class="panel-body collapse #if (showTable)in#end" id="insertsizeTable">
+<!-- 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">${libId}</a></td> #end
+ #{
+ val prefixPath = List("samples", sample) ::: (if (libId.isEmpty) Nil else List("libraries", libId)) ::: List("bammetrics", "stats")
+
+ val fieldValues = for (field <- fields) yield {
+ summary.getValue((prefixPath ::: List("CollectInsertSizeMetrics", "metrics", field.toUpperCase)):_*).getOrElse(prefixPath ::: metricsTag :: Nil)
+ }
+ }#
+ #for (value <- fieldValues)
+ <td>${value}</td>
+ #end
+ </tr>
+ #end
+ #end
+ </tbody>
+</table>
+
+</div>
diff --git a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/rna.ssp b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/rna.ssp
new file mode 100644
index 0000000000000000000000000000000000000000..8701c981a774cf44daf0bd39ccf837a7d69afe1b
--- /dev/null
+++ b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/rna.ssp
@@ -0,0 +1,3 @@
+#{ //TODO: Need content }#
+
+Todo
\ No newline at end of file
diff --git a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/target.ssp b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/target.ssp
new file mode 100644
index 0000000000000000000000000000000000000000..8701c981a774cf44daf0bd39ccf837a7d69afe1b
--- /dev/null
+++ b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/target.ssp
@@ -0,0 +1,3 @@
+#{ //TODO: Need content }#
+
+Todo
\ No newline at end of file
diff --git a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp
new file mode 100644
index 0000000000000000000000000000000000000000..106608cc023365f0851acdd8f006aafb75231bd7
--- /dev/null
+++ b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp
@@ -0,0 +1,93 @@
+#import(nl.lumc.sasc.biopet.core.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("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 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>
+ Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nunc risus est, volutpat quis enim sit amet, lacinia posuere ante. Mauris eget massa efficitur, luctus nisl ut, placerat nibh. Pellentesque id nulla maximus, rutrum dui nec, lobortis odio. Fusce eu enim ac sem auctor congue. Ut ac ullamcorper quam, eget sollicitudin felis. Maecenas posuere sagittis blandit. Proin mollis magna lectus, id gravida est consectetur vitae. Nulla id risus at tellus laoreet finibus in id lacus. Duis lobortis commodo nisl viverra tempor. Curabitur sit amet pretium dui, sit amet tincidunt mauris. Duis volutpat eu purus ut molestie.
+ </p>
+ </div>
+ </div>
+#end
+
+#if (showPlot)
+ #{ BammetricsReport.wgsHistogramPlot(outputDir, "wgs", summary, !sampleLevel, sampleId = sampleId) }#
+
+ <div class="panel-body">
+ <img src="wgs.png" class="img-responsive" />
+ </div>
+ <div class="panel-footer">
+ #if (showTable)
+ <button type="button" class="btn btn-info" data-toggle="collapse" data-target="#wgsTable">Hide table</button>
+ #else
+ <button type="button" class="btn btn-info" data-toggle="collapse" data-target="#wgsTable">Show table</button>
+ #end
+ <i class="glyphicon glyphicon-file"></i> <a href="wgs.tsv">tsv file</a>
+ </div>
+#end
+
+<div class="panel-body collapse #if (showTable)in#end" id="wgsTable">
+<!-- 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">${libId}</a></td> #end
+ #{
+ val prefixPath = List("samples", sample) ::: (if (libId.isEmpty) Nil else List("libraries", libId)) ::: List("bammetrics", "stats")
+
+ val fieldValues = for (field <- fields) yield {
+ summary.getValue((prefixPath ::: List("wgs", "metrics", field.toUpperCase)):_*).getOrElse(prefixPath ::: metricsTag :: Nil)
+ }
+ }#
+ #for (value <- fieldValues)
+ <td>${value}</td>
+ #end
+ </tr>
+ #end
+ #end
+ </tbody>
+</table>
+
+</div>
diff --git a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
index 2547108e449440da76afffe519945a156356127f..32c4553f5d3ced53ab6539ff279fc56a55a05171 100644
--- a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
+++ b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
@@ -156,8 +156,10 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
//FIXME:should use piping
add(BedtoolsCoverage(this, inputBam, intervals.bed, coverageFile, depth = true), true)
val covStats = CoverageStats(this, coverageFile, targetDir)
+ covStats.title = Some("Coverage for " + targetName)
+ covStats.subTitle = Some(".")
add(covStats)
- addSummarizable(covStats, "cov_stats")
+ addSummarizable(covStats, targetName + "_cov_stats")
}
addSummaryJobs
diff --git a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
new file mode 100644
index 0000000000000000000000000000000000000000..d12c307cb8b2e5c8213d3e444832880a230fe9f9
--- /dev/null
+++ b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
@@ -0,0 +1,256 @@
+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.summary.{ SummaryValue, Summary }
+import nl.lumc.sasc.biopet.extensions.rscript.{ XYPlot, StackedBarPlot }
+
+/**
+ * Created by pjvan_thof on 3/30/15.
+ */
+object BammetricsReport extends ReportBuilder {
+ // FIXME: Not yet finished
+
+ val reportName = "Bam Metrics"
+
+ def indexPage = ReportPage(List(), List(), Map())
+
+ def bamMetricsPage(summary: Summary, sampleId: Option[String], libId: Option[String]) = {
+ val targets = (
+ summary.getLibraryValue(sampleId, libId, "bammetrics", "settings", "amplicon_name"),
+ summary.getLibraryValue(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)
+ case _ => Nil
+ }
+
+ ReportPage(
+ (if (targets.isEmpty) List() else List("Targets" -> ReportPage(
+ List(),
+ targets.map(t => (t -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp", Map("target" -> t)))),
+ 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))
+ ),
+ Map()
+ )
+ }
+
+ def alignmentSummaryPlot(outputDir: File,
+ prefix: String,
+ summary: Summary,
+ libraryLevel: Boolean = false,
+ sampleId: 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.print("Library") else tsvWriter.print("Sample")
+ tsvWriter.println("\tMapped\tDuplicates\tUnmapped\tSecondary")
+
+ def getLine(summary: Summary, sample: String, lib: Option[String] = None): String = {
+ val mapped = new SummaryValue(List("bammetrics", "stats", "biopet_flagstat", "Mapped"),
+ summary, Some(sample), lib).value.getOrElse(0).toString.toLong
+ val duplicates = new SummaryValue(List("bammetrics", "stats", "biopet_flagstat", "Duplicates"),
+ summary, Some(sample), lib).value.getOrElse(0).toString.toLong
+ val total = new SummaryValue(List("bammetrics", "stats", "biopet_flagstat", "All"),
+ summary, Some(sample), lib).value.getOrElse(0).toString.toLong
+ val secondary = new SummaryValue(List("bammetrics", "stats", "biopet_flagstat", "NotPrimaryAlignment"),
+ summary, Some(sample), lib).value.getOrElse(0).toString.toLong
+ val sb = new StringBuffer()
+ if (lib.isDefined) sb.append(sample + "-" + lib.get + "\t") else sb.append(sample + "\t")
+ sb.append((mapped - duplicates) + "\t")
+ sb.append(duplicates + "\t")
+ sb.append((total - mapped - secondary) + "\t")
+ sb.append(secondary)
+ sb.toString
+ }
+
+ if (libraryLevel) {
+ for (
+ sample <- summary.samples if (sampleId.isEmpty || sample == sampleId.get);
+ lib <- summary.libraries(sample)
+ ) {
+ tsvWriter.println(getLine(summary, sample, Some(lib)))
+ }
+ } else {
+ for (sample <- summary.samples if (sampleId.isEmpty || sample == sampleId.get)) {
+ tsvWriter.println(getLine(summary, sample))
+ }
+ }
+
+ tsvWriter.close()
+
+ val plot = new StackedBarPlot(null)
+ plot.input = tsvFile
+ plot.output = pngFile
+ plot.ylabel = Some("Reads")
+ if (libraryLevel) {
+ plot.width = Some(200 + (summary.libraries.filter(s => sampleId.getOrElse(s._1) == s._1).foldLeft(0)(_ + _._2.size) * 10))
+ } else plot.width = Some(200 + (summary.samples.filter(s => sampleId.getOrElse(s) == s).size * 10))
+ plot.title = Some("Aligned reads")
+ plot.runLocal()
+ }
+
+ def insertSizePlot(outputDir: File,
+ prefix: String,
+ summary: Summary,
+ libraryLevel: Boolean = false,
+ sampleId: 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)
+ ) 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, Int]] = Map()
+
+ def fill(sample: String, lib: Option[String]): Unit = {
+
+ val insertSize = new SummaryValue(List("bammetrics", "stats", "CollectInsertSizeMetrics", "histogram", "insert_size"),
+ summary, Some(sample), lib).value.getOrElse(List())
+ val counts = new SummaryValue(List("bammetrics", "stats", "CollectInsertSizeMetrics", "histogram", "All_Reads.fr_count"),
+ 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.toInt
+ val old = map.getOrElse(insertSize, Map())
+ if (libraryLevel) map += insertSize -> (old + ((s"$sample-" + lib.get) -> count))
+ else map += insertSize -> (old + (sample -> count))
+ })
+ }
+ case _ => throw new IllegalStateException("Must be a list")
+ }
+ }
+
+ if (libraryLevel) {
+ for (
+ sample <- summary.samples if (sampleId.isEmpty || sampleId.get == sample);
+ lib <- summary.libraries(sample)
+ ) fill(sample, Some(lib))
+ } else if (sampleId.isDefined) fill(sampleId.get, None)
+ else summary.samples.foreach(fill(_, None))
+
+ for ((insertSize, counts) <- map) {
+ tsvWriter.print(insertSize)
+ if (libraryLevel) {
+ for (
+ sample <- summary.samples if (sampleId.isEmpty || sampleId.get == sample);
+ lib <- summary.libraries(sample)
+ ) tsvWriter.print("\t" + counts.getOrElse(s"$sample-$lib", "0"))
+ } else {
+ for (sample <- summary.samples if (sampleId.isEmpty || sampleId.get == sample)) {
+ tsvWriter.print("\t" + counts.getOrElse(sample, "0"))
+ }
+ }
+ tsvWriter.println()
+ }
+
+ tsvWriter.close()
+
+ val plot = new XYPlot(null)
+ plot.input = tsvFile
+ plot.output = pngFile
+ plot.ylabel = Some("Reads")
+ plot.xlabel = Some("Insert size")
+ plot.width = Some(1200)
+ plot.removeZero = true
+ plot.title = Some("Insert size")
+ plot.runLocal()
+ }
+
+ def wgsHistogramPlot(outputDir: File,
+ prefix: String,
+ summary: Summary,
+ libraryLevel: Boolean = false,
+ sampleId: Option[String] = None): Unit = {
+ val tsvFile = new File(outputDir, prefix + ".tsv")
+ val pngFile = new File(outputDir, prefix + ".png")
+ val tsvWriter = new PrintWriter(tsvFile)
+ if (libraryLevel) {
+ tsvWriter.println((for (
+ sample <- summary.samples if (sampleId.isEmpty || sampleId.get == sample);
+ lib <- summary.libraries(sample)
+ ) yield s"$sample-$lib")
+ .mkString("library\t", "\t", ""))
+ } else {
+ sampleId match {
+ case Some(sample) => tsvWriter.println("\t" + sample)
+ case _ => tsvWriter.println(summary.samples.mkString("Sample\t", "\t", ""))
+ }
+ }
+
+ var map: Map[Int, Map[String, Int]] = Map()
+
+ def fill(sample: String, lib: Option[String]): Unit = {
+
+ val insertSize = new SummaryValue(List("bammetrics", "stats", "wgs", "histogram", "coverage"),
+ summary, Some(sample), lib).value.getOrElse(List())
+ val counts = new SummaryValue(List("bammetrics", "stats", "wgs", "histogram", "count"),
+ summary, Some(sample), lib).value.getOrElse(List())
+
+ (insertSize, counts) match {
+ case (l: List[_], l2: List[_]) => {
+ l.zip(l2).foreach(i => {
+ val insertSize = i._1.toString.toInt
+ val count = i._2.toString.toInt
+ val old = map.getOrElse(insertSize, Map())
+ if (libraryLevel) map += insertSize -> (old + ((s"$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)
+ ) 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)
+ ) 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 XYPlot(null)
+ plot.input = tsvFile
+ plot.output = pngFile
+ plot.ylabel = Some("Bases")
+ plot.xlabel = Some("Coverage")
+ plot.width = Some(1200)
+ plot.removeZero = true
+ plot.title = Some("Whole genome coverage")
+ plot.runLocal()
+ }
+}
diff --git a/public/biopet-framework/pom.xml b/public/biopet-framework/pom.xml
index 905ae9fda5733ccb769a159669c6bfbfaa0a19b1..360e07bb2cc0c001ad3184376135ac9cbcb33b84 100644
--- a/public/biopet-framework/pom.xml
+++ b/public/biopet-framework/pom.xml
@@ -55,14 +55,14 @@
</dependency>
<dependency>
<groupId>org.scalatest</groupId>
- <artifactId>scalatest_2.11</artifactId>
+ <artifactId>scalatest_2.10</artifactId>
<version>2.2.1</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.scala-lang</groupId>
<artifactId>scala-library</artifactId>
- <version>2.11.2</version>
+ <version>2.10.2</version>
</dependency>
<dependency>
<groupId>org.broadinstitute.gatk</groupId>
@@ -87,7 +87,7 @@
</dependency>
<dependency>
<groupId>io.argonaut</groupId>
- <artifactId>argonaut_2.11</artifactId>
+ <artifactId>argonaut_2.10</artifactId>
<version>6.1-M4</version>
</dependency>
<dependency>
@@ -110,6 +110,11 @@
<artifactId>scopt_2.10</artifactId>
<version>3.3.0</version>
</dependency>
+ <dependency>
+ <groupId>org.scalatra.scalate</groupId>
+ <artifactId>scalate-core_2.10</artifactId>
+ <version>1.7.0</version>
+ </dependency>
<dependency>
<groupId>org.yaml</groupId>
<artifactId>snakeyaml</artifactId>
diff --git a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/executables.ssp b/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/executables.ssp
new file mode 100644
index 0000000000000000000000000000000000000000..24e70a5bd96b18d63338dfaac2b9b6ba9462b806
--- /dev/null
+++ b/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/executables.ssp
@@ -0,0 +1,33 @@
+#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] = None %>
+<%@ var libId: Option[String] = None %>
+#{
+ 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]]]
+}#
+
+<table class="table">
+ <thead>
+ <tr>
+ <th>Name</th>
+ <th>Version</th>
+ </tr>
+ </thead>
+ <tbody>
+ #for (name <- executables.keySet.toList.sorted)
+ <tr>
+ <td>${name}</td>
+ #{
+ val version = executables(name).get("version") match {
+ case Some(x) if x != None => x.toString
+ case _ => "N/A"
+ }
+ }#
+ <td>${version}</td>
+ </tr>
+ #end
+ </tbody>
+</table>
\ No newline at end of file
diff --git a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/bootstrap-theme.min.css b/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/bootstrap-theme.min.css
new file mode 100644
index 0000000000000000000000000000000000000000..cefa3d1ae367429a366230ca2c4c995616bb0790
--- /dev/null
+++ b/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/bootstrap-theme.min.css
@@ -0,0 +1,5 @@
+/*!
+ * Bootstrap v3.3.4 (http://getbootstrap.com)
+ * Copyright 2011-2015 Twitter, Inc.
+ * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
+ */.btn-danger,.btn-default,.btn-info,.btn-primary,.btn-success,.btn-warning{text-shadow:0 -1px 0 rgba(0,0,0,.2);-webkit-box-shadow:inset 0 1px 0 rgba(255,255,255,.15),0 1px 1px rgba(0,0,0,.075);box-shadow:inset 0 1px 0 rgba(255,255,255,.15),0 1px 1px rgba(0,0,0,.075)}.btn-danger.active,.btn-danger:active,.btn-default.active,.btn-default:active,.btn-info.active,.btn-info:active,.btn-primary.active,.btn-primary:active,.btn-success.active,.btn-success:active,.btn-warning.active,.btn-warning:active{-webkit-box-shadow:inset 0 3px 5px rgba(0,0,0,.125);box-shadow:inset 0 3px 5px rgba(0,0,0,.125)}.btn-danger .badge,.btn-default .badge,.btn-info .badge,.btn-primary .badge,.btn-success .badge,.btn-warning .badge{text-shadow:none}.btn.active,.btn:active{background-image:none}.btn-default{text-shadow:0 1px 0 #fff;background-image:-webkit-linear-gradient(top,#fff 0,#e0e0e0 100%);background-image:-o-linear-gradient(top,#fff 0,#e0e0e0 100%);background-image:-webkit-gradient(linear,left top,left bottom,from(#fff),to(#e0e0e0));background-image:linear-gradient(to bottom,#fff 0,#e0e0e0 100%);filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffffff', endColorstr='#ffe0e0e0', GradientType=0);filter:progid:DXImageTransform.Microsoft.gradient(enabled=false);background-repeat:repeat-x;border-color:#dbdbdb;border-color:#ccc}.btn-default:focus,.btn-default:hover{background-color:#e0e0e0;background-position:0 -15px}.btn-default.active,.btn-default:active{background-color:#e0e0e0;border-color:#dbdbdb}.btn-default.disabled,.btn-default:disabled,.btn-default[disabled]{background-color:#e0e0e0;background-image:none}.btn-primary{background-image:-webkit-linear-gradient(top,#337ab7 0,#265a88 100%);background-image:-o-linear-gradient(top,#337ab7 0,#265a88 100%);background-image:-webkit-gradient(linear,left top,left bottom,from(#337ab7),to(#265a88));background-image:linear-gradient(to bottom,#337ab7 0,#265a88 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diff --git a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/bootstrap.min.css b/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/bootstrap.min.css
new file mode 100644
index 0000000000000000000000000000000000000000..cd1c616ad862823506143fda108e7caa2a58d1ed
--- /dev/null
+++ b/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/bootstrap.min.css
@@ -0,0 +1,5 @@
+/*!
