Commit bb2dac47 authored by Wai Yi Leung's avatar Wai Yi Leung

TinyCap report base

parent 574ccefb
#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
<%@ var summary: Summary %>
<%@ var rootPath: String %>
<%@ var pipeline: String %>
<table class="table">
<tbody>
<tr><th>Pipeline</th><td>${pipeline}</td></tr>
<tr><th>Version</th><td>${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>Reference</th><td>${summary.getValue(pipeline, "settings", "reference", "species")} - ${summary.getValue(pipeline, "settings", "reference", "name")}</td></tr>
<tr><th>Number of samples</th><td>${summary.samples.size}</td></tr>
</tbody>
</table>
<br/>
<div class="row">
<div class="col-md-1"></div>
<div class="col-md-6">
<p>
In this web document you can find your <em>${pipeline}</em> pipeline report.
Different categories of data can be found in the left-side menu.
Statistics per sample and library can be accessed through the top-level menu.
Some statistics for target regions can be found in the regions tab.
Futhermore, you can view all versions of software tools used by selecting <em>Versions</em> from the top menu.
</p>
<p>
<small>Brought to you by <a href="https://sasc.lumc.nl" target="_blank"><abbr
title="Sequence Analysis Support Core">SASC</abbr></a> and <a
href="https://www.lumc.nl/org/klinische-genetica/" target="_blank"><abbr title="Clinical Genetics LUMC">KG</abbr></a>,
LUMC.
</small>
</p>
</div>
</div>
\ No newline at end of file
package nl.lumc.sasc.biopet.pipelines.tinycap
import nl.lumc.sasc.biopet.core.{ PipelineCommand, Reference }
import nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
import nl.lumc.sasc.biopet.core.{PipelineCommand, Reference}
import nl.lumc.sasc.biopet.extensions.HtseqCount
import nl.lumc.sasc.biopet.pipelines.mapping.MultisampleMappingTrait
import nl.lumc.sasc.biopet.utils.config.Configurable
......@@ -85,6 +86,13 @@ class TinyCap(val root: Configurable) extends QScript with MultisampleMappingTra
"annotationGff" -> annotationGff
)
override def reportClass: Option[ReportBuilderExtension] = {
val report = new TinyCapReport(this)
report.outputDir = new File(outputDir, "report")
report.summaryFile = summaryFile
Some(report)
}
override def addMultiSampleJobs = {
super.addMultiSampleJobs
}
......
package nl.lumc.sasc.biopet.pipelines.tinycap
import nl.lumc.sasc.biopet.core.report.{ReportPage, ReportSection, ReportBuilderExtension}
import nl.lumc.sasc.biopet.pipelines.mapping.MultisampleMappingReportTrait
import nl.lumc.sasc.biopet.utils.config.Configurable
/**
* Created by wyleung on 4-2-16.
*/
class TinyCapReport(val root: Configurable) extends ReportBuilderExtension {
def builder = TinyCapReport
}
object TinyCapReport extends MultisampleMappingReportTrait {
/** Name of the report */
def reportName = "TinyCap Report"
/** Front section for the report */
override def frontSection: ReportSection = ReportSection("/nl/lumc/sasc/biopet/pipelines/tinycap/tinycapFront.ssp")
override def pipelineName = "tinycap"
/** Root page for the carp report */
override def indexPage = {
val wgsExecuted = summary.getSampleValues("bammetrics", "stats", "wgs").values.exists(_.isDefined)
val rnaExecuted = summary.getSampleValues("bammetrics", "stats", "rna").values.exists(_.isDefined)
ReportPage(
List("Samples" -> generateSamplesPage(pageArgs)) ++
Map("Reference" -> ReportPage(List(), List(
"Reference" -> ReportSection("/nl/lumc/sasc/biopet/core/report/reference.ssp", Map("pipeline" -> pipelineName))
), Map()),
"Files" -> filesPage,
"Versions" -> ReportPage(List(), List("Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp"
)), Map())
),
List(
"Report" -> frontSection,
"Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",
Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)
)) ++
(if (wgsExecuted) List("Whole genome coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp",
Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)))
else Nil) ++
(if (rnaExecuted) List("Rna coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp",
Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)))
else Nil) ++
List("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 ++ Map("pipeline" -> pipelineName)
)
}
}
......@@ -6,7 +6,7 @@
<table class="table">
<tbody>
<tr><th>Pipeline</th><td>Shiva</td></tr>
<tr><th>Pipeline</th><td>${pipeline}</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>
......
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