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biopet.biopet
Commit 6b6ea1fe authored by Peter van 't Hof's avatar Peter van 't Hof
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Added flexiprep files to Shiva report

parent 066efc37
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Showing with 186 additions and 28 deletions
public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp
View file @ 6b6ea1fe
#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] %>
<%@ 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 %>
#{
def getPlot = {
(if (libId.isDefined) summary.getLibraryValue(sampleId.get, libId.get, metricsTag, "files", "insert_size_metrics", "output_histogram", "path")
else summary.getSampleValue(sampleId.get, metricsTag, "files", "insert_size_metrics", "output_histogram", "path")).collect {
case value => {
val file = new File(value.toString)
val newFile = new File(outputDir, file.getName)
FileUtils.copyFile(file, newFile)
newFile.getName
}
}
val samples = sampleId match {
case Some(sample) => {
List(sample.toString)
}
case _ => summary.samples.toList
}
}#
<iframe src="${getPlot}" style="width:400px; height:400px;" frameborder="0"></iframe>
#if (showPlot)
#{ BammetricsReport.insertSizePlot(outputDir, "insertsize", summary, !sampleLevel, sampleId = sampleId) }#
<div class="panel-body">
<img src="insertsize.png" class="img-responsive" />
</div>
<div class="panel-footer">
<i class="glyphicon glyphicon-file"></i> <a href="insertsize.tsv">tsv file</a>
</div>
#end
#if (showTable)
<div class="panel-body">
<!-- Table -->
<table class="table sortable-theme-bootstrap" data-sortable>
<thead><tr>
<th data-sorted="true" data-sorted-direction="ascending">Sample</th>
#if (!sampleLevel) <th>Library</th> #end
#for (field <- fields)
<th>${field}</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")
<table>
<tbody>
#for (field <- fields)
<tr><th>${field}</th><td>
#if (libId.isDefined)
${summary.getLibraryValue(sampleId.get, libId.get, metricsTag, "stats", "insert_size_metrics", field)}
#else
${summary.getSampleValue(sampleId.get, metricsTag, "stats", "insert_size_metrics", field)}
val fieldValues = for (field <- fields) yield {
summary.getValue((prefixPath ::: List(metricsTag, "stats", "insert_size_metrics", field)):_*)
}
}#
#for (value <- fieldValues)
<td>${value}</td>
#end
</tr>
#end
#end
</td></tr>
#end
</tbody>
</table>
</tbody>
</table>
</div>
#end
public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
View file @ 6b6ea1fe
......@@ -27,7 +27,7 @@ object BammetricsReport extends ReportBuilder {
List(
"Summary" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"),
"Bam Stats" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/bamStats.ssp"),
"Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp"),
"Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp", Map("showPlot" -> true)),
"RNA (optional)" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/rna.ssp"),
"Target (optional)" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/target.ssp"),
"GC Bias" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/gcBias.ssp")
......
public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepInputfiles.ssp 0 → 100644
View file @ 6b6ea1fe
#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
}
}#
<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>${read}</td>
<td>${summary.getLibraryValue(sample, libId, "flexiprep", "files", "pipeline", "input_" + read, "path")}</td>
<td>${summary.getLibraryValue(sample, libId, "flexiprep", "files", "pipeline", "input_" + read, "md5")}</td>
#end
</tr>
#end
#end
</tbody>
</table>
\ No newline at end of file
public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepOutputfiles.ssp 0 → 100644
View file @ 6b6ea1fe
#import(nl.lumc.sasc.biopet.core.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport)
#import(java.io.File)
<%@ var summary: Summary %>
<%@ var sampleId: Option[String] = None %>
<%@ var libId: Option[String] = None %>
<%@ var rootPath: String %>
<%@ var outputDir: File %>
<%@ var showPlot: Boolean = false %>
<%@ var showTable: Boolean = true %>
#{
val samples = sampleId match {
case Some(sample) => List(sample.toString)
case _ => summary.samples.toList
}
}#
<table class="table sortable-theme-bootstrap" data-sortable>
<thead><tr>
<th data-sorted="true" data-sorted-direction="ascending">Sample</th>
<th colspan="2">Library</th>
<th>Path</th>
<th>MD5</th>
</tr></thead>
<tbody>
#for (sample <- samples.toList.sorted)
#{
val libs = libId match {
case Some(libId) => List(libId.toString)
case _ => summary.libraries(sample).toList
}
val sampleRowspan = {
libs.size +
libs.count(summary.getLibraryValue(sample, _, "flexiprep", "settings", "paired").getOrElse(false) == true)
}
}#
<tr><td rowspan="${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>${summary.getLibraryValue(sample, libId, "flexiprep", "files", "pipeline", "output_" + read, "path")}</td>
<td>${summary.getLibraryValue(sample, libId, "flexiprep", "files", "pipeline", "output_" + read, "md5")}</td>
#end
</tr>
#end
#end
</tbody>
</table>
\ No newline at end of file
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
View file @ 6b6ea1fe
......@@ -28,12 +28,19 @@ object ShivaReport extends MultisampleReportBuilder {
Map("showPlot" -> true, "showTable" -> true)),
"Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",
Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> true)),
"Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp",
Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> true)),
"QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp",
Map("showPlot" -> true, "showTable" -> true)),
"QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp",
Map("showPlot" -> true, "showTable" -> true))
), Map()),
"Samples" -> generateSamplesPage(pageArgs)
"Samples" -> generateSamplesPage(pageArgs),
"Files" -> ReportPage(Map(), 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")
), Map()),
"Versions" -> ReportPage(Map(), List(), Map())
),
List(
"Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/shivaFront.ssp"),
......@@ -42,8 +49,10 @@ object ShivaReport extends MultisampleReportBuilder {
"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)),
"QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp",
Map("showPlot" -> true, "showTable" -> false)),
Map("showPlot" -> true, "showTable" -> true)),
"QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp",
Map("showPlot" -> true, "showTable" -> false))
),
......
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