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\ No newline at end of file
diff --git a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/bootstrap_dashboard.css b/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/bootstrap_dashboard.css
new file mode 100644
index 0000000000000000000000000000000000000000..d705f1f35f05d1a3fe8007c3e044e0011b3e25cd
--- /dev/null
+++ b/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/bootstrap_dashboard.css
@@ -0,0 +1,165 @@
+/*
+ * Base structure
+ */
+
+/* Move down content because we have a fixed navbar that is 50px tall */
+body {
+ padding-top: 50px;
+}
+
+/*
+ * Global add-ons
+ */
+
+.sub-header {
+ padding-bottom: 10px;
+ border-bottom: 1px solid #eee;
+}
+
+/*
+ * Top navigation
+ * Hide default border to remove 1px line.
+ */
+.navbar-fixed-top {
+ border: 0;
+}
+
+/*
+ * Sidebar
+ */
+
+/* Hide for mobile, show later */
+.sidebar {
+ display: none;
+}
+
+@media (min-width: 768px) {
+ .sidebar {
+ position: fixed;
+ top: 51px;
+ bottom: 0;
+ left: 0;
+ z-index: 1000;
+ display: block;
+ padding: 20px;
+ overflow-x: hidden;
+ overflow-y: auto; /* Scrollable contents if viewport is shorter than content. */
+ background-color: #f5f5f5;
+ border-right: 1px solid #eee;
+ }
+}
+
+/* Sidebar navigation */
+.nav-sidebar {
+ margin-right: -21px; /* 20px padding + 1px border */
+ margin-bottom: 20px;
+ margin-left: -20px;
+}
+
+.nav-sidebar > li > a {
+ padding-right: 20px;
+ padding-left: 20px;
+}
+
+.nav-sidebar > .active > a,
+.nav-sidebar > .active > a:hover,
+.nav-sidebar > .active > a:focus {
+ color: #fff;
+ background-color: #428bca;
+}
+
+/*
+ * Main content
+ */
+
+.main {
+ padding: 20px;
+}
+
+@media (min-width: 768px) {
+ .main {
+ padding-right: 40px;
+ padding-left: 40px;
+ }
+}
+
+.main .page-header {
+ margin-top: 0;
+}
+
+/*
+ * Placeholder dashboard ideas
+ */
+
+.placeholders {
+ margin-bottom: 30px;
+ text-align: center;
+}
+
+.placeholders h4 {
+ margin-bottom: 0;
+}
+
+.placeholder {
+ margin-bottom: 20px;
+}
+
+.placeholder img {
+ display: inline-block;
+ border-radius: 50%;
+}
+
+/*
+ * dropdown menu
+ */
+
+ .dropdown-submenu{
+ position:relative;
+ }
+ .dropdown-submenu > .dropdown-menu
+ {
+ top:0;
+ left:100%;
+ margin-top:-6px;
+ margin-left:-1px;
+ -webkit-border-radius:0 6px 6px 6px;
+ -moz-border-radius:0 6px 6px 6px;
+ border-radius:0 6px 6px 6px;
+ }
+ .dropdown-submenu:hover > .dropdown-menu{
+ display:block;
+ }
+
+ .dropdown-submenu > a:after{
+ display:block;
+ content:" ";
+ float:right;
+ width:0;
+ height:0;
+ border-color:transparent;
+ border-style:solid;
+ border-width:5px 0 5px 5px;
+ border-left-color:#cccccc;
+ margin-top:5px;
+ margin-right:-10px;
+ }
+
+ .dropdown-submenu:hover > a:after{
+ border-left-color:#ffffff;
+ }
+
+ .dropdown-submenu .pull-left{
+ float:none;
+ }
+
+ .dropdown-submenu.pull-left > .dropdown-menu{
+ left:-100%;
+ margin-left:10px;
+ -webkit-border-radius:6px 0 6px 6px;
+ -moz-border-radius:6px 0 6px 6px;
+ border-radius:6px 0 6px 6px;
+ }
+
+ .root:hover > .dropdown-menu{
+ display: block;
+ }
\ No newline at end of file
diff --git a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/sortable-theme-bootstrap.css b/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/sortable-theme-bootstrap.css
new file mode 100644
index 0000000000000000000000000000000000000000..ff68918cba21d3ad223530e6c195842ed3805951
--- /dev/null
+++ b/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/css/sortable-theme-bootstrap.css
@@ -0,0 +1,90 @@
+/* line 2, ../sass/_sortable.sass */
+table[data-sortable] {
+ border-collapse: collapse;
+ border-spacing: 0;
+}
+/* line 6, ../sass/_sortable.sass */
+table[data-sortable] th {
+ vertical-align: bottom;
+ font-weight: bold;
+}
+/* line 10, ../sass/_sortable.sass */
+table[data-sortable] th, table[data-sortable] td {
+ text-align: left;
+ padding: 10px;
+}
+/* line 14, ../sass/_sortable.sass */
+table[data-sortable] th:not([data-sortable="false"]) {
+ -webkit-user-select: none;
+ -moz-user-select: none;
+ -ms-user-select: none;
+ -o-user-select: none;
+ user-select: none;
+ -webkit-tap-highlight-color: rgba(0, 0, 0, 0);
+ -webkit-touch-callout: none;
+ cursor: pointer;
+}
+/* line 26, ../sass/_sortable.sass */
+table[data-sortable] th:after {
+ content: "";
+ visibility: hidden;
+ display: inline-block;
+ vertical-align: inherit;
+ height: 0;
+ width: 0;
+ border-width: 5px;
+ border-style: solid;
+ border-color: transparent;
+ margin-right: 1px;
+ margin-left: 10px;
+ float: right;
+}
+/* line 40, ../sass/_sortable.sass */
+table[data-sortable] th[data-sorted="true"]:after {
+ visibility: visible;
+}
+/* line 43, ../sass/_sortable.sass */
+table[data-sortable] th[data-sorted-direction="descending"]:after {
+ border-top-color: inherit;
+ margin-top: 8px;
+}
+/* line 47, ../sass/_sortable.sass */
+table[data-sortable] th[data-sorted-direction="ascending"]:after {
+ border-bottom-color: inherit;
+ margin-top: 3px;
+}
+
+/* line 5, ../sass/sortable-theme-bootstrap.sass */
+table[data-sortable].sortable-theme-bootstrap {
+ font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;
+ font-size: 14px;
+ line-height: 20px;
+ color: #333333;
+ background: white;
+}
+/* line 12, ../sass/sortable-theme-bootstrap.sass */
+table[data-sortable].sortable-theme-bootstrap thead th {
+ border-bottom: 2px solid #e0e0e0;
+}
+/* line 15, ../sass/sortable-theme-bootstrap.sass */
+table[data-sortable].sortable-theme-bootstrap tbody td {
+ border-top: 1px solid #e0e0e0;
+}
+/* line 18, ../sass/sortable-theme-bootstrap.sass */
+table[data-sortable].sortable-theme-bootstrap th[data-sorted="true"] {
+ color: #3a87ad;
+ background: #d9edf7;
+ border-bottom-color: #bce8f1;
+}
+/* line 23, ../sass/sortable-theme-bootstrap.sass */
+table[data-sortable].sortable-theme-bootstrap th[data-sorted="true"][data-sorted-direction="descending"]:after {
+ border-top-color: #3a87ad;
+}
+/* line 26, ../sass/sortable-theme-bootstrap.sass */
+table[data-sortable].sortable-theme-bootstrap th[data-sorted="true"][data-sorted-direction="ascending"]:after {
+ border-bottom-color: #3a87ad;
+}
+/* line 31, ../sass/sortable-theme-bootstrap.sass */
+table[data-sortable].sortable-theme-bootstrap.sortable-theme-bootstrap-striped tbody > tr:nth-child(odd) > td {
+ background-color: #f9f9f9;
+}
\ No newline at end of file
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diff --git a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/js/bootstrap.min.js b/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/js/bootstrap.min.js
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--- /dev/null
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diff --git a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/js/jquery.min.js b/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/js/jquery.min.js
new file mode 100644
index 0000000000000000000000000000000000000000..e6a051d0d1d32752ae08d9cf30fe5952da22a9b0
--- /dev/null
+++ b/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/js/jquery.min.js
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0})}),m.each({Height:"height",Width:"width"},function(a,b){m.each({padding:"inner"+a,content:b,"":"outer"+a},function(c,d){m.fn[d]=function(d,e){var f=arguments.length&&(c||"boolean"!=typeof d),g=c||(d===!0||e===!0?"margin":"border");return V(this,function(b,c,d){var e;return m.isWindow(b)?b.document.documentElement["client"+a]:9===b.nodeType?(e=b.documentElement,Math.max(b.body["scroll"+a],e["scroll"+a],b.body["offset"+a],e["offset"+a],e["client"+a])):void 0===d?m.css(b,c,g):m.style(b,c,d,g)},b,f?d:void 0,f,null)}})}),m.fn.size=function(){return this.length},m.fn.andSelf=m.fn.addBack,"function"==typeof define&&define.amd&&define("jquery",[],function(){return m});var ed=a.jQuery,fd=a.$;return m.noConflict=function(b){return a.$===m&&(a.$=fd),b&&a.jQuery===m&&(a.jQuery=ed),m},typeof b===K&&(a.jQuery=a.$=m),m});
diff --git a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/js/sortable.min.js b/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/js/sortable.min.js
new file mode 100644
index 0000000000000000000000000000000000000000..242074c43328498a4e3a861331c370512204728b
--- /dev/null
+++ b/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/ext/js/sortable.min.js
@@ -0,0 +1,2 @@
+/*! sortable.js 0.5.0 */
+(function(){var a,b,c,d,e,f;a="table[data-sortable]",c=/^-?[£$¤]?[\d,.]+%?$/,f=/^\s+|\s+$/g,e="ontouchstart"in document.documentElement,b=e?"touchstart":"click",d={init:function(){var b,c,e,f,g;for(c=document.querySelectorAll(a),g=[],e=0,f=c.length;f>e;e++)b=c[e],g.push(d.initTable(b));return g},initTable:function(a){var b,c,e,f,g;if(1===a.tHead.rows.length&&"true"!==a.getAttribute("data-sortable-initialized")){for(a.setAttribute("data-sortable-initialized","true"),e=a.querySelectorAll("th"),b=f=0,g=e.length;g>f;b=++f)c=e[b],"false"!==c.getAttribute("data-sortable")&&d.setupClickableTH(a,c,b);return a}},setupClickableTH:function(a,c,e){var f;return f=d.getColumnType(a,e),c.addEventListener(b,function(){var b,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u;for(j="true"===this.getAttribute("data-sorted"),k=this.getAttribute("data-sorted-direction"),b=j?"ascending"===k?"descending":"ascending":f.defaultSortDirection,m=this.parentNode.querySelectorAll("th"),n=0,q=m.length;q>n;n++)c=m[n],c.setAttribute("data-sorted","false"),c.removeAttribute("data-sorted-direction");for(this.setAttribute("data-sorted","true"),this.setAttribute("data-sorted-direction",b),l=a.tBodies[0],h=[],t=l.rows,o=0,r=t.length;r>o;o++)g=t[o],h.push([d.getNodeValue(g.cells[e]),g]);for(j?h.reverse():h.sort(f.compare),u=[],p=0,s=h.length;s>p;p++)i=h[p],u.push(l.appendChild(i[1]));return u})},getColumnType:function(a,b){var e,f,g,h,i;for(i=a.tBodies[0].rows,g=0,h=i.length;h>g;g++)if(e=i[g],f=d.getNodeValue(e.cells[b]),""!==f&&f.match(c))return d.types.numeric;return d.types.alpha},getNodeValue:function(a){return a?null!==a.getAttribute("data-value")?a.getAttribute("data-value"):"undefined"!=typeof a.innerText?a.innerText.replace(f,""):a.textContent.replace(f,""):""},types:{numeric:{defaultSortDirection:"descending",compare:function(a,b){var c,d;return c=parseFloat(a[0].replace(/[^0-9.-]/g,"")),d=parseFloat(b[0].replace(/[^0-9.-]/g,"")),isNaN(c)&&(c=0),isNaN(d)&&(d=0),d-c}},alpha:{defaultSortDirection:"ascending",compare:function(a,b){var c,d;return c=a[0].toLowerCase(),d=b[0].toLowerCase(),c===d?0:d>c?-1:1}}}},setTimeout(d.init,0),window.Sortable=d}).call(this);
\ No newline at end of file
diff --git a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/librariesList.ssp b/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/librariesList.ssp
new file mode 100644
index 0000000000000000000000000000000000000000..f13c6e2a3557dd4ecb7eedda272e447c1fe49d70
--- /dev/null
+++ b/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/librariesList.ssp
@@ -0,0 +1,13 @@
+#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] = None %>
+<table class="table">
+<thead><tr></tr><th>Libraries</th></thead></tr>
+<tbody>
+#for (lib <- summary.libraries(sampleId.get))
+ <tr><td><a href="${rootPath}Samples/${sampleId.get}/Libraries/${lib}/index.html">${lib}</a></td></tr>
+#end
+</tbody>
+</table>
\ No newline at end of file
diff --git a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/main.ssp b/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/main.ssp
new file mode 100644
index 0000000000000000000000000000000000000000..2bf9f3f8a6d8f15eb477a912741f1f4556c58bac
--- /dev/null
+++ b/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/main.ssp
@@ -0,0 +1,154 @@
+#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.core.report.ReportPage)
+<%@ var summary: Summary %>
+<%@ var indexPage: ReportPage %>
+<%@ var reportName: String %>
+<%@ var page: ReportPage %>
+<%@ var path: List[String] %>
+<%@ var args: Map[String, Any] %>
+<%@ var rootPath: String %>
+#{
+ def createMenu(page: ReportPage, path: List[String] = Nil, first: Boolean = true): String = {
+ val buffer: StringBuffer = new StringBuffer()
+
+ if (page.subPages.size > 0){
+ buffer.append("<ul class=\"dropdown-menu\">")
+ }
+
+ for (subPage <- page.subPages) {
+ val href: String = {
+ if (path.isEmpty) rootPath + subPage._1 + "/index.html"
+ else rootPath + path.mkString("","/","/") + subPage._1 + "/index.html"
+ }
+
+ buffer.append("<li")
+ if(subPage._2.subPages.size > 0) buffer.append(" class=\"dropdown-submenu\"")
+ buffer.append("><a href=\"" + href + "\"")
+ if (first) buffer.append(" tabindex=\"-1\"")
+ buffer.append(">" + subPage._1 + "</a>")
+ buffer.append(createMenu(subPage._2, path ::: subPage._1 :: Nil, false))
+ buffer.append("</li>")
+ }
+ if(page.subPages.size > 0) {
+ buffer.append("</ul>\n")
+ }
+ buffer.toString
+ }
+
+ def getSubPage(path:List[String]): ReportPage = {
+ path.foldLeft(indexPage)((c, p) => {
+ val foundPages = c.subPages.filter(_._1 == p)
+ require(foundPages.size == 1, "Name of page not found or duplicate is found, page:: " + p + " in path: " + path)
+ foundPages.head._2
+ })
+ }
+}#
+<!DOCTYPE html>
+<html>
+ <head>
+ <title>${reportName}</title>
+
+ <!-- Bootstrap core JavaScript
+ ================================================== -->
+ <!-- Placed at the end of the document so the pages load faster -->
+ <script src="${rootPath}ext/js/jquery.min.js"></script>
+
+ <!-- Latest compiled and minified CSS -->
+ <link rel="stylesheet" href="${rootPath}ext/css/bootstrap.min.css">
+
+ <!-- Optional theme -->
+ <link rel="stylesheet" href="${rootPath}ext/css/bootstrap-theme.min.css">
+
+ <!-- Latest compiled and minified JavaScript -->
+ <script src="${rootPath}ext/js/bootstrap.min.js"></script>
+
+ <link rel="stylesheet" type="text/css" href="${rootPath}ext/css/bootstrap_dashboard.css">
+ <link rel="stylesheet" type="text/css" href="${rootPath}ext/css/sortable-theme-bootstrap.css">
+
+ <!-- sortable tables //-->
+ <script src="${rootPath}ext/js/sortable.min.js"></script>
+ <script language="JavaScript">
+ <!--
+ $(document).ready(function() {
+ Sortable.init()
+
+ });
+ //-->
+ </script>
+ </head>
+<body>
+
+<nav class="navbar navbar-inverse navbar-fixed-top">
+<div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".navbar-ex1-collapse">
+ <span class="sr-only">Toggle navigation</span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+
+ <ul class="nav navbar-nav">
+ <li class="root #if (path.size == 0) active #end">
+ <a class="navbar-brand" href="${rootPath}index.html">${reportName}
+ #if (indexPage.subPages.size > 0) <b class="caret"></b> #end
+ </a>
+ ${unescape(createMenu(indexPage))}
+ </li>
+ </ul>
+ </div>
+
+ <div class="collapse navbar-collapse navbar-ex1-collapse">
+ <ul class="nav navbar-nav">
+ <!-- ${path.size} //-->
+ <!-- ${path} //-->
+ #for (t <- 1 to path.size)
+ #if(t == 0)
+ <li class="root">
+ <a href="${rootPath}index.html">Home
+ #if (indexPage.subPages.size > 0) <b class="caret"></b> #end
+ </a>
+ ${unescape(createMenu(indexPage))}
+ </li>
+ #else
+ <li class="root #if (t == path.size) active #end">
+ <a href="${rootPath}${path.slice(0,t).mkString("", "/", "/")}index.html">${path( t - 1 )}
+ #if (getSubPage(path.slice(0, t)).subPages.size > 0) <b class="caret"></b> #end
+ </a>
+ ${unescape(createMenu(getSubPage(path.slice(0, t)), path.slice(0, t)))}
+ </li>
+ #end
+ #end
+
+ </ul>
+ </div>
+ <!--/.nav-collapse -->
+</div>
+</nav>
+
+<div class="container-fluid">
+<div class="row">
+ <div id="side-nav" class="col-sm-3 col-md-2 sidebar">
+ <ul class="nav nav-sidebar nav-list">
+ #for ((name, url) <- page.sections)
+ <li><a href="#${name}">${name}</a></li>
+ #end
+ </ul>
+ </div>
+ <div class="col-sm-9 col-sm-offset-3 col-md-10 col-md-offset-2 main content">
+ #for ((name, section) <- page.sections)
+ <div id="${name}" class="panel panel-primary">
+ <div class="panel-heading">
+ <h3 class="panel-title" id="panel-title">
+ ${name}
+ </h3>
+ </div>
