Skip to content

GitLab

Commit be30372c authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files
Options

Added bam and vcf files to report of Shiva

parent 6b6ea1fe
Hide whitespace changes
Inline Side-by-side
Showing with 161 additions and 6 deletions
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/Summary.scala
View file @ be30372c
......@@ -46,6 +46,14 @@ class Summary(file: File) {
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: _*)
......
public/mapping/src/main/resources/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp 0 → 100644
View file @ be30372c
#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 %>
#{
val samples = sampleId match {
case Some(sample) => {
List(sample.toString)
}
case _ => summary.samples.toList
}
}#
<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>${summary.getLibraryValue(sample, libId, "mapping", "files", "pipeline", "output_bamfile", "path")}</td>
<td>${summary.getLibraryValue(sample, libId, "mapping", "files", "pipeline", "output_bamfile", "md5")}</td>
</tr>
#end
#end
</tbody>
</table>
</div>
public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/outputBamfiles.ssp 0 → 100644
View file @ be30372c
#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 samples = sampleId match {
case Some(sample) => {
List(sample.toString)
}
case _ => summary.samples.toList
}
}#
<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>${summary.getLibraryValue(sample, libId, "shiva", "files", "pipeline", "preProcessBam", "path")}</td>
<td>${summary.getLibraryValue(sample, libId, "shiva", "files", "pipeline", "preProcessBam", "md5")}</td>
</tr>
#end
#end
</tbody>
</table>
</div>
public/shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/outputVcfFiles.ssp 0 → 100644
View file @ be30372c
#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]]
}#
<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>${summary.getLibraryValue(sampleId, libId, "shivavariantcalling", "files", "pipeline", "final", "path")}</td>
<td>${summary.getLibraryValue(sampleId, libId, "shivavariantcalling", "files", "pipeline", "final", "md5")}</td>
</tr>
#end
#for (variantCaller <- variantCallers)
<tr>
<td>${variantCaller}</td>
<td>${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>
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
View file @ be30372c
......@@ -36,10 +36,7 @@ object ShivaReport extends MultisampleReportBuilder {
Map("showPlot" -> true, "showTable" -> true))
), Map()),
"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()),
"Files" -> filesPage,
"Versions" -> ReportPage(Map(), List(), Map())
),
List(
......@@ -60,10 +57,19 @@ object ShivaReport extends MultisampleReportBuilder {
)
}
def filesPage = 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"),
"Bam files per lib" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp"),
"Preprocessed bam files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/outputBamfiles.ssp"),
"VCF files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/outputVcfFiles.ssp", Map("sampleId" -> None))
), Map())
def samplePage(sampleId: String, args: Map[String, Any]) = {
ReportPage(Map(
"Libraries" -> generateLibraryPage(args),
"Alignment" -> BammetricsReport.bamMetricsPage
"Alignment" -> BammetricsReport.bamMetricsPage,
"Files" -> filesPage
), List(
"Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",
if (summary.libraries(sampleId).size > 1) Map("showPlot" -> true) else Map()),
......
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
View file @ be30372c
......@@ -72,7 +72,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
/** 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()
}
}
......
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