Commit 6a754e68 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Adding front page for shiva

parent 5fda5828
#import(nl.lumc.sasc.biopet.core.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
<%@ var summary: Summary %>
<%@ var rootPath: String %>
<table>
<tbody>
<tr><th>Pipeline</th><td>Shiva</td></tr>
<tr><th><a href="${rootPath}/Samples/index.html">Samples</a></th><td>${summary.samples.size}</td></tr>
</tbody>
</table>
\ No newline at end of file
...@@ -10,19 +10,20 @@ object ShivaReport extends MultisampleReportBuilder { ...@@ -10,19 +10,20 @@ object ShivaReport extends MultisampleReportBuilder {
def indexPage = ReportPage( def indexPage = ReportPage(
Map( Map(
"General" -> ReportPage(Map(), List( "General" -> ReportPage(Map(), List(
"Variantcalling" -> ReportSection("/nl/lumc/sasc/biopet/core/report/ShivaVariantcalling.ssp"), "Variantcalling" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp"),
"QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"), "QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
"QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp") "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp")
), Map()), ), Map()),
"Samples" -> generateSamplesPage(pageArgs) "Samples" -> generateSamplesPage(pageArgs)
), ),
Nil, List("Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/shivaFront.ssp")),
pageArgs pageArgs
) )
def samplePage(sampleId: String, args: Map[String, Any]) = { def samplePage(sampleId: String, args: Map[String, Any]) = {
ReportPage(Map("Libraries" -> generateLibraryPage(args)), List( ReportPage(Map("Libraries" -> generateLibraryPage(args)), List(
"Variantcalling" -> ReportSection("/nl/lumc/sasc/biopet/core/report/ShivaVariantcalling.ssp"), "Libraries" -> ReportSection("/nl/lumc/sasc/biopet/core/report/librariesList.ssp"),
"Variantcalling" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp"),
"QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"), "QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
"QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp") "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp")
), args) ), args)
......
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