+ ${unescape(section.render(args))}
+ </div>
+ #end
+ </div>
+</div>
+</div>
+
+</body>
+</html>
\ No newline at end of file
diff --git a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/samplesList.ssp b/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/samplesList.ssp
new file mode 100644
index 0000000000000000000000000000000000000000..e82c1428b6590420d395e35596f61ecaba09c62b
--- /dev/null
+++ b/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/core/report/samplesList.ssp
@@ -0,0 +1,12 @@
+#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.core.report.ReportPage)
+<%@ var summary: Summary %>
+<%@ var rootPath: String %>
+<table class="table sortable-theme-bootstrap" data-sortable>
+ <thead><tr></tr><th data-sorted="true" data-sorted-direction="ascending">Sample</th></thead></tr>
+ <tbody>
+ #for (sample <- summary.samples)
+ <tr><td><a href="${rootPath}Samples/${sample}/index.html">${sample}</a></td></tr>
+ #end
+ </tbody>
+</table>
\ No newline at end of file
diff --git a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/extensions/rscript/plotXY.R b/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/extensions/rscript/plotXY.R
new file mode 100644
index 0000000000000000000000000000000000000000..eee20c030b280c9246ce77428d3415173ea1b796
--- /dev/null
+++ b/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/extensions/rscript/plotXY.R
@@ -0,0 +1,40 @@
+library(reshape2)
+library(ggplot2)
+library(argparse)
+
+parser <- ArgumentParser(description='Process some integers')
+parser$add_argument('--input', dest='input', type='character', help='Input tsv file', required=TRUE)
+parser$add_argument('--output', dest='output', type='character', help='Output png file', required=TRUE)
+parser$add_argument('--width', dest='width', type='integer', default = 500)
+parser$add_argument('--height', dest='height', type='integer', default = 500)
+parser$add_argument('--xlabel', dest='xlabel', type='character')
+parser$add_argument('--ylabel', dest='ylabel', type='character', required=TRUE)
+parser$add_argument('--llabel', dest='llabel', type='character')
+parser$add_argument('--title', dest='title', type='character')
+parser$add_argument('--removeZero', dest='removeZero', type='character', default="false")
+
+arguments <- parser$parse_args()
+
+png(filename = arguments$output, width = arguments$width, height = arguments$height)
+
+DF <- read.table(arguments$input, header=TRUE)
+
+if (is.null(arguments$xlabel)) xlab <- colnames(DF)[1] else xlab <- arguments$xlabel
+
+colnames(DF)[1] <- "Rank"
+
+DF1 <- melt(DF, id.var="Rank")
+
+if (arguments$removeZero == "true") DF1 <- DF1[DF1$value > 0, ]
+if (arguments$removeZero == "true") print("Removed 0 values")
+
+ggplot(DF1, aes(x = Rank, y = value, group = variable, color = variable)) +
+ xlab(xlab) +
+ ylab(arguments$ylabel) +
+ guides(fill=guide_legend(title=arguments$llabel)) +
+ theme(axis.text.x = element_text(angle = 90, hjust = 1, size = 8)) +
+ ggtitle(arguments$title) +
+ theme_bw() +
+ geom_line()
+
+dev.off()
diff --git a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/extensions/rscript/stackedBar.R b/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/extensions/rscript/stackedBar.R
new file mode 100644
index 0000000000000000000000000000000000000000..0ae7f942cc69d1047ab2a642342381d5e8f2eade
--- /dev/null
+++ b/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/extensions/rscript/stackedBar.R
@@ -0,0 +1,35 @@
+library(reshape2)
+library(ggplot2)
+library(argparse)
+
+parser <- ArgumentParser(description='Process some integers')
+parser$add_argument('--input', dest='input', type='character', help='Input tsv file', required=TRUE)
+parser$add_argument('--output', dest='output', type='character', help='Output png file', required=TRUE)
+parser$add_argument('--width', dest='width', type='integer', default = 500)
+parser$add_argument('--height', dest='height', type='integer', default = 500)
+parser$add_argument('--xlabel', dest='xlabel', type='character')
+parser$add_argument('--ylabel', dest='ylabel', type='character', required=TRUE)
+parser$add_argument('--llabel', dest='llabel', type='character')
+parser$add_argument('--title', dest='title', type='character')
+
+arguments <- parser$parse_args()
+
+png(filename = arguments$output, width = arguments$width, height = arguments$height)
+
+DF <- read.table(arguments$input, header=TRUE)
+
+if (is.null(arguments$xlabel)) xlab <- colnames(DF)[1] else xlab <- arguments$xlabel
+
+colnames(DF)[1] <- "Rank"
+
+DF1 <- melt(DF, id.var="Rank")
+
+ggplot(DF1, aes(x = Rank, y = value, fill = variable)) +
+ xlab(xlab) +
+ ylab(arguments$ylabel) +
+ guides(fill=guide_legend(title=arguments$llabel)) +
+ theme(axis.text.x = element_text(angle = 90, hjust = 1, size = 8)) +
+ geom_bar(stat = "identity", width=1) +
+ ggtitle(arguments$title)
+
+dev.off()
diff --git a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/scripts/bedtools_cov_stats.py b/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/scripts/bedtools_cov_stats.py
index d4be9ee6f1d6af2315c9135e6f7f07ffdf6eb097..71c60d37a8daa5a52e80a777d21d1d413f3d9936 100755
--- a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/scripts/bedtools_cov_stats.py
+++ b/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/scripts/bedtools_cov_stats.py
@@ -318,14 +318,4 @@ if __name__ == '__main__':
title=title, out_img=args.plot)
stats = {'coverage': {k: v.get_quick_stats() for k, v in coverages.items()}}
- if args.plot is not None:
- files = {'plot_coverage': {
- 'path': os.path.abspath(args.plot),
- 'checksum_sha1': None,
- }
- }
- else:
- files = {}
-
- json.dump({'stats': stats, 'files': files}, sys.stdout, sort_keys=True, indent=4,
- separators=(',', ': '))
\ No newline at end of file
+ json.dump(stats, sys.stdout, sort_keys=True, indent=4, separators=(',', ': '))
\ No newline at end of file
diff --git a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/tools/plotXY.R b/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/tools/plotXY.R
deleted file mode 100644
index 63fd7b03262d94094a9f151b22cca812f10cee1f..0000000000000000000000000000000000000000
--- a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/tools/plotXY.R
+++ /dev/null
@@ -1,20 +0,0 @@
-library('ggplot2')
-library('reshape2')
-
-args <- commandArgs(TRUE)
-inputArg <- args[1]
-outputArg <- args[2]
-
-tsv<-read.table(inputArg, header = 1, sep= '\t', stringsAsFactors = F)
-
-data <- melt(tsv)
-
-data$X <- as.numeric(data$X)
-data <- na.omit(data)
-data <- data[data$value > 0,]
-
-print("Starting to plot")
-png(file = outputArg, width = 1500, height = 1500)
-ggplot(data, aes(x=X, y=value, color=variable, group=variable)) + geom_line()
-dev.off()
-print("plot done")
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
index 8b7748a24fd77018092d65bb0a5366c1a58ac9d1..6154e7660ba1ea6b59a8ce046c2a614af3cb3705 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
@@ -18,6 +18,7 @@ package nl.lumc.sasc.biopet.core
import java.io.File
import java.io.PrintWriter
import nl.lumc.sasc.biopet.core.config.{ ConfigValueIndex, Config, Configurable }
+import nl.lumc.sasc.biopet.core.report.{ ReportBuilderExtension, ReportBuilder }
import org.broadinstitute.gatk.utils.commandline.Argument
import org.broadinstitute.gatk.queue.QSettings
import org.broadinstitute.gatk.queue.function.QFunction
@@ -57,6 +58,9 @@ trait BiopetQScript extends Configurable with GatkLogging {
/** Pipeline itself */
def biopetScript
+ /** Returns the extension to make the report */
+ def reportClass: Option[ReportBuilderExtension] = None
+
/** Script from queue itself, final to force some checks for each pipeline and write report */
final def script() {
outputDir = config("output_dir")
@@ -81,6 +85,8 @@ trait BiopetQScript extends Configurable with GatkLogging {
globalConfig.writeReport(qSettings.runName, new File(outputDir, ".log/" + qSettings.runName))
else BiopetQScript.addError("Parent of output dir: '" + outputDir.getParent + "' is not writeable, outputdir can not be created")
+ reportClass.foreach(add(_))
+
BiopetQScript.checkErrors
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala
index 86bc96d1e670589eb97fdf8cbdfeb098137d6909..549b356a10fcfb5030f464dbe4f8067ec422b6bd 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala
@@ -54,4 +54,8 @@ trait ToolCommand extends MainCommand with Logging {
protected type Args <: AbstractArgs
protected type OptParser <: AbstractOptParser
+}
+
+trait ToolCommandFuntion extends BiopetJavaCommandLineFunction {
+ override def getVersion = Some("Biopet " + FullVersion)
}
\ No newline at end of file
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/MultisampleReportBuilder.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/MultisampleReportBuilder.scala
new file mode 100644
index 0000000000000000000000000000000000000000..3b43b435bf5a60862506fec8c41b99d499eb530b
--- /dev/null
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/MultisampleReportBuilder.scala
@@ -0,0 +1,41 @@
+package nl.lumc.sasc.biopet.core.report
+
+/**
+ * Created by pjvan_thof on 3/30/15.
+ */
+trait MultisampleReportBuilder extends ReportBuilder {
+ def samplePage(sampleId: String, args: Map[String, Any]): ReportPage
+
+ def samplesSections: List[(String, ReportSection)] = {
+ List(
+ ("Samples", ReportSection("/nl/lumc/sasc/biopet/core/report/samplesList.ssp"))
+ )
+ }
+
+ def libraryPage(sampleId: String, libraryId: String, args: Map[String, Any]): ReportPage
+
+ def libririesSections: List[(String, ReportSection)] = {
+ List(
+ ("Libraries", ReportSection("/nl/lumc/sasc/biopet/core/report/librariesList.ssp"))
+ )
+ }
+
+ def generateSamplesPage(args: Map[String, Any]): ReportPage = {
+ val samplePages = summary.samples
+ .map(sampleId => (sampleId -> samplePage(sampleId, args ++ Map("sampleId" -> Some(sampleId)))))
+ .toList
+ ReportPage(samplePages, samplesSections, args)
+ }
+
+ def generateLibraryPage(args: Map[String, Any]): ReportPage = {
+ val sampleId = args("sampleId") match {
+ case Some(x) => x.toString
+ case None => throw new IllegalStateException("Sample not found")
+ }
+
+ val libPages = summary.libraries(sampleId)
+ .map(libId => (libId -> libraryPage(sampleId, libId, args ++ Map("libId" -> Some(libId)))))
+ .toList
+ ReportPage(libPages, libririesSections, args)
+ }
+}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
new file mode 100644
index 0000000000000000000000000000000000000000..bf40c89ee83b432f9659117919299871b37ca35f
--- /dev/null
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
@@ -0,0 +1,176 @@
+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.summary.Summary
+import org.broadinstitute.gatk.utils.commandline.Input
+import org.fusesource.scalate.{ TemplateSource, TemplateEngine }
+import nl.lumc.sasc.biopet.utils.IoUtils
+
+/**
+ * Created by pjvan_thof on 3/27/15.
+ */
+trait ReportBuilderExtension extends ToolCommandFuntion {
+
+ val builder: ReportBuilder
+
+ @Input(required = true)
+ var summaryFile: File = _
+
+ var outputDir: File = _
+
+ var args: Map[String, String] = Map()
+
+ override def beforeGraph: Unit = {
+ super.beforeGraph
+ jobOutputFile = new File(outputDir, ".report.log.out")
+ javaMainClass = builder.getClass.getName.takeWhile(_ != '$')
+ }
+
+ override def commandLine: String = {
+ super.commandLine +
+ required("--summary", summaryFile) +
+ required("--outputDir", outputDir) +
+ args.map(x => required(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
+
+ class OptParser extends AbstractOptParser {
+ opt[File]('s', "summary") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
+ c.copy(summary = x)
+ }
+ opt[File]('o', "outputDir") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
+ c.copy(outputDir = x)
+ }
+ opt[Map[String, String]]('a', "args") action { (x, c) =>
+ c.copy(pageArgs = c.pageArgs ++ x)
+ }
+ }
+
+ private var setSummary: Summary = _
+
+ final def summary = setSummary
+
+ def pageArgs: Map[String, Any] = Map()
+
+ private var done = 0
+ private var total = 0
+
+ def main(args: Array[String]): Unit = {
+ logger.info("Start")
+
+ val argsParser = new OptParser
+ val cmdArgs: Args = argsParser.parse(args, Args()) getOrElse sys.exit(1)
+
+ require(cmdArgs.outputDir.exists(), "Output dir does not exist")
+ require(cmdArgs.outputDir.isDirectory, "Output dir is not a directory")
+
+ 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
+ val extOutputDir: File = new File(cmdArgs.outputDir, "ext")
+ val resourceDir: String = "/nl/lumc/sasc/biopet/core/report/ext/"
+ val extFiles = List(
+ "css/bootstrap_dashboard.css",
+ "css/bootstrap.min.css",
+ "css/bootstrap-theme.min.css",
+ "css/sortable-theme-bootstrap.css",
+ "js/jquery.min.js",
+ "js/sortable.min.js",
+ "js/bootstrap.min.js",
+ "fonts/glyphicons-halflings-regular.woff",
+ "fonts/glyphicons-halflings-regular.ttf",
+ "fonts/glyphicons-halflings-regular.woff2"
+ )
+
+ for (resource <- extFiles.par) {
+ IoUtils.copyStreamToFile(getClass.getResourceAsStream(resourceDir + resource), new File(extOutputDir, resource), true)
+ }
+
+ logger.info("Parsing summary")
+ setSummary = new Summary(cmdArgs.summary)
+
+ total = countPages(indexPage)
+ logger.info(total + " pages to be generated")
+
+ logger.info("Generate pages")
+ val jobs = generatePage(summary, indexPage, cmdArgs.outputDir,
+ args = pageArgs ++ cmdArgs.pageArgs ++
+ Map("summary" -> summary, "reportName" -> reportName, "indexPage" -> indexPage))
+
+ logger.info(jobs + " Done")
+ }
+
+ def indexPage: ReportPage
+
+ def reportName: String
+
+ def countPages(page: ReportPage): Int = {
+ page.subPages.map(x => countPages(x._2)).fold(1)(_ + _)
+ }
+
+ def generatePage(summary: Summary,
+ page: ReportPage,
+ outputDir: File,
+ path: List[String] = Nil,
+ args: Map[String, Any] = Map()): Int = {
+
+ val pageOutputDir = new File(outputDir, path.mkString(File.separator))
+ pageOutputDir.mkdirs()
+ val rootPath = "./" + Array.fill(path.size)("../").mkString("")
+ val pageArgs = args ++ page.args ++
+ Map("page" -> page,
+ "path" -> path,
+ "outputDir" -> pageOutputDir,
+ "rootPath" -> rootPath
+ )
+
+ // Generating subpages
+ val jobs = for ((name, subPage) <- page.subPages.par) yield {
+ generatePage(summary, subPage, outputDir, path ::: name :: Nil, pageArgs)
+ }
+
+ val output = ReportBuilder.renderTemplate("/nl/lumc/sasc/biopet/core/report/main.ssp",
+ pageArgs ++ Map("args" -> pageArgs))
+
+ val file = new File(pageOutputDir, "index.html")
+ val writer = new PrintWriter(file)
+ writer.println(output)
+ writer.close()
+
+ done += 1
+ if (done % 100 == 0) logger.info(done + " Done, " + (done.toDouble / total * 100) + "%")
+ jobs.fold(0)(_ + _) + 1
+ }
+}
+
+object ReportBuilder {
+
+ protected val engine = new TemplateEngine()
+
+ private var templateCache: Map[String, File] = Map()
+
+ /**
+ * This method will render a template that is located in the classpath / jar
+ * @param location location in the classpath / jar
+ * @param args Additional arguments, not required
+ * @return Rendered result of template
+ */
+ def renderTemplate(location: String, args: Map[String, Any] = Map()): String = {
+ val templateFile: File = templateCache.get(location) match {
+ case Some(template) => template
+ case _ => {
+ val tempFile = File.createTempFile("ssp-template", new File(location).getName)
+ IoUtils.copyStreamToFile(getClass.getResourceAsStream(location), tempFile)
+ templateCache += location -> tempFile
+ tempFile
+ }
+ }
+ engine.layout(TemplateSource.fromFile(templateFile), args)
+ }
+}
\ No newline at end of file
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportPage.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportPage.scala
new file mode 100644
index 0000000000000000000000000000000000000000..533c18384cda6ea60dbce4c587f8224611568ccf
--- /dev/null
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportPage.scala
@@ -0,0 +1,8 @@
+package nl.lumc.sasc.biopet.core.report
+
+/**
+ * Created by pjvan_thof on 3/27/15.
