Skip to content

GitLab

Commit 6b6ea1fe authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added flexiprep files to Shiva report

parent 066efc37
Hide whitespace changes
Inline Side-by-side
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))
),
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment