Commit 9ac622a9 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added sample / lib to report

parent 128e3f39
...@@ -2,6 +2,8 @@ ...@@ -2,6 +2,8 @@
#import(nl.lumc.sasc.biopet.core.report.ReportPage) #import(nl.lumc.sasc.biopet.core.report.ReportPage)
<%@ var summary: Summary %> <%@ var summary: Summary %>
<%@ var rootPath: String %> <%@ var rootPath: String %>
<%@ var sampleId: Option[String] = None %>
<%@ var libId: Option[String] = None %>
<table class="table"> <table class="table">
<tbody> <tbody>
...@@ -9,6 +11,8 @@ ...@@ -9,6 +11,8 @@
<tr><th>Version</th><td>${summary.getValue("meta", "pipeline_version")}</td></tr> <tr><th>Version</th><td>${summary.getValue("meta", "pipeline_version")}</td></tr>
<tr><th>Last commit hash</th><td>${summary.getValue("meta", "last_commit_hash")}</td></tr> <tr><th>Last commit hash</th><td>${summary.getValue("meta", "last_commit_hash")}</td></tr>
<tr><th>Output directory</th><td>${summary.getValue("meta", "output_dir")}</td></tr> <tr><th>Output directory</th><td>${summary.getValue("meta", "output_dir")}</td></tr>
#if(sampleId.isDefined) <tr><th>Sample</th><td>${sampleId}</td></tr> #end
#if(libId.isDefined) <tr><th>Library</th><td>${libId}</td></tr> #end
</tbody> </tbody>
</table> </table>
<br/> <br/>
......
...@@ -5,11 +5,8 @@ ...@@ -5,11 +5,8 @@
<%@ var sampleId: Option[String] = None %> <%@ var sampleId: Option[String] = None %>
<%@ var libId: Option[String] = None %> <%@ var libId: Option[String] = None %>
<%@ var rootPath: String %> <%@ var rootPath: String %>
<%@ var outputDir: File %>
<%@ var showPlot: Boolean = true %> <%@ var showPlot: Boolean = true %>
<%@ var showTable: Boolean = true %>
<%@ var showIntro: Boolean = true %> <%@ var showIntro: Boolean = true %>
<%@ var multisample: Boolean = false %>
#{ #{
val samples = sampleId match { val samples = sampleId match {
case Some(sample) => List(sample.toString) case Some(sample) => List(sample.toString)
...@@ -59,7 +56,7 @@ ...@@ -59,7 +56,7 @@
<script type="application/ecmascript"> <script type="application/ecmascript">
#{ #{
val rawreport = Map("kraken" -> summary.getValue("gears", "stats", "krakenreport")) val rawreport = Map("kraken" -> summary.getValue(sampleId, libId, "gears", "stats", "krakenreport"))
val bla = ConfigUtils.mapToJson(rawreport) val bla = ConfigUtils.mapToJson(rawreport)
}# }#
......
...@@ -69,6 +69,8 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript with Sam ...@@ -69,6 +69,8 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript with Sam
val gears = new GearsReport(this) val gears = new GearsReport(this)
gears.outputDir = new File(outputDir, "report") gears.outputDir = new File(outputDir, "report")
gears.summaryFile = summaryFile gears.summaryFile = summaryFile
sampleId.foreach(gears.args += "sampleId" -> _)
libId.foreach(gears.args += "libId" -> _)
Some(gears) Some(gears)
} }
......
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