+ */
+case class ReportPage(subPages: List[(String, ReportPage)],
+ sections: List[(String, ReportSection)],
+ args: Map[String, Any])
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportSection.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportSection.scala
new file mode 100644
index 0000000000000000000000000000000000000000..a2a258f2aa348114ca6356c6e49c22969d6e89a8
--- /dev/null
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportSection.scala
@@ -0,0 +1,16 @@
+package nl.lumc.sasc.biopet.core.report
+
+/**
+ * Created by pjvan_thof on 4/8/15.
+ */
+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)
+ }
+}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summary.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summary.scala
new file mode 100644
index 0000000000000000000000000000000000000000..662ec704850f28a64bc1df154030f1454b5eb075
--- /dev/null
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summary.scala
@@ -0,0 +1,68 @@
+package nl.lumc.sasc.biopet.core.summary
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.utils.ConfigUtils
+
+/**
+ * Created by pjvan_thof on 3/26/15.
+ */
+class Summary(file: File) {
+ val map = ConfigUtils.fileToConfigMap(file)
+
+ lazy val samples: Set[String] = {
+ ConfigUtils.getValueFromPath(map, List("samples")) match {
+ case Some(samples) => ConfigUtils.any2map(samples).keySet
+ case _ => Set()
+ }
+ }
+
+ lazy val libraries: Map[String, Set[String]] = {
+ (for (sample <- samples) yield sample -> {
+ ConfigUtils.getValueFromPath(map, List("samples", sample, "libraries")) match {
+ case Some(libs) => ConfigUtils.any2map(libs).keySet
+ case _ => Set[String]()
+ }
+ }).toMap
+ }
+
+ def getValue(path: String*): Option[Any] = {
+ ConfigUtils.getValueFromPath(map, path.toList)
+ }
+
+ def getSampleValue(sampleId: String, path: String*): Option[Any] = {
+ ConfigUtils.getValueFromPath(map, "samples" :: sampleId :: path.toList)
+ }
+
+ def getSampleValues(path: String*): Map[String, Option[Any]] = {
+ (for (sample <- samples) yield sample -> getSampleValue(sample, path: _*)).toMap
+ }
+
+ def getSampleValues(function: (Summary, String) => Option[Any]): Map[String, Option[Any]] = {
+ (for (sample <- samples) yield sample -> function(this, sample)).toMap
+ }
+
+ 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] = {
+ (sampleId, libId) match {
+ case (Some(sample), Some(lib)) => getLibraryValue(sample, lib, path: _*)
+ case (Some(sample), _) => getSampleValue(sample, path: _*)
+ case _ => getValue(path: _*)
+ }
+ }
+
+ def getLibraryValues(path: String*): Map[(String, String), Option[Any]] = {
+ (for (sample <- samples; lib <- libraries.getOrElse(sample, Set())) yield {
+ (sample, lib) -> getLibraryValue(sample, lib, path: _*)
+ }).toMap
+ }
+
+ def getLibraryValues(function: (Summary, String, String) => Option[Any]): Map[(String, String), Option[Any]] = {
+ (for (sample <- samples; lib <- libraries.getOrElse(sample, Set())) yield {
+ (sample, lib) -> function(this, sample, lib)
+ }).toMap
+ }
+}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryValue.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryValue.scala
new file mode 100644
index 0000000000000000000000000000000000000000..b4cf349d6efd391af39a2c8fa64a83479948370f
--- /dev/null
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryValue.scala
@@ -0,0 +1,66 @@
+package nl.lumc.sasc.biopet.core.summary
+
+import java.math.BigDecimal
+
+/**
+ * Created by pjvan_thof on 4/23/15.
+ */
+case class SummaryValue(val value: Option[Any]) {
+
+ def this(path: List[String],
+ summary: Summary,
+ sampleId: Option[String] = None,
+ libId: Option[String] = None) = {
+ this((sampleId, libId) match {
+ case (Some(sample), Some(lib)) => summary.getLibraryValue(sample, lib, path: _*)
+ case (Some(sample), _) => summary.getSampleValue(sample, path: _*)
+ case _ => summary.getValue(path: _*)
+ })
+ }
+
+ def +(that: SummaryValue): SummaryValue = {
+ (this.value, that.value) match {
+ case (Some(a: Double), Some(b)) => SummaryValue(Some(a + b.toString.toDouble))
+ case (Some(a: Int), Some(b)) => SummaryValue(Some(a + b.toString.toInt))
+ case (Some(a), Some(b)) => SummaryValue(Some(a.toString.toDouble + b.toString.toDouble))
+ case _ => SummaryValue(None)
+ }
+ }
+
+ def -(that: SummaryValue): SummaryValue = {
+ (this.value, that.value) match {
+ case (Some(a: Double), Some(b)) => SummaryValue(Some(a - b.toString.toDouble))
+ case (Some(a: Int), Some(b)) => SummaryValue(Some(a - b.toString.toInt))
+ case (Some(a), Some(b)) => SummaryValue(Some(a.toString.toDouble - b.toString.toDouble))
+ case _ => SummaryValue(None)
+ }
+ }
+
+ def /(that: SummaryValue): SummaryValue = {
+ (this.value, that.value) match {
+ case (Some(a: Double), Some(b)) => SummaryValue(Some(a / b.toString.toDouble))
+ case (Some(a: Int), Some(b)) => SummaryValue(Some(a / b.toString.toInt))
+ case (Some(a), Some(b)) => SummaryValue(Some(a.toString.toDouble / b.toString.toDouble))
+ case _ => SummaryValue(None)
+ }
+ }
+
+ def *(that: SummaryValue): SummaryValue = {
+ (this.value, that.value) match {
+ case (Some(a: Double), Some(b)) => SummaryValue(Some(a * b.toString.toDouble))
+ case (Some(a: Int), Some(b)) => SummaryValue(Some(a * b.toString.toInt))
+ case (Some(a), Some(b)) => SummaryValue(Some(a.toString.toDouble * b.toString.toDouble))
+ case _ => SummaryValue(None)
+ }
+ }
+
+ def %(that: SummaryValue): SummaryValue = {
+ (this.value, that.value) match {
+ case (Some(a: Double), Some(b)) => SummaryValue(Some(a % b.toString.toDouble))
+ case (Some(a: Int), Some(b)) => SummaryValue(Some(a % b.toString.toInt))
+ case (Some(a), Some(b)) => SummaryValue(Some(a.toString.toDouble % b.toString.toDouble))
+ case _ => SummaryValue(None)
+ }
+ }
+}
+
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
index 2b9d14276a2d1ef10052fdad64cfb1d45e6d4fc7..f28b4db04416373bd58e5f5cc5bc79c4a8dbccf8 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
@@ -106,13 +106,17 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
(v1: Any, v2: Any, key: String) => summarizable.resolveSummaryConflict(v1, v2, key))
}).foldRight(pipelineMap)((a, b) => ConfigUtils.mergeMaps(a._1, b, a._2))
- val combinedMap = Map("meta" -> Map(
- "last_commit_hash" -> LastCommitHash,
- "pipeline_version" -> Version
- )) ++
- (for (qscript <- qscript.summaryQScripts) yield {
- ConfigUtils.fileToConfigMap(qscript.summaryFile)
- }).foldRight(jobsMap)((a, b) => ConfigUtils.mergeMaps(a, b))
+ val combinedMap = (for (qscript <- qscript.summaryQScripts) yield {
+ ConfigUtils.fileToConfigMap(qscript.summaryFile)
+ }).foldRight(jobsMap)((a, b) => ConfigUtils.mergeMaps(a, b)) ++
+ Map("meta" -> Map(
+ "last_commit_hash" -> LastCommitHash,
+ "pipeline_version" -> Version,
+ "pipeline_name" -> qscript.summaryName,
+ "output_dir" -> qscript.outputDir,
+ "run_name" -> config("run_name", default = qSettings.runName).asString,
+ "summary_creation" -> System.currentTimeMillis()
+ ))
val writer = new PrintWriter(out)
writer.println(ConfigUtils.mapToJson(combinedMap).nospaces)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala
index a8ccef5a0ea581f90b123655ed68f47d591a1476..7ed63f27c9f31775b68ffb32c885c2cc0590ea2d 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala
@@ -17,20 +17,20 @@ package nl.lumc.sasc.biopet.extensions
import java.io.File
-import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.core.{ Reference, BiopetCommandLineFunction }
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
/**
* Created by pjvan_thof on 3/3/15.
*/
-class Freebayes(val root: Configurable) extends BiopetCommandLineFunction {
+class Freebayes(val root: Configurable) extends BiopetCommandLineFunction with Reference {
@Input(required = true)
var bamfiles: List[File] = Nil
@Input(required = true)
- var reference: File = config("reference")
+ var reference: File = _
@Output(required = true)
var outputVcf: File = null
@@ -42,6 +42,11 @@ class Freebayes(val root: Configurable) extends BiopetCommandLineFunction {
override val versionRegex = """version: (.*)""".r
override def versionCommand = executable + " --version"
+ override def beforeGraph: Unit = {
+ super.beforeGraph
+ reference = referenceFasta()
+ }
+
def cmdLine = executable +
required("--fasta-reference", reference) +
repeat("--bam", bamfiles) +
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala
index a4d5bbc0056131ca7ce89948ec907d758fe0c0bc..2c720f63630222e25d40042938c745713242ab40 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala
@@ -29,6 +29,9 @@ class Gzip(val root: Configurable) extends BiopetCommandLineFunction {
executable = config("exe", default = "gzip")
+ override val versionRegex = """gzip (.*)""".r
+ override def versionCommand = executable + " --version"
+
def cmdLine = required(executable) + " -c " + repeat(input) + " > " + required(output)
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Md5sum.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Md5sum.scala
index fa177b8fe4cd52cfee1307dbb4e9aeeb5ded4e08..e2ce9c6bc4181d659263e17fd880535597975a55 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Md5sum.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Md5sum.scala
@@ -33,6 +33,9 @@ class Md5sum(val root: Configurable) extends BiopetCommandLineFunction {
executable = config("exe", default = "md5sum")
+ override val versionRegex = """md5sum \(GNU coreutils\) (.*)""".r
+ override def versionCommand = executable + " --version"
+
/** return commandline to execute */
def cmdLine = required(executable) + required(input) + " > " + required(output)
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RscriptCommandLineFunction.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RscriptCommandLineFunction.scala
index e25f026885c4e8f4997ee7e2184ad46636bbe788..d5da78b7632538fe8e0079249ec514f7411454f6 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RscriptCommandLineFunction.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RscriptCommandLineFunction.scala
@@ -64,7 +64,14 @@ trait RscriptCommandLineFunction extends BiopetCommandLineFunction {
def runLocal(logger: ProcessLogger): Unit = {
checkScript(local = true)
- Process(cmdLine).run(logger)
+ this.logger.info(cmdLine)
+
+ val cmd = cmdLine.stripPrefix(" '").stripSuffix("' ").split("' *'")
+
+ this.logger.info(cmd.mkString(" "))
+
+ val process = Process(cmd.toSeq).run(logger)
+ this.logger.info(process.exitValue())
}
/**
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala
index e8fa8cd7cbddf8714975386fb0d7a426c24144bc..51735af04705760812572e88c0b1286d429b837b 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala
@@ -30,6 +30,9 @@ class Zcat(val root: Configurable) extends BiopetCommandLineFunction {
executable = config("exe", default = "zcat")
+ override val versionRegex = """zcat \(gzip\) (.*)""".r
+ override def versionCommand = executable + " --version"
+
/** Returns command to execute */
def cmdLine = required(executable) + required(input) + " > " + required(output)
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/Gatk.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/Gatk.scala
index 27b9c81111a0322db9e1046b2625398a8ecead99..10122b2bd8593667b1d5beba809d449c1a16d6ce 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/Gatk.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/Gatk.scala
@@ -48,6 +48,11 @@ abstract class Gatk extends BiopetJavaCommandLineFunction with Reference {
@Input(required = false)
var pedigree: List[File] = config("pedigree", default = Nil)
+ override val versionRegex = """(.*)""".r
+ override val versionExitcode = List(0, 1)
+ override def versionCommand = executable + " -jar " + jarFile + " -version"
+
+ override def getVersion = super.getVersion.collect { case version => "Gatk " + version }
override def dictRequired = true
override def beforeGraph: Unit = {
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectWgsMetrics.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectWgsMetrics.scala
index f62ca954cf5b96f48fec290930dfd865d8d531f3..cab00c424684a140ee526bf43e4d3660183afadd 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectWgsMetrics.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectWgsMetrics.scala
@@ -57,5 +57,8 @@ class CollectWgsMetrics(val root: Configurable) extends Picard with Summarizable
def summaryFiles: Map[String, File] = Map()
/** Returns stats for summary */
- def summaryStats = Picard.getMetrics(output).getOrElse(Map())
+ def summaryStats = Map(
+ "metrics" -> Picard.getMetrics(output),
+ "histogram" -> Picard.getHistogram(output)
+ )
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
index 77d2ec0a477c04143def73aa34fb2346f713b961..d4f60ee54cf92f101bf6866d88dc2879234580d5 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
@@ -15,7 +15,7 @@
*/
package nl.lumc.sasc.biopet.extensions.picard
-import java.io.File
+import java.io.{ FileReader, File }
import scala.io.Source
import org.broadinstitute.gatk.utils.commandline.Argument
@@ -63,6 +63,11 @@ abstract class Picard extends BiopetJavaCommandLineFunction {
override val defaultCoreMemory = 3.0
+ override def getVersion = {
+ if (jarFile == null) Picard.getBiopetPicardVersion
+ else super.getVersion
+ }
+
override def commandLine = super.commandLine +
required("TMP_DIR=" + jobTempDir) +
optional("VERBOSITY=", verbosity, spaceSeparated = false) +
@@ -76,6 +81,29 @@ abstract class Picard extends BiopetJavaCommandLineFunction {
object Picard extends Logging {
+ lazy val getBiopetPicardVersion: Option[String] = {
+ val reader = Source.fromInputStream(getClass.getResourceAsStream("/dependency_list.txt"))
+ val dependencies = reader.getLines().map(_.trim.split(":")).filter(_.size == 5).map(line => Map(
+ "groupId" -> line(0),
+ "artifactId" -> line(1),
+ "type" -> line(2),
+ "version" -> line(3),
+ "scope" -> line(4)
+ )).toList
+
+ logger.debug("dependencies: " + dependencies)
+
+ val htsjdk = dependencies.find(dep => dep("groupId") == "samtools" && dep("artifactId") == "htsjdk").collect {
+ case dep =>
+ "samtools htsjdk " + dep("version")
+ }
+
+ dependencies.find(dep => dep("groupId") == "picard" && dep("artifactId") == "picard").collect {
+ case dep =>
+ "Picard " + dep("version") + " using " + htsjdk.getOrElse("unknown htsjdk")
+ }
+ }
+
def getMetrics(file: File, tag: String = "METRICS CLASS",
groupBy: Option[String] = None): Option[Any] = {
getMetricsContent(file, tag) match {
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/StackedBarPlot.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/StackedBarPlot.scala
new file mode 100644
index 0000000000000000000000000000000000000000..436812377c779a7ec5f768e3aa7967cf35330cf7
--- /dev/null
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/StackedBarPlot.scala
@@ -0,0 +1,37 @@
+package nl.lumc.sasc.biopet.extensions.rscript
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.extensions.RscriptCommandLineFunction
+import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
+
+/**
+ * Created by pjvan_thof on 4/29/15.
+ */
+class StackedBarPlot(val root: Configurable) extends RscriptCommandLineFunction {
+ protected var script: File = config("script", default = "stackedBar.R")
+
+ @Input
+ var input: File = _
+
+ @Output
+ var output: File = _
+
+ var width: Option[Int] = config("width")
+ var height: Option[Int] = config("height")
+ var xlabel: Option[String] = config("xlabel")
+ var ylabel: Option[String] = config("ylabel")
+ var llabel: Option[String] = config("llabel")
+ var title: Option[String] = config("title")
+
+ override def cmdLine: String = super.cmdLine +
+ required("--input", input) +
+ required("--output", output) +
+ optional("--width", width) +
+ optional("--height", height) +
+ optional("--xlabel", xlabel) +
+ required("--ylabel", ylabel) +
+ optional("--llabel", llabel) +
+ optional("--title", title)
+}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/XYPlot.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/XYPlot.scala
new file mode 100644
index 0000000000000000000000000000000000000000..bfaea724001d84856c21523be0428690981bbd3f
--- /dev/null
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/XYPlot.scala
@@ -0,0 +1,39 @@
+package nl.lumc.sasc.biopet.extensions.rscript
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.extensions.RscriptCommandLineFunction
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
+/**
+ * Created by pjvan_thof on 4/29/15.
+ */
+class XYPlot(val root: Configurable) extends RscriptCommandLineFunction {
+ protected var script: File = config("script", default = "plotXY.R")
+
+ @Input
+ var input: File = _
+
+ @Output
+ var output: File = _
+
+ var width: Option[Int] = config("width")
+ var height: Option[Int] = config("height")
+ var xlabel: Option[String] = config("xlabel")
+ var ylabel: Option[String] = config("ylabel")
+ var llabel: Option[String] = config("llabel")
+ var title: Option[String] = config("title")
+ var removeZero: Boolean = config("removeZero", default = false)
+
+ override def cmdLine: String = super.cmdLine +
+ required("--input", input) +
+ required("--output", output) +
+ optional("--width", width) +
+ optional("--height", height) +
+ optional("--xlabel", xlabel) +
+ required("--ylabel", ylabel) +
+ optional("--llabel", llabel) +
+ optional("--title", title) +
+ optional("--removeZero", removeZero)
+}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala
index 0ac4feac1587a26b18f0b85ba01422a6559a4f2b..49dfc1a62fad0aa6bb511e50c57874df8f59ce70 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala
@@ -15,12 +15,13 @@
*/
package nl.lumc.sasc.biopet.extensions.samtools
+import nl.lumc.sasc.biopet.core.Reference
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import java.io.File
/** Extension for samtools mpileup */
-class SamtoolsMpileup(val root: Configurable) extends Samtools {
+class SamtoolsMpileup(val root: Configurable) extends Samtools with Reference {
@Input(doc = "Bam File")
var input: List[File] = Nil
@@ -28,7 +29,7 @@ class SamtoolsMpileup(val root: Configurable) extends Samtools {
var output: File = _
@Input(doc = "Reference fasta")
- var reference: File = config("reference")
+ var reference: File = _
@Input(doc = "Interval bed", required = false)
var intervalBed: Option[File] = config("interval_bed")
@@ -40,6 +41,11 @@ class SamtoolsMpileup(val root: Configurable) extends Samtools {
var depth: Option[Int] = config("depth")
var outputMappingQuality: Boolean = config("output_mapping_quality", default = false)
+ override def beforeGraph: Unit = {
+ super.beforeGraph
+ reference = referenceFasta()
+ }
+
def cmdBase = required(executable) +
required("mpileup") +
optional("-f", reference) +
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/scripts/CoverageStats.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/scripts/CoverageStats.scala
index c5f5d8ace92cb348e8f5313b23a0d74481ffeae6..37c6cfe938f1f7b89baf6efba87706c40fedf149 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/scripts/CoverageStats.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/scripts/CoverageStats.scala
@@ -18,6 +18,7 @@ package nl.lumc.sasc.biopet.scripts
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.core.summary.Summarizable
import nl.lumc.sasc.biopet.extensions.PythonCommandLineFunction
+import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import java.io.File
@@ -33,14 +34,23 @@ class CoverageStats(val root: Configurable) extends PythonCommandLineFunction wi
@Output(doc = "plot File (png)")
var plot: File = _
+ var title: Option[String] = None
+ var subTitle: Option[String] = None
+
override val defaultCoreMemory = 9.0
def cmdLine = getPythonCommand +
- required(input) + required("--plot", plot) + " > " + required(output)
+ required(input) +
+ required("--plot", plot) +
+ optional("--title", title) +
+ optional("--subtitle", subTitle) +
+ " > " + required(output)
- def summaryFiles: Map[String, File] = Map("output" -> output, "plot" -> plot)
+ def summaryFiles: Map[String, File] = Map("plot" -> plot)
- def summaryStats: Map[String, Any] = Map()
+ def summaryStats: Map[String, Any] = {
+ ConfigUtils.fileToConfigMap(output)
+ }
}
object CoverageStats {
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala
index 84976169e5f0255bb1977df10070d08c095f46f0..7f6de262b7a5a08d7a4d44879ee6842681e63bd1 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala
@@ -22,7 +22,7 @@ import htsjdk.tribble.bed.BEDCodec
import htsjdk.variant.variantcontext.VariantContextBuilder
import htsjdk.variant.variantcontext.writer.{ VariantContextWriterBuilder, AsyncVariantContextWriter }
import htsjdk.variant.vcf.{ VCFHeaderLineType, VCFHeaderLineCount, VCFInfoHeaderLine, VCFFileReader }
-import nl.lumc.sasc.biopet.core.ToolCommand
+import nl.lumc.sasc.biopet.core.{ ToolCommandFuntion, ToolCommand }
import scala.collection.JavaConverters.asScalaIteratorConverter
import scala.collection.JavaConversions._
import scala.collection.mutable
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
index 8f9f3155a8c0ec12b312a6bde3beb236cd463412..19752d72b4c19426050388351fcd6e6b613bf57d 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
@@ -21,15 +21,14 @@ import htsjdk.variant.variantcontext.VariantContext
import htsjdk.variant.vcf.VCFFileReader
import java.io.File
import java.io.PrintWriter
-import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
-import nl.lumc.sasc.biopet.core.ToolCommand
+import nl.lumc.sasc.biopet.core.{ ToolCommandFuntion, BiopetJavaCommandLineFunction, ToolCommand }
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import scala.collection.JavaConversions._
import nl.lumc.sasc.biopet.utils.VcfUtils._
import scala.collection.mutable.ListBuffer
-class BastyGenerateFasta(val root: Configurable) extends BiopetJavaCommandLineFunction {
+class BastyGenerateFasta(val root: Configurable) extends ToolCommandFuntion {
javaMainClass = getClass.getName
@Input(doc = "Input vcf file", required = false)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
index ddfb57439ae4c16bc702173c4176b4246126ec00..0a3df85f0d9100370d97e9975de6d918d2ab7363 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
@@ -17,8 +17,7 @@ package nl.lumc.sasc.biopet.tools
import htsjdk.samtools.{ SAMSequenceRecord, SamReaderFactory }
import java.io.File
-import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
-import nl.lumc.sasc.biopet.core.ToolCommand
+import nl.lumc.sasc.biopet.core.{ ToolCommandFuntion, BiopetJavaCommandLineFunction, ToolCommand }
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import java.io.PrintWriter
@@ -27,7 +26,7 @@ import scala.io.Source
/**
* @deprecated Use picard.util.BedToIntervalList instead
*/
-class BedToInterval(val root: Configurable) extends BiopetJavaCommandLineFunction {
+class BedToInterval(val root: Configurable) extends ToolCommandFuntion {
javaMainClass = getClass.getName
@Input(doc = "Input Bed file", required = true)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala
index 6502f46c2fde94876789c7190fbc636c3cc19c3c..a55e6270b1812773db8f9617febf3c0316300cae 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala
@@ -17,8 +17,7 @@ package nl.lumc.sasc.biopet.tools
import java.io.File
import java.io.PrintWriter
-import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
-import nl.lumc.sasc.biopet.core.ToolCommand
+import nl.lumc.sasc.biopet.core.{ ToolCommandFuntion, BiopetJavaCommandLineFunction, ToolCommand }
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import scala.collection.JavaConversions._
@@ -26,7 +25,7 @@ import scala.collection.SortedMap
import scala.collection.mutable.Map
import scala.io.Source
-class BedtoolsCoverageToCounts(val root: Configurable) extends BiopetJavaCommandLineFunction {
+class BedtoolsCoverageToCounts(val root: Configurable) extends ToolCommandFuntion {
javaMainClass = getClass.getName
@Input(doc = "Input fasta", shortName = "input", required = true)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
index f72ea06d54fb65861ffbfb066f99bae58c64f638..bffbe4c36bda11242d120042bd517702c7ab4958 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
@@ -17,15 +17,14 @@ package nl.lumc.sasc.biopet.tools
import htsjdk.samtools.{ SAMRecord, SamReaderFactory }
import java.io.{ PrintWriter, File }
-import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
-import nl.lumc.sasc.biopet.core.ToolCommand
+import nl.lumc.sasc.biopet.core.{ ToolCommandFuntion, BiopetJavaCommandLineFunction, ToolCommand }
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.core.summary.Summarizable
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import scala.collection.JavaConversions._
-class BiopetFlagstat(val root: Configurable) extends BiopetJavaCommandLineFunction with Summarizable {
+class BiopetFlagstat(val root: Configurable) extends ToolCommandFuntion with Summarizable {
javaMainClass = getClass.getName
@Input(doc = "Input bam", shortName = "input", required = true)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala
index 569a3f234e8192025f366f2d06985137b1577ed6..88fdc9a709624fde4a84e034abcaf8dc2bf140c3 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala
@@ -17,8 +17,7 @@ package nl.lumc.sasc.biopet.tools
import java.io.File
import htsjdk.samtools.fastq.{ AsyncFastqWriter, FastqReader, BasicFastqWriter }
-import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
-import nl.lumc.sasc.biopet.core.ToolCommand
+import nl.lumc.sasc.biopet.core.{ ToolCommandFuntion, BiopetJavaCommandLineFunction, ToolCommand }
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import scala.collection.JavaConversions._
@@ -27,7 +26,7 @@ import scala.collection.JavaConversions._
* Queue extension for the FastqSplitter
* @param root Parent object
*/
-class FastqSplitter(val root: Configurable) extends BiopetJavaCommandLineFunction {
+class FastqSplitter(val root: Configurable) extends ToolCommandFuntion {
javaMainClass = getClass.getName
@Input(doc = "Input fastq", shortName = "input", required = true)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
index a4881e73e900edd9c7570397a83d8bdc362a0445..be422716c8c9d29072dba77e675bac7df02ace4f 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
@@ -27,7 +27,7 @@ import scala.collection.JavaConverters._
import htsjdk.samtools.fastq.{ AsyncFastqWriter, BasicFastqWriter, FastqReader, FastqRecord }
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
-import nl.lumc.sasc.biopet.core.{ BiopetExecutable, BiopetJavaCommandLineFunction, ToolCommand }
+import nl.lumc.sasc.biopet.core.{ ToolCommandFuntion, BiopetExecutable, BiopetJavaCommandLineFunction, ToolCommand }
import nl.lumc.sasc.biopet.core.config.Configurable
/**
@@ -35,7 +35,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
*
* @param root Configuration object for the pipeline
*/
-class FastqSync(val root: Configurable) extends BiopetJavaCommandLineFunction with Summarizable {
+class FastqSync(val root: Configurable) extends ToolCommandFuntion with Summarizable {
javaMainClass = getClass.getName
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
index 72abb6ceab1fa146fb1f711e6d5b3ca4b100a4e3..3b49ef5e4e07380866333cb669fdb6d924af0716 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
@@ -24,15 +24,14 @@ import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
import htsjdk.variant.vcf.VCFFileReader
import htsjdk.variant.vcf.VCFHeader
import java.io.File
-import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
-import nl.lumc.sasc.biopet.core.ToolCommand
+import nl.lumc.sasc.biopet.core.{ ToolCommandFuntion, BiopetJavaCommandLineFunction, ToolCommand }
import scala.collection.SortedMap
import scala.collection.mutable.{ Map, Set }
import nl.lumc.sasc.biopet.core.config.Configurable
import scala.collection.JavaConversions._
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
-class MergeAlleles(val root: Configurable) extends BiopetJavaCommandLineFunction {
+class MergeAlleles(val root: Configurable) extends ToolCommandFuntion {
javaMainClass = getClass.getName
@Input(doc = "Input vcf files", shortName = "input", required = true)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeTables.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeTables.scala
index 7da65a63c49cb1ac51de35766936a53f80e73fa4..6d01e051ca46d2bc3dea8f496215dd4239bfd97b 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeTables.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeTables.scala
@@ -19,8 +19,7 @@ import java.io.{ File, BufferedWriter, FileWriter, OutputStreamWriter }
import scala.io.{ BufferedSource, Source }
import scala.collection.mutable.{ Set => MutSet }
-import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
-import nl.lumc.sasc.biopet.core.ToolCommand
+import nl.lumc.sasc.biopet.core.{ ToolCommandFuntion, BiopetJavaCommandLineFunction, ToolCommand }
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
@@ -29,7 +28,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
*
* @param root [[Configurable]] object
*/
-class MergeTables(val root: Configurable) extends BiopetJavaCommandLineFunction {
+class MergeTables(val root: Configurable) extends ToolCommandFuntion {
javaMainClass = getClass.getName
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
index f0df8cfe87a0c3d557dec7bce10d20d7420f33d6..8ebe6fc7b212ec35bcfe797d81b84d6595eaec3c 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
@@ -18,8 +18,7 @@ package nl.lumc.sasc.biopet.tools
import java.io.File
import java.io.PrintWriter
import htsjdk.samtools.SamReaderFactory
-import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
-import nl.lumc.sasc.biopet.core.ToolCommand
+import nl.lumc.sasc.biopet.core.{ Reference, ToolCommandFuntion, BiopetJavaCommandLineFunction, ToolCommand }
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup
import nl.lumc.sasc.biopet.utils.ConfigUtils
@@ -30,7 +29,7 @@ import scala.math.round
import scala.math.floor
import scala.collection.JavaConversions._
-class MpileupToVcf(val root: Configurable) extends BiopetJavaCommandLineFunction {
+class MpileupToVcf(val root: Configurable) extends ToolCommandFuntion with Reference {
javaMainClass = getClass.getName
@Input(doc = "Input mpileup file", shortName = "mpileup", required = false)
@@ -47,7 +46,7 @@ class MpileupToVcf(val root: Configurable) extends BiopetJavaCommandLineFunction
var homoFraction: Option[Double] = config("homoFraction")
var ploidy: Option[Int] = config("ploidy")
var sample: String = _
- var reference: String = config("reference")
+ var reference: String = _
override val defaultCoreMemory = 3.0
@@ -56,6 +55,7 @@ class MpileupToVcf(val root: Configurable) extends BiopetJavaCommandLineFunction
override def beforeGraph {
super.beforeGraph
+ reference = referenceFasta().getAbsolutePath
val samtoolsMpileup = new SamtoolsMpileup(this)
}
@@ -72,6 +72,7 @@ class MpileupToVcf(val root: Configurable) extends BiopetJavaCommandLineFunction
override def commandLine = {
(if (inputMpileup == null) {
val samtoolsMpileup = new SamtoolsMpileup(this)
+ samtoolsMpileup.reference = referenceFasta()
samtoolsMpileup.input = List(inputBam)
samtoolsMpileup.cmdPipe + " | "
} else "") +
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/PrefixFastq.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/PrefixFastq.scala
index 6dfc152219a65bfe2becdf7922e466120ccc8eda..101b9f9b4b05cb4879bf00df35501229fd41ad3d 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/PrefixFastq.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/PrefixFastq.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.tools
import java.io.File
-import nl.lumc.sasc.biopet.core.{ BiopetJavaCommandLineFunction, ToolCommand }
+import nl.lumc.sasc.biopet.core.{ ToolCommandFuntion, BiopetJavaCommandLineFunction, ToolCommand }
import htsjdk.samtools.fastq.{ FastqRecord, AsyncFastqWriter, FastqReader, BasicFastqWriter }
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Output, Input }
@@ -28,7 +28,7 @@ import scala.collection.JavaConversions._
*
* Created by pjvan_thof on 1/13/15.
*/
-class PrefixFastq(val root: Configurable) extends BiopetJavaCommandLineFunction {
+class PrefixFastq(val root: Configurable) extends ToolCommandFuntion {
javaMainClass = getClass.getName
override val defaultCoreMemory = 1.0
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala
index 464346febec95c126463369bc2a6cafa796e6ade..86c7215a19c9f177f013f3f48a0d77a0e9e0444d 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala
@@ -17,8 +17,7 @@ package nl.lumc.sasc.biopet.tools
import java.io.File
import java.io.PrintWriter
-import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
-import nl.lumc.sasc.biopet.core.ToolCommand
+import nl.lumc.sasc.biopet.core.{ ToolCommandFuntion, BiopetJavaCommandLineFunction, ToolCommand }
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import org.biojava3.sequencing.io.fastq.{ SangerFastqReader, StreamListener, Fastq }
@@ -27,7 +26,7 @@ import scala.collection.SortedMap
import scala.collection.mutable.Map
import java.io.FileReader
-class SageCountFastq(val root: Configurable) extends BiopetJavaCommandLineFunction {
+class SageCountFastq(val root: Configurable) extends ToolCommandFuntion {
javaMainClass = getClass.getName
@Input(doc = "Input fasta", shortName = "input", required = true)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala
index 3f5af4439a54e69949905f2e77ab6215aff0d0e1..dc1cb1e0a32dfe9125ff22ee743d5526572f7d1a 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala
@@ -17,8 +17,7 @@ package nl.lumc.sasc.biopet.tools
import java.io.File
import java.io.PrintWriter
-import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
-import nl.lumc.sasc.biopet.core.ToolCommand
+import nl.lumc.sasc.biopet.core.{ ToolCommandFuntion, BiopetJavaCommandLineFunction, ToolCommand }
import nl.lumc.sasc.biopet.core.config.Configurable
import org.biojava3.core.sequence.DNASequence
import org.biojava3.core.sequence.io.FastaReaderHelper
@@ -28,7 +27,7 @@ import scala.collection.mutable.{ Map, Set }
import scala.collection.JavaConversions._
import scala.util.matching.Regex
-class SageCreateLibrary(val root: Configurable) extends BiopetJavaCommandLineFunction {
+class SageCreateLibrary(val root: Configurable) extends ToolCommandFuntion {
javaMainClass = getClass.getName
@Input(doc = "Input fasta", shortName = "input", required = true)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala
index 075b90f440d798343eb00805ba205094fd7afc14..cb95df0c973a37ab91d837e1f6375b45beb258da 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala
@@ -17,15 +17,14 @@ package nl.lumc.sasc.biopet.tools
import java.io.File
import java.io.PrintWriter
-import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
-import nl.lumc.sasc.biopet.core.ToolCommand
+import nl.lumc.sasc.biopet.core.{ ToolCommandFuntion, BiopetJavaCommandLineFunction, ToolCommand }
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import scala.io.Source
import scala.collection.mutable.Map
import scala.collection.SortedMap
-class SageCreateTagCounts(val root: Configurable) extends BiopetJavaCommandLineFunction {
+class SageCreateTagCounts(val root: Configurable) extends ToolCommandFuntion {
javaMainClass = getClass.getName
@Input(doc = "Raw count file", shortName = "input", required = true)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/Seqstat.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/Seqstat.scala
index 7688edc1a02ddb80cdcc77efbe67c90a169e4a07..b273687431629a8eacec39c5d45254ce2a3f15ba 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/Seqstat.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/Seqstat.scala
@@ -29,8 +29,7 @@ import htsjdk.samtools.fastq.{ FastqReader, FastqRecord }
import scalaz._, Scalaz._
import argonaut._, Argonaut._
-import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
-import nl.lumc.sasc.biopet.core.ToolCommand
+import nl.lumc.sasc.biopet.core.{ ToolCommandFuntion, BiopetJavaCommandLineFunction, ToolCommand }
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.utils.ConfigUtils
@@ -39,7 +38,7 @@ import nl.lumc.sasc.biopet.utils.ConfigUtils
*
* @param root Configuration object for the pipeline
*/
-class Seqstat(val root: Configurable) extends BiopetJavaCommandLineFunction with Summarizable {
+class Seqstat(val root: Configurable) extends ToolCommandFuntion with Summarizable {
javaMainClass = getClass.getName
@Input(doc = "Input FASTQ", shortName = "input", required = true)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SummaryToTsv.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SummaryToTsv.scala
new file mode 100644
index 0000000000000000000000000000000000000000..731e7039e2092d927d2a0ebe5146371a50453d5b
--- /dev/null
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SummaryToTsv.scala
@@ -0,0 +1,62 @@
+package nl.lumc.sasc.biopet.tools
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.ToolCommand
+import nl.lumc.sasc.biopet.core.summary.Summary
+
+/**
+ * Created by pjvan_thof on 4/23/15.
+ */
+object SummaryToTsv extends ToolCommand {
+ case class Args(summary: File = null,
+ outputFile: Option[File] = None,
+ values: List[String] = Nil,
+ mode: String = "root") extends AbstractArgs
+
+ class OptParser extends AbstractOptParser {
+ opt[File]('s', "summary") required () unbounded () maxOccurs (1) valueName ("<file>") action { (x, c) =>
+ c.copy(summary = x)
+ }
+ opt[File]('o', "output") maxOccurs (1) unbounded () valueName ("<file>") action { (x, c) =>
+ c.copy(outputFile = Some(x))
+ }
+ opt[String]('p', "path") required () unbounded () valueName ("<value>") action { (x, c) =>
+ c.copy(values = c.values ::: x :: Nil)
+ }
+ opt[String]('m', "mode") maxOccurs (1) unbounded () valueName ("<root|sample|lib>") action { (x, c) =>
+ c.copy(mode = x)
+ }
+
+ }
+
+ def main(args: Array[String]): Unit = {
+ val argsParser = new OptParser
+ val cmdArgs: Args = argsParser.parse(args, Args()) getOrElse sys.exit(1)
+
+ val summary = new Summary(cmdArgs.summary)
+
+ val paths = cmdArgs.values.map(x => {
+ val split = x.split("=", 2)
+ split(0) -> split(1).split(":")
+ })
+
+ val values = fetchValues(summary, paths.toMap, sample = cmdArgs.mode == "sample", lib = cmdArgs.mode == "lib")
+
+ println(paths.map(_._1).mkString("\t", "\t", ""))
+
+ for (lineId <- values.head._2.keys) {
+ println(paths.map(x => values(x._1)(lineId).getOrElse("")).mkString(lineId + "\t", "\t", ""))
+ }
+ }
+
+ def fetchValues(summary: Summary, paths: Map[String, Array[String]],
+ sample: Boolean = false,
+ lib: Boolean = false) = {
+ for ((name, path) <- paths) yield name -> {
+ if (lib) summary.getLibraryValues(path: _*).map(a => (a._1._1 + "-" + a._1._2) -> a._2)
+ else if (sample) summary.getSampleValues(path: _*)
+ else Map("value" -> summary.getValue(path: _*))
+ }
+ }
+}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
index 5d002e7aaa8f1d40c37935bff72a14d110285cd4..1fc34adcb9877d3e2fd93bb14c0b6108435d0053 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
@@ -20,14 +20,13 @@ import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
import htsjdk.variant.vcf.VCFFileReader
import htsjdk.variant.variantcontext.VariantContext
import java.io.File
-import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
-import nl.lumc.sasc.biopet.core.ToolCommand
+import nl.lumc.sasc.biopet.core.{ ToolCommandFuntion, BiopetJavaCommandLineFunction, ToolCommand }
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
import scala.collection.JavaConversions._
import scala.io.Source
-class VcfFilter(val root: Configurable) extends BiopetJavaCommandLineFunction {
+class VcfFilter(val root: Configurable) extends ToolCommandFuntion {
javaMainClass = getClass.getName
@Input(doc = "Input vcf", shortName = "I", required = true)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
index 89e41067c16a32e0e4a27ba3c03e5bf5f1fdcea8..77ae5c23cb1e252861430739458cc4af6d6eebb4 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
@@ -21,7 +21,7 @@ import htsjdk.samtools.reference.FastaSequenceFile
import htsjdk.variant.variantcontext.{ Allele, VariantContext, Genotype }
import htsjdk.variant.vcf.VCFFileReader
import nl.lumc.sasc.biopet.core.summary.{ SummaryQScript, Summarizable }
-import nl.lumc.sasc.biopet.core.{ BiopetJavaCommandLineFunction, ToolCommand }
+import nl.lumc.sasc.biopet.core.{ Reference, ToolCommandFuntion, BiopetJavaCommandLineFunction, ToolCommand }
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
import scala.collection.JavaConversions._
@@ -35,7 +35,7 @@ import scala.util.Random
/**
* Created by pjvan_thof on 1/10/15.
*/
-class VcfStats(val root: Configurable) extends BiopetJavaCommandLineFunction with Summarizable {
+class VcfStats(val root: Configurable) extends ToolCommandFuntion with Summarizable with Reference {
javaMainClass = getClass.getName
@Input(doc = "Input fastq", shortName = "I", required = true)
@@ -59,9 +59,10 @@ class VcfStats(val root: Configurable) extends BiopetJavaCommandLineFunction wit
var genotypeTags: List[String] = Nil
var allInfoTags = false
var allGenotypeTags = false
- var reference: File = config("reference")
+ var reference: File = _
override def beforeGraph: Unit = {
+ reference = referenceFasta()
index = new File(input.getAbsolutePath + ".tbi")
}
@@ -346,7 +347,7 @@ object VcfStats extends ToolCommand {
}
// Triple for loop to not keep all bins in memory
- val stats = (for (intervals <- Random.shuffle(intervals).grouped(intervals.size / 4).toList.par) yield {
+ val stats = (for (intervals <- Random.shuffle(intervals).grouped(intervals.size / (if (intervals.size > 10) 4 else 1)).toList.par) yield {
val chunkStats = for (intervals <- intervals.grouped(25)) yield {
val binStats = for (interval <- intervals.par) yield {
val reader = new VCFFileReader(commandArgs.inputFile, true)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala
index c290e2cc56ece077e6e8de745c0f469484ace11d..3b97e6702c85c6fcce3714ae1d80c77180b27039 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala
@@ -25,7 +25,7 @@ import htsjdk.variant.variantcontext.writer.{ AsyncVariantContextWriter, Variant
import htsjdk.variant.vcf._
import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
-import nl.lumc.sasc.biopet.core.{ BiopetJavaCommandLineFunction, ToolCommand }
+import nl.lumc.sasc.biopet.core.{ ToolCommandFuntion, BiopetJavaCommandLineFunction, ToolCommand }
import nl.lumc.sasc.biopet.core.config.Configurable
/**
@@ -38,7 +38,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
* Created by ahbbollen on 10/27/14.
*/
-class VepNormalizer(val root: Configurable) extends BiopetJavaCommandLineFunction {
+class VepNormalizer(val root: Configurable) extends ToolCommandFuntion {
javaMainClass = getClass.getName
@Input(doc = "Input VCF, may be indexed", shortName = "InputFile", required = true)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala
index 9df2f0b6869ee7bdd8d6d9e0f3be0fc49a672768..56bc3e8dd0b44d6fd0d33b6f6e11f491be5f7872 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala
@@ -34,8 +34,7 @@ import htsjdk.tribble.bed.BEDCodec
import org.apache.commons.io.FilenameUtils.getExtension
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
-import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
-import nl.lumc.sasc.biopet.core.ToolCommand
+import nl.lumc.sasc.biopet.core.{ ToolCommandFuntion, BiopetJavaCommandLineFunction, ToolCommand }
import nl.lumc.sasc.biopet.core.config.Configurable
// TODO: finish implementation for usage in pipelines
@@ -44,7 +43,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
*
* @param root Configuration object for the pipeline
*/
-class WipeReads(val root: Configurable) extends BiopetJavaCommandLineFunction {
+class WipeReads(val root: Configurable) extends ToolCommandFuntion {
javaMainClass = getClass.getName
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/IoUtils.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/IoUtils.scala
new file mode 100644
index 0000000000000000000000000000000000000000..04f2c082b1ded6dcbda85dda0bad542031c6abfc
--- /dev/null
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/IoUtils.scala
@@ -0,0 +1,33 @@
+package nl.lumc.sasc.biopet.utils
+
+import java.io.{ FileOutputStream, InputStream, FileInputStream, File }
+
+/**
+ * Created by pjvan_thof on 6/4/15.
+ */
+object IoUtils {
+ def copyFile(in: File, out: File, createDirs: Boolean = false): Unit = {
+ copyStreamToFile(new FileInputStream(in), out, createDirs)
+ }
+
+ def copyStreamToFile(in: InputStream, out: File, createDirs: Boolean = false): Unit = {
+ if (createDirs) out.getParentFile.mkdirs()
+ val os = new FileOutputStream(out)
+
+ org.apache.commons.io.IOUtils.copy(in, os)
+ os.close()
+ in.close()
+ }
+
+ def copyDir(inputDir: File, externalDir: File): Unit = {
+ require(inputDir.isDirectory)
+ externalDir.mkdirs()
+ for (srcFile <- inputDir.listFiles) {
+ if (srcFile.isDirectory) copyDir(new File(inputDir, srcFile.getName), new File(externalDir, srcFile.getName))
+ else {
+ val newFile = new File(externalDir, srcFile.getName)
+ copyFile(srcFile, newFile)
+ }
+ }
+ }
+}
diff --git a/public/carp/pom.xml b/public/carp/pom.xml
index bba9a5848e14a5d5c9d3c998bbbd4eb018243951..3e01cecbd0dd0629c5b852178e50ed299e753703 100644
--- a/public/carp/pom.xml
+++ b/public/carp/pom.xml
@@ -52,7 +52,7 @@
</dependency>
<dependency>
<groupId>org.scalatest</groupId>
- <artifactId>scalatest_2.11</artifactId>
+ <artifactId>scalatest_2.10</artifactId>
<version>2.2.1</version>
<scope>test</scope>
</dependency>
diff --git a/public/flexiprep/pom.xml b/public/flexiprep/pom.xml
index 499d32020c82e40c7fddad364b39e7cdf7cf5536..53cc99ebd970b1c8591295446f065454cfe9c5e1 100644
--- a/public/flexiprep/pom.xml
+++ b/public/flexiprep/pom.xml
@@ -47,7 +47,7 @@
</dependency>
<dependency>
<groupId>org.scalatest</groupId>
- <artifactId>scalatest_2.11</artifactId>
+ <artifactId>scalatest_2.10</artifactId>
<version>2.2.1</version>
<scope>test</scope>
</dependency>
diff --git a/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp b/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp
new file mode 100644
index 0000000000000000000000000000000000000000..d4085dd163c6e6d47c4be3f7304083320c01d0c5
--- /dev/null
+++ b/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp
@@ -0,0 +1,107 @@
+#import(nl.lumc.sasc.biopet.core.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 %>
+<%@ 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>
+ Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nunc risus est, volutpat quis enim sit amet, lacinia posuere ante. Mauris eget massa efficitur, luctus nisl ut, placerat nibh. Pellentesque id nulla maximus, rutrum dui nec, lobortis odio. Fusce eu enim ac sem auctor congue. Ut ac ullamcorper quam, eget sollicitudin felis. Maecenas posuere sagittis blandit. Proin mollis magna lectus, id gravida est consectetur vitae. Nulla id risus at tellus laoreet finibus in id lacus. Duis lobortis commodo nisl viverra tempor. Curabitur sit amet pretium dui, sit amet tincidunt mauris. Duis volutpat eu purus ut molestie.
+ </p>
+ </div>
+ </div>
+#end
+#if (showPlot)
+ #{
+ FlexiprepReport.baseSummaryPlot(outputDir, "QC_Bases_R1","R1", summary, sampleId = sampleId)
+ FlexiprepReport.baseSummaryPlot(outputDir, "QC_Bases_R2","R2", summary, sampleId = sampleId)
+ }#
+ <div class="panel-body">
+ <div class="row">
+ <div class="col-sm-6 col-md-6">
+ <img src="QC_Bases_R1.png" class="img-responsive" />
+ </div>
+ <div class="col-sm-6 col-md-6">
+ <img src="QC_Bases_R2.png" class="img-responsive" />
+ </div>
+ </div>
+
+ </div>
+ <div class="panel-footer">
+ #if (showTable)
+ <button type="button" class="btn btn-info" data-toggle="collapse" data-target="#QC_BasesTable">Hide table</button>
+ #else
+ <button type="button" class="btn btn-info" data-toggle="collapse" data-target="#QC_BasesTable">Show table</button>
+ #end
+ <i class="glyphicon glyphicon-file"></i> <a href="QC_Bases_R1.tsv">R1 reads stats</a> -
+ <i class="glyphicon glyphicon-file"></i> <a href="QC_Bases_R2.tsv">R2 reads stats</a>
+ </div>
+#end
+
+<div class="panel-body collapse #if (showTable)in#end" id="QC_BasesTable">
+
+<!-- Table -->
+<table class="table sortable-theme-bootstrap">
+
+ <thead><tr>
+ <th>Sample</th>
+ <th colspan="2">Library</th>
+ <th>Before QC</th>
+ <th>Discarded</th>
+ <th>(%)</th>
+ <th>After QC</th>
+ </tr></thead>
+ <tbody>
+ #for (sample <- samples.toList.sorted)
+ #{
+ val libs = libId match {
+ case Some(libId) => List(libId.toString)
+ case _ => summary.libraries(sample).toList
+ }
+
+ 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
+ #{
+ val beforeTotal = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_" + read, "bases", "num_total").getOrElse(0).asInstanceOf[Long]
+ val afterTotal = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_" + read + "_after", "bases", "num_total").getOrElse(0).asInstanceOf[Long]
+ }#
+ <td>${read}</td>
+ <td>${beforeTotal}</td>
+ <td>${beforeTotal - afterTotal}</td>
+ <td>${(beforeTotal - afterTotal).toDouble / beforeTotal * 100}%</td>
+ <td>${afterTotal}</td>
+ #end
+ </tr>
+ #end
+ #end
+ </tbody>
+</table>
+
+</div>
diff --git a/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFastaqcPlot.ssp b/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFastaqcPlot.ssp
new file mode 100644
index 0000000000000000000000000000000000000000..b28ae9049e4920ca113e0cae2f73cb08f070c94a
--- /dev/null
+++ b/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFastaqcPlot.ssp
@@ -0,0 +1,51 @@
+#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.core.report.ReportPage)
+#import(org.apache.commons.io.FileUtils)
+#import(java.io.File)
+<%@ var summary: Summary %>
+<%@ var sampleId: Option[String] %>
+<%@ var libId: Option[String] %>
+<%@ var plot: String %>
+<%@ var outputDir: File %>
+#{
+ val paired: Boolean = summary.getLibraryValue(sampleId.get, libId.get, "flexiprep", "settings", "paired").get.asInstanceOf[Boolean]
+ val skipClip: Boolean = summary.getLibraryValue(sampleId.get, libId.get, "flexiprep", "settings", "skip_clip").get.asInstanceOf[Boolean]
+ val skipTrim: Boolean = summary.getLibraryValue(sampleId.get, libId.get, "flexiprep", "settings", "skip_trim").get.asInstanceOf[Boolean]
+
+ def getPlot(read:String) = {
+ summary.getLibraryValue(sampleId.get, libId.get, "flexiprep", "files", read, plot, "path").collect {
+ case value => {
+ val file = new File(value.toString)
+ val newFile = new File(outputDir, read + "_" + file.getName)
+ if (file.exists()) FileUtils.copyFile(file, newFile)
+ newFile.getName
+ }
+ }
+ }
+}#
+
+<div class="row">
+ <div class="col-md-1"></div>
+ <div class="col-md-5"><b>Before QC</b></div>
+ #if (!skipTrim || !skipClip) <div class="col-md-5"><b>After QC</b></div> #end
+</div>
+<div class="row">
+ <div class="col-md-1"><b>R1</b></div>
+ <div class="col-md-5"><img class="img-responsive" src="${getPlot("fastqc_R1")}" /></div>
+ #if (!skipTrim || !skipClip)
+ <div class="col-md-5">
+ <img class="img-responsive" src="${getPlot("fastqc_R1_qc")}" />
+ </div>
+ #end
+</div>
+#if (paired)
+ <div class="row">
+ <div class="col-md-1"><b>R2</b></div>
+ <div class="col-md-5"><img class="img-responsive" src="${getPlot("fastqc_R2")}" /></div>
+ #if (!skipTrim || !skipClip)
+ <div class="col-md-5">
+ <img class="img-responsive" src="${getPlot("fastqc_R2_qc")}" />
+ </div>
+ #end
+ </div>
+#end
diff --git a/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFront.ssp b/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFront.ssp
new file mode 100644
index 0000000000000000000000000000000000000000..8701c981a774cf44daf0bd39ccf837a7d69afe1b
--- /dev/null
+++ b/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFront.ssp
@@ -0,0 +1,3 @@
+#{ //TODO: Need content }#
+
+Todo
\ No newline at end of file
diff --git a/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepInputfiles.ssp b/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepInputfiles.ssp
new file mode 100644
index 0000000000000000000000000000000000000000..ced6349bb7752fc5a86df328f2216f6650a1aaef
--- /dev/null
+++ b/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepInputfiles.ssp
@@ -0,0 +1,63 @@
+#import(nl.lumc.sasc.biopet.core.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)
+ else a
+ }
+ }
+}#
+
+<table class="table sortable-theme-bootstrap" data-sortable>
+
+<thead><tr>
+ <th data-sorted="true" data-sorted-direction="ascending">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)
+ case _ => summary.libraries(sample).toList
+ }
+
+ 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
diff --git a/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepOutputfiles.ssp b/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepOutputfiles.ssp
new file mode 100644
index 0000000000000000000000000000000000000000..439fa99f6b0b206e8898ad39deea447ad28aff30
--- /dev/null
+++ b/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepOutputfiles.ssp
@@ -0,0 +1,63 @@
+#import(nl.lumc.sasc.biopet.core.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)
+ else a
+ }
+ }
+}#
+
+<table class="table sortable-theme-bootstrap" data-sortable>
+
+<thead><tr>
+ <th data-sorted="true" data-sorted-direction="ascending">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)
+ case _ => summary.libraries(sample).toList
+ }
+
+ 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>
+ <td>${summary.getLibraryValue(sample, libId, "flexiprep", "files", "pipeline", "output_" + read, "md5")}</td>
+ #end
+ </tr>
+ #end
+ #end
+</tbody>
+</table>
\ No newline at end of file
diff --git a/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp b/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp
new file mode 100644
index 0000000000000000000000000000000000000000..6aff81a3be7078fef447151151fa38446b9a2286
--- /dev/null
+++ b/public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp
@@ -0,0 +1,109 @@
+#import(nl.lumc.sasc.biopet.core.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 %>
+<%@ 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>
+ Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nunc risus est, volutpat quis enim sit amet, lacinia posuere ante. Mauris eget massa efficitur, luctus nisl ut, placerat nibh. Pellentesque id nulla maximus, rutrum dui nec, lobortis odio. Fusce eu enim ac sem auctor congue. Ut ac ullamcorper quam, eget sollicitudin felis. Maecenas posuere sagittis blandit. Proin mollis magna lectus, id gravida est consectetur vitae. Nulla id risus at tellus laoreet finibus in id lacus. Duis lobortis commodo nisl viverra tempor. Curabitur sit amet pretium dui, sit amet tincidunt mauris. Duis volutpat eu purus ut molestie.
+ </p>
+ </div>
+ </div>
+#end
+
+#if (showPlot)
+ #{
+ FlexiprepReport.readSummaryPlot(outputDir, "QC_Reads_R1","R1", summary, sampleId = sampleId)
+ FlexiprepReport.readSummaryPlot(outputDir, "QC_Reads_R2","R2", summary, sampleId = sampleId)
+ }#
+ <div class="panel-body">
+ <div class="row">
+ <div class="col-sm-6 col-md-6">
+ <img src="QC_Reads_R1.png" class="img-responsive">
+ </div>
+ <div class="col-sm-6 col-md-6">
+ <img src="QC_Reads_R2.png" class="img-responsive">
+ </div>
+ </div>
+
+ </div>
+ <div class="panel-footer">
+ #if (showTable)
+ <button type="button" class="btn btn-info" data-toggle="collapse" data-target="#QC_ReadsTable">Hide table</button>
+ #else
+ <button type="button" class="btn btn-info" data-toggle="collapse" data-target="#QC_ReadsTable">Show table</button>
+ #end
+ <i class="glyphicon glyphicon-file"></i> <a href="QC_Reads_R1.tsv">R1 reads stats</a> -
+ <i class="glyphicon glyphicon-file"></i> <a href="QC_Reads_R2.tsv">R2 reads stats</a>
+ </div>
+#end
+
+<div class="panel-body collapse #if (showTable)in#end" id="QC_ReadsTable">
+
+<!-- Table -->
+<table class="table sortable-theme-bootstrap">
+ <thead><tr>
+ <th>Sample</th>
+ <th colspan="2">Library</th>
+ <th>Before QC</th>
+ <th>Clipping</th>
+ <th>Trimming</th>
+ <th>After QC</th>
+ </tr></thead>
+ <tbody>
+ #for (sample <- samples.toList.sorted)
+ #{
+ val libs = libId match {
+ case Some(libId) => List(libId.toString)
+ case _ => summary.libraries(sample).toList
+ }
+ 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">${libId}</a></td>
+ #{ val reads = if (paired == true) List("R1", "R2") else List("R1") }#
+ #for (read <- reads)
+ #if (read == "R2") </tr><tr> #end
+ #{
+ val beforeTotal = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_" + read, "reads", "num_total")
+ val afterTotal = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_" + read + "_after", "reads", "num_total")
+ val clippingDiscardedToShort = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "clipping_" + read, "num_reads_discarded_too_short").getOrElse(0).asInstanceOf[Long]
+ val clippingDiscardedToLong = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "clipping_" + read, "num_reads_discarded_too_long").getOrElse(0).asInstanceOf[Long]
+ val trimmingDiscarded = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "trimming", "num_reads_discarded_" + read).getOrElse(0).asInstanceOf[Long]
+ }#
+ <td>${read}</td>
+ <td>${beforeTotal}</td>
+ <td>${clippingDiscardedToShort + clippingDiscardedToLong}</td>
+ <td>${trimmingDiscarded}</td>
+ <td>${afterTotal}</td>
+ #end
+ </tr>
+ #end
+ #end
+ </tbody>
+
+</table>
+</div>
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
new file mode 100644
index 0000000000000000000000000000000000000000..5981f2a33f3bd166f72a27337677cbeabc79a622
--- /dev/null
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
@@ -0,0 +1,135 @@
+package nl.lumc.sasc.biopet.pipelines.flexiprep
+
+import java.io.{ PrintWriter, File }
+
+import nl.lumc.sasc.biopet.core.report.{ ReportSection, ReportPage, ReportBuilder }
+import nl.lumc.sasc.biopet.core.summary.{ SummaryValue, Summary }
+import nl.lumc.sasc.biopet.extensions.rscript.StackedBarPlot
+
+/**
+ * Created by pjvan_thof on 3/30/15.
+ */
+object FlexiprepReport extends ReportBuilder {
+ val reportName = "Flexiprep"
+
+ def indexPage = ReportPage(List(
+ "QC" -> flexiprepPage
+ ), List(
+ "Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFront.ssp")
+ ),
+ Map()
+ )
+
+ def flexiprepPage = ReportPage(
+ List(),
+ List(
+ "Read Summary" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
+ "Base Summary" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp"),
+ fastqcPlotSection("Base quality", "plot_per_base_quality"),
+ fastqcPlotSection("Sequence quality", "plot_per_sequence_quality"),
+ fastqcPlotSection("Base GC content", "plot_per_base_gc_content"),
+ fastqcPlotSection("Sequence GC content", "plot_per_sequence_gc_content"),
+ fastqcPlotSection("Base seqeunce content", "plot_per_base_sequence_content"),
+ fastqcPlotSection("Duplication", "plot_duplication_levels"),
+ fastqcPlotSection("Kmers", "plot_kmer_profiles"),
+ fastqcPlotSection("Length distribution", "plot_sequence_length_distribution")
+ ),
+ Map()
+ )
+
+ protected def fastqcPlotSection(name: String, tag: String) = {
+ name -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFastaqcPlot.ssp", Map("plot" -> tag))
+ }
+
+ // FIXME: Not yet finished
+
+ def readSummaryPlot(outputDir: File,
+ prefix: String,
+ read: String,
+ summary: Summary,
+ sampleId: Option[String] = None): Unit = {
+ val tsvFile = new File(outputDir, prefix + ".tsv")
+ val pngFile = new File(outputDir, prefix + ".png")
+ val tsvWriter = new PrintWriter(tsvFile)
+ tsvWriter.println("Library\tAfter_QC\tClipping\tTrimming\tSynced")
+
+ def getLine(summary: Summary, sample: String, lib: String): String = {
+ val beforeTotal = new SummaryValue(List("flexiprep", "stats", "seqstat_" + read, "reads", "num_total"),
+ summary, Some(sample), Some(lib)).value.getOrElse(0).toString.toLong
+ val afterTotal = new SummaryValue(List("flexiprep", "stats", "seqstat_" + read + "_after", "reads", "num_total"),
+ summary, Some(sample), Some(lib)).value.getOrElse(0).toString.toLong
+ val clippingDiscardedToShort = new SummaryValue(List("flexiprep", "stats", "clipping_" + read, "num_reads_discarded_too_short"),
+ summary, Some(sample), Some(lib)).value.getOrElse(0).toString.toLong
+ val clippingDiscardedToLong = new SummaryValue(List("flexiprep", "stats", "clipping_" + read, "num_reads_discarded_too_long"),
+ summary, Some(sample), Some(lib)).value.getOrElse(0).toString.toLong
+ val trimmingDiscarded = new SummaryValue(List("flexiprep", "stats", "trimming", "num_reads_discarded_" + read),
+ summary, Some(sample), Some(lib)).value.getOrElse(0).toString.toLong
+
+ val sb = new StringBuffer()
+ sb.append(sample + "-" + lib + "\t")
+ sb.append(afterTotal + "\t")
+ sb.append((clippingDiscardedToShort + clippingDiscardedToLong) + "\t")
+ sb.append(trimmingDiscarded + "\t")
+ sb.append(beforeTotal - afterTotal - trimmingDiscarded - clippingDiscardedToShort - clippingDiscardedToLong)
+ sb.toString
+ }
+
+ for (
+ sample <- summary.samples if (sampleId.isEmpty || sample == sampleId.get);
+ lib <- summary.libraries(sample)
+ ) {
+ tsvWriter.println(getLine(summary, sample, lib))
+ }
+
+ tsvWriter.close()
+
+ val plot = new StackedBarPlot(null)
+ plot.input = tsvFile
+ plot.output = pngFile
+ plot.ylabel = Some("Reads")
+ plot.width = Some(200 + (summary.libraries.filter(s => sampleId.getOrElse(s._1) == s._1).foldLeft(0)(_ + _._2.size) * 10))
+ plot.title = Some("QC summary on " + read + " reads")
+ plot.runLocal()
+ }
+
+ def baseSummaryPlot(outputDir: File,
+ prefix: String,
+ read: String,
+ summary: Summary,
+ sampleId: Option[String] = None): Unit = {
+ val tsvFile = new File(outputDir, prefix + ".tsv")
+ val pngFile = new File(outputDir, prefix + ".png")
+ val tsvWriter = new PrintWriter(tsvFile)
+ tsvWriter.println("Library\tAfter_QC\tDiscarded")
+
+ def getLine(summary: Summary, sample: String, lib: String): String = {
+ val beforeTotal = new SummaryValue(List("flexiprep", "stats", "seqstat_" + read, "bases", "num_total"),
+ summary, Some(sample), Some(lib)).value.getOrElse(0).toString.toLong
+ val afterTotal = new SummaryValue(List("flexiprep", "stats", "seqstat_" + read + "_after", "bases", "num_total"),
+ summary, Some(sample), Some(lib)).value.getOrElse(0).toString.toLong
+
+ val sb = new StringBuffer()
+ sb.append(sample + "-" + lib + "\t")
+ sb.append(afterTotal + "\t")
+ sb.append(beforeTotal - afterTotal)
+ sb.toString
+ }
+
+ for (
+ sample <- summary.samples if (sampleId.isEmpty || sample == sampleId.get);
+ lib <- summary.libraries(sample)
+ ) {
+ tsvWriter.println(getLine(summary, sample, lib))
+ }
+
+ tsvWriter.close()
+
+ val plot = new StackedBarPlot(null)
+ plot.input = tsvFile
+ plot.output = pngFile
+ plot.ylabel = Some("Bases")
+ plot.width = Some(200 + (summary.libraries.filter(s => sampleId.getOrElse(s._1) == s._1).foldLeft(0)(_ + _._2.size) * 10))
+ plot.title = Some("QC summary on " + read + " bases")
+ plot.runLocal()
+ }
+}
diff --git a/public/gears/pom.xml b/public/gears/pom.xml
index 3182044285c3f9e7f0230ec3210ef947a55e4fef..4dd3396244ed60c04cbced6f70aa6144162918cd 100644
--- a/public/gears/pom.xml
+++ b/public/gears/pom.xml
@@ -48,7 +48,7 @@
</dependency>
<dependency>
<groupId>org.scalatest</groupId>
- <artifactId>scalatest_2.11</artifactId>
+ <artifactId>scalatest_2.10</artifactId>
<version>2.2.1</version>
<scope>test</scope>
</dependency>
diff --git a/public/gentrap/pom.xml b/public/gentrap/pom.xml
index 585d6e2dad2b07cb3293a255f234e301c18abd63..abfad9a314da96da82bed0fb8db411973b13f57d 100644
--- a/public/gentrap/pom.xml
+++ b/public/gentrap/pom.xml
@@ -52,7 +52,7 @@
</dependency>
<dependency>
<groupId>org.scalatest</groupId>
- <artifactId>scalatest_2.11</artifactId>
+ <artifactId>scalatest_2.10</artifactId>
<version>2.2.1</version>
<scope>test</scope>
</dependency>
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/CufflinksProducer.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/CufflinksProducer.scala
index 84e771f47871191ff452f5b0d39599fd96abee43..b3b0fc8c3a373c5dfbe88ebcdd3a20a5330547b8 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/CufflinksProducer.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/CufflinksProducer.scala
@@ -21,12 +21,18 @@ import scalaz._, Scalaz._
import nl.lumc.sasc.biopet.extensions.{ Cufflinks, Ln }
/** General trait for containing cufflinks results */
-trait CufflinksProducer { this: Gentrap#Sample =>
+trait CufflinksProducer {
import Gentrap._
import Gentrap.ExpMeasures._
import Gentrap.StrandProtocol._
+ //TODO: move vars that are used in gentrep
+ protected def sampleDir: File
+ protected def sampleId: String
+ protected def pipeline: Gentrap
+ protected def alnFile: File
+
/** Valid cufflink measure types */
protected val cufflinksMeasures = Set(CufflinksStrict, CufflinksGuided, CufflinksBlind)
diff --git a/public/mapping/pom.xml b/public/mapping/pom.xml
index 91da3c4399daf5eeec772de6b0ade409f7e38d67..3b2fb7aa00f8f2b1e6ac71baa21a264f2dd2e326 100644
--- a/public/mapping/pom.xml
+++ b/public/mapping/pom.xml
@@ -57,7 +57,7 @@
</dependency>
<dependency>
<groupId>org.scalatest</groupId>
- <artifactId>scalatest_2.11</artifactId>
+ <artifactId>scalatest_2.10</artifactId>
<version>2.2.1</version>
<scope>test</scope>
</dependency>
diff --git a/public/mapping/src/main/resources/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp b/public/mapping/src/main/resources/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp
new file mode 100644
index 0000000000000000000000000000000000000000..4570ad240a6220dd06eb4412fc1456d426b36ffe
--- /dev/null
+++ b/public/mapping/src/main/resources/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp
@@ -0,0 +1,59 @@
+#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.core.report.ReportPage)
+#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
+#import(java.io.File)
+<%@ var summary: Summary %>
+<%@ var sampleId: Option[String] = None %>
+<%@ var libId: Option[String] = None %>
+<%@ var sampleLevel: Boolean = true %>
+<%@ var rootPath: String %>
+<%@ var outputDir: File %>
+<%@ var pipelineName: String = "mapping" %>
+<%@ var fileTag: String = "output_bamfile" %>
+#{
+ 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)
+ else a
+ }
+ }
+}#
+
+<div class="panel-body">
+<!-- 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
+ <th>Path</th>
+ <th>MD5</th>
+ </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
+ <td>${removeDir(summary.getLibraryValue(Some(sample), (if (sampleLevel) None else Some(libId)), pipelineName, "files", "pipeline", fileTag, "path"))}</td>
+ <td>${summary.getLibraryValue(Some(sample), (if (sampleLevel) None else Some(libId)), pipelineName, "files", "pipeline", fileTag, "md5")}</td>
+ </tr>
+ #end
+ #end
+ </tbody>
+</table>
+
+</div>
diff --git a/public/pom.xml b/public/pom.xml
index b786c88bd52a30db07d20e70848a689e30908bf6..0fbfc79e5738fcc4a91dc2823310b0f76e5fe5f2 100644
--- a/public/pom.xml
+++ b/public/pom.xml
@@ -67,6 +67,23 @@
</resource>
</resources>
<plugins>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-dependency-plugin</artifactId>
+ <version>2.10</version>
+ <executions>
+ <execution>
+ <id>copy-installed</id>
+ <phase>prepare-package</phase>
+ <goals>
+ <goal>list</goal>
+ </goals>
+ <configuration>
+ <outputFile>${project.build.outputDirectory}/dependency_list.txt</outputFile>
+ </configuration>
+ </execution>
+ </executions>
+ </plugin>
<plugin>
<groupId>net.alchim31.maven</groupId>
<artifactId>scala-maven-plugin</artifactId>
@@ -212,7 +229,7 @@
<artifactId>scoverage-maven-plugin</artifactId>
<version>${scoverage.plugin.version}</version>
<configuration>
- <scalaVersion>2.11.4</scalaVersion>
+ <scalaVersion>2.10.2</scalaVersion>
<!-- other parameters -->
</configuration>
</plugin>
diff --git a/public/shiva/pom.xml b/public/shiva/pom.xml
index ad5563fb93ddeba577f4925c85970b175506b42d..1fb9ebde57502336c489d03a3c713b1448b8fbd1 100644
--- a/public/shiva/pom.xml
+++ b/public/shiva/pom.xml
@@ -48,7 +48,7 @@
</dependency>
<dependency>
<groupId>org.scalatest</groupId>
- <artifactId>scalatest_2.11</artifactId>
+ <artifactId>scalatest_2.10</artifactId>
<version>2.2.1</version>
<scope>test</scope>
</dependency>
diff --git a/public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/outputVcfFiles.ssp b/public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/outputVcfFiles.ssp
new file mode 100644
index 0000000000000000000000000000000000000000..a17e87c9e17596abbdba6ca55110779ac6d246d8
--- /dev/null
+++ b/public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/outputVcfFiles.ssp
@@ -0,0 +1,48 @@
+#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.core.report.ReportPage)
+#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
+#import(java.io.File)
+<%@ var summary: Summary %>
+<%@ var sampleId: Option[String] = None %>
+<%@ var libId: Option[String] = None %>
+<%@ var sampleLevel: Boolean = true %>
+<%@ var rootPath: String %>
+<%@ var outputDir: File %>
+#{
+ val variantCallers = summary.getLibraryValue(sampleId, libId, "shivavariantcalling", "settings", "variantcallers").get.asInstanceOf[List[String]]
+ 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)
+ else a
+ }
+ }
+}#
+
+<div class="panel-body">
+<!-- Table -->
+<table class="table sortable-theme-bootstrap" data-sortable>
+ <thead><tr>
+ <th>Variantcaller</th>
+ <th>Path</th>
+ <th>MD5</th>
+ </tr></thead>
+ <tbody>
+ #if (variantCallers.size > 1)
+ <tr>
+ <td>Final (merged)</td>
+ <td>${removeDir(summary.getLibraryValue(sampleId, libId, "shivavariantcalling", "files", "pipeline", "final", "path"))}</td>
+ <td>${summary.getLibraryValue(sampleId, libId, "shivavariantcalling", "files", "pipeline", "final", "md5")}</td>
+ </tr>
+ #end
+ #for (variantCaller <- variantCallers)
+ <tr>
+ <td>${variantCaller}</td>
+ <td>${removeDir(summary.getLibraryValue(sampleId, libId, "shivavariantcalling", "files", "pipeline", variantCaller, "path"))}</td>
+ <td>${summary.getLibraryValue(sampleId, libId, "shivavariantcalling", "files", "pipeline", variantCaller, "md5")}</td>
+ </tr>
+ #end
+ </tbody>
+</table>
+
+</div>
diff --git a/public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp b/public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp
new file mode 100644
index 0000000000000000000000000000000000000000..27121ca4ee08e1a1b68c5c8bd96368d562e64618
--- /dev/null
+++ b/public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp
@@ -0,0 +1,64 @@
+#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.core.report.ReportPage)
+#import(nl.lumc.sasc.biopet.pipelines.shiva.ShivaReport)
+#import(java.io.File)
+<%@ var summary: Summary %>
+<%@ var sampleId: Option[String] = None %>
+<%@ var rootPath: String %>
+<%@ var outputDir: File %>
+<%@ var showPlot: Boolean = false %>
+<%@ var showTable: Boolean = true %>
+<%@ var showIntro: Boolean = true%>
+#{
+ val fields = List("Hom", "HomVar", "Het", "HomRef", "NoCall", "Variant", "Total")
+ 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>
+ Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nunc risus est, volutpat quis enim sit amet, lacinia posuere ante. Mauris eget massa efficitur, luctus nisl ut, placerat nibh. Pellentesque id nulla maximus, rutrum dui nec, lobortis odio. Fusce eu enim ac sem auctor congue. Ut ac ullamcorper quam, eget sollicitudin felis. Maecenas posuere sagittis blandit. Proin mollis magna lectus, id gravida est consectetur vitae. Nulla id risus at tellus laoreet finibus in id lacus. Duis lobortis commodo nisl viverra tempor. Curabitur sit amet pretium dui, sit amet tincidunt mauris. Duis volutpat eu purus ut molestie.
+ </p>
+ </div>
+ </div>
+#end
+
+#if (showPlot)
+ #{ ShivaReport.variantSummaryPlot(outputDir, "variantSummary", summary, sampleId = sampleId) }#
+ <div class="panel-body">
+ <img src="variantSummary.png" class="img-responsive" />
+ </div>
+ <div class="panel-footer">
+ #if (showTable)
+ <button type="button" class="btn btn-info" data-toggle="collapse" data-target="#variantSummaryTable">Hide table</button>
+ #else
+ <button type="button" class="btn btn-info" data-toggle="collapse" data-target="#variantSummaryTable">Show table</button>
+ #end
+ <i class="glyphicon glyphicon-file"></i> <a href="variantSummary.tsv">tsv file</a>
+ </div>
+#end
+
+<div class="panel-body collapse #if (showTable)in#end" id="variantSummaryTable">
+
+<!-- Table -->
+<table class="table sortable-theme-bootstrap" data-sortable>
+ <thead><tr><th data-sorted="true" data-sorted-direction="ascending">Sample</th>
+ #for (field <- fields) <th>${field}</th> #end
+ </tr></thead>
+ <tbody>
+ #for (sample <- samples.toList.sorted)
+ <tr><td><a href="${rootPath}Samples/${sample}/index.html">${sample}</a></td>
+ #for (field <- fields)
+ <td>${summary.getSampleValue(sample, "shivavariantcalling", "stats", "multisample-vcfstats-final", "genotype", field)}</td>
+ #end
+ </tr>
+ #end
+ </tbody>
+</table>
+</div>
diff --git a/public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/shivaFront.ssp b/public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/shivaFront.ssp
new file mode 100644
index 0000000000000000000000000000000000000000..2a76fe50d1e84ddab3ecd52cec18b302668bcf56
--- /dev/null
+++ b/public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/shivaFront.ssp
@@ -0,0 +1,27 @@
+#import(nl.lumc.sasc.biopet.core.summary.Summary)
+#import(nl.lumc.sasc.biopet.core.report.ReportPage)
+<%@ var summary: Summary %>
+<%@ var rootPath: String %>
+
+<table class="table">
+<tbody>
+ <tr><th>Pipeline</th><td>Shiva</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>${summary.getValue("meta", "output_dir")}</td></tr>
+ <tr>
+ <th>Variantcallers</th>
+ <td>${summary.getValue("shivavariantcalling", "settings", "variantcallers").get.asInstanceOf[List[String]].mkString(", ")}</td>
+ </tr>
+ <tr><th>Number of samples</th><td>${summary.samples.size}</td></tr>
+</tbody>
+</table>
+<br/>
+<div class="row">
+ <div class="col-md-1"></div>
+ <div class="col-md-6">
+ <p>
+ Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nunc risus est, volutpat quis enim sit amet, lacinia posuere ante. Mauris eget massa efficitur, luctus nisl ut, placerat nibh. Pellentesque id nulla maximus, rutrum dui nec, lobortis odio. Fusce eu enim ac sem auctor congue. Ut ac ullamcorper quam, eget sollicitudin felis. Maecenas posuere sagittis blandit. Proin mollis magna lectus, id gravida est consectetur vitae. Nulla id risus at tellus laoreet finibus in id lacus. Duis lobortis commodo nisl viverra tempor. Curabitur sit amet pretium dui, sit amet tincidunt mauris. Duis volutpat eu purus ut molestie.
+ </p>
+ </div>
+</div>
\ No newline at end of file
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
new file mode 100644
index 0000000000000000000000000000000000000000..e3a2634896730962d8fd636eac7861e02506055f
--- /dev/null
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
@@ -0,0 +1,181 @@
+package nl.lumc.sasc.biopet.pipelines.shiva
+
+import java.io.{ PrintWriter, File }
+
+import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.core.report._
+import nl.lumc.sasc.biopet.core.summary.{ SummaryValue, Summary }
+import nl.lumc.sasc.biopet.extensions.rscript.StackedBarPlot
+import nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport
+import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
+
+/**
+ * Created by pjvan_thof on 3/30/15.
+ */
+class ShivaReport(val root: Configurable) extends ReportBuilderExtension {
+ val builder = ShivaReport
+
+ override val defaultCoreMemory = 3.0
+}
+
+object ShivaReport extends MultisampleReportBuilder {
+
+ // FIXME: Not yet finished
+
+ def indexPage = {
+ val regions = regionsPage
+ ReportPage(
+ List("Samples" -> generateSamplesPage(pageArgs)) ++
+ (if (regions.isDefined) Map(regions.get) else Map()) ++
+ Map("Files" -> filesPage,
+ "Versions" -> ReportPage(List(), List((
+ "Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp"
+ ))), Map())
+ ),
+ List(
+ "Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/shivaFront.ssp"),
+ "Variantcalling" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp",
+ Map("showPlot" -> true, "showTable" -> false)),
+ "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",
+ Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)
+ ),
+ "Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp",
+ Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)),
+ "Whole genome coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp",
+ Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)),
+ "QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp",
+ Map("showPlot" -> true, "showTable" -> false)),
+ "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp",
+ Map("showPlot" -> true, "showTable" -> false))
+ ),
+ pageArgs
+ )
+ }
+
+ def regionsPage = {
+ val roi = summary.getValue("shiva", "settings", "regions_of_interest")
+ val amplicon = summary.getValue("shiva", "settings", "amplicon_bed")
+
+ var regionPages: Map[String, ReportPage] = Map()
+
+ def createPage(name: String, amplicon: Boolean = false): ReportPage = {
+ ReportPage(
+ List(),
+ List("Coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp")),
+ Map("target" -> name)
+ )
+ }
+
+ amplicon match {
+ case Some(x: String) => regionPages += (x + " (Amplicon)") -> createPage(x, true)
+ case _ =>
+ }
+
+ roi match {
+ case Some(x: String) => regionPages += x -> createPage(x, false)
+ case Some(x: List[_]) => x.foreach(x => regionPages += x.toString -> createPage(x.toString, false))
+ case _ =>
+ }
+
+ if (regionPages.nonEmpty) Some("Regions" -> ReportPage(
+ List(),
+ regionPages.map(p => (p._1 -> ReportSection(
+ "/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp",
+ Map("target" -> p._1.stripSuffix(" (Amplicon)"))
+ ))).toList.sortBy(_._1),
+ Map())
+ )
+ else None
+ }
+
+ def filesPage = ReportPage(List(), List(
+ "Input fastq files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepInputfiles.ssp"),
+ "After QC fastq files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepOutputfiles.ssp"),
+ "Bam files per lib" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp", Map("sampleLevel" -> false)),
+ "Preprocessed bam files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp",
+ Map("pipelineName" -> "shiva", "fileTag" -> "preProcessBam")),
+ "VCF files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/outputVcfFiles.ssp", Map("sampleId" -> None))
+ ), Map())
+
+ def samplePage(sampleId: String, args: Map[String, Any]) = {
+ ReportPage(List(
+ "Libraries" -> generateLibraryPage(args),
+ "Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), None),
+ "Files" -> filesPage
+ ), List(
+ "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",
+ if (summary.libraries(sampleId).size > 1) Map("showPlot" -> true) else Map()),
+ "Preprocessing" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp", Map("sampleLevel" -> true)),
+ "Variantcalling" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp"),
+ "QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
+ "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp")
+ ), args)
+ }
+
+ def libraryPage(sampleId: String, libId: String, args: Map[String, Any]) = {
+ ReportPage(List(
+ "Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), Some(libId)),
+ "QC" -> FlexiprepReport.flexiprepPage
+ ), List(
+ "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"),
+ "QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
+ "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp")
+ ), args)
+ }
+
+ def reportName = "Shiva Report"
+
+ def variantSummaryPlot(outputDir: File,
+ prefix: String,
+ summary: Summary,
+ libraryLevel: Boolean = false,
+ sampleId: 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.print("Library") else tsvWriter.print("Sample")
+ tsvWriter.println("\tHomVar\tHet\tHomRef\tNoCall")
+
+ def getLine(summary: Summary, sample: String, lib: Option[String] = None): String = {
+ val homVar = new SummaryValue(List("shivavariantcalling", "stats", "multisample-vcfstats-final", "genotype", "HomVar"),
+ summary, Some(sample), lib).value.getOrElse(0).toString.toLong
+ val homRef = new SummaryValue(List("shivavariantcalling", "stats", "multisample-vcfstats-final", "genotype", "HomRef"),
+ summary, Some(sample), lib).value.getOrElse(0).toString.toLong
+ val noCall = new SummaryValue(List("shivavariantcalling", "stats", "multisample-vcfstats-final", "genotype", "NoCall"),
+ summary, Some(sample), lib).value.getOrElse(0).toString.toLong
+ val het = new SummaryValue(List("shivavariantcalling", "stats", "multisample-vcfstats-final", "genotype", "Het"),
+ summary, Some(sample), lib).value.getOrElse(0).toString.toLong
+ val sb = new StringBuffer()
+ if (lib.isDefined) sb.append(sample + "-" + lib.get + "\t") else sb.append(sample + "\t")
+ sb.append(homVar + "\t")
+ sb.append(het + "\t")
+ sb.append(homRef + "\t")
+ sb.append(noCall)
+ sb.toString
+ }
+
+ if (libraryLevel) {
+ for (
+ sample <- summary.samples if (sampleId.isEmpty || sample == sampleId.get);
+ lib <- summary.libraries(sample)
+ ) {
+ tsvWriter.println(getLine(summary, sample, Some(lib)))
+ }
+ } else {
+ for (sample <- summary.samples if (sampleId.isEmpty || sample == sampleId.get)) {
+ tsvWriter.println(getLine(summary, sample))
+ }
+ }
+
+ tsvWriter.close()
+
+ val plot = new StackedBarPlot(null)
+ plot.input = tsvFile
+ plot.output = pngFile
+ plot.ylabel = Some("VCF records")
+ if (libraryLevel) {
+ plot.width = Some(200 + (summary.libraries.filter(s => sampleId.getOrElse(s._1) == s._1).foldLeft(0)(_ + _._2.size) * 10))
+ } else plot.width = Some(200 + (summary.samples.filter(s => sampleId.getOrElse(s) == s).size * 10))
+ plot.runLocal()
+ }
+}
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
index 696216d716e1cb72d1baf95fc3f431a0a4744d5c..d95169cfcd351dd4fae8d01d7c6923e9ca61fcf7 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
@@ -45,6 +45,13 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
addSummaryJobs
}
+ override def reportClass = {
+ val shiva = new ShivaReport(this)
+ shiva.outputDir = new File(outputDir, "report")
+ shiva.summaryFile = summaryFile
+ Some(shiva)
+ }
+
/** Method to make the variantcalling submodule of shiva */
def makeVariantcalling(multisample: Boolean = false): ShivaVariantcallingTrait = {
if (multisample) new ShivaVariantcalling(qscript) {
@@ -65,7 +72,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
/** Sample specific files to add to summary */
def summaryFiles: Map[String, File] = {
preProcessBam match {
- case Some(preProcessBam) => Map("bamFile" -> preProcessBam)
+ case Some(preProcessBam) => Map("preProcessBam" -> preProcessBam)
case _ => Map()
}
}
@@ -286,7 +293,16 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
def summaryFile = new File(outputDir, "Shiva.summary.json")
/** Settings of pipeline for summary */
- def summarySettings = Map("reference" -> referenceSummary)
+ def summarySettings = {
+ val roiBedFiles: List[File] = config("regions_of_interest", Nil)
+ val ampliconBedFile: Option[File] = config("amplicon_bed")
+
+ Map(
+ "reference" -> referenceSummary,
+ "regions_of_interest" -> roiBedFiles.map(_.getName.stripSuffix(".bed")),
+ "amplicon_bed" -> ampliconBedFile.map(_.getName.stripSuffix(".bed"))
+ )
+ }
/** Files for the summary */
def summaryFiles = Map("referenceFasta" -> referenceFasta())