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biopet.biopet
Commits
9ac622a9
Commit
9ac622a9
authored
Oct 31, 2015
by
Peter van 't Hof
Browse files
Added sample / lib to report
parent
128e3f39
Changes
3
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public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsFront.ssp
View file @
9ac622a9
...
...
@@ -2,6 +2,8 @@
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
<%@ var summary: Summary %>
<%@ var rootPath: String %>
<%@ var sampleId: Option[String] = None %>
<%@ var libId: Option[String] = None %>
<table class="table">
<tbody>
...
...
@@ -9,6 +11,8 @@
<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>${summary.getValue("meta", "output_dir")}</td></tr>
#if(sampleId.isDefined) <tr><th>Sample</th><td>${sampleId}</td></tr> #end
#if(libId.isDefined) <tr><th>Library</th><td>${libId}</td></tr> #end
</tbody>
</table>
<br/>
...
...
public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsSunburst.ssp
View file @
9ac622a9
...
...
@@ -5,11 +5,8 @@
<%@ var sampleId: Option[String] = None %>
<%@ var libId: Option[String] = None %>
<%@ var rootPath: String %>
<%@ var outputDir: File %>
<%@ var showPlot: Boolean = true %>
<%@ var showTable: Boolean = true %>
<%@ var showIntro: Boolean = true %>
<%@ var multisample: Boolean = false %>
#{
val samples = sampleId match {
case Some(sample) => List(sample.toString)
...
...
@@ -59,7 +56,7 @@
<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)
}#
...
...
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
View file @
9ac622a9
...
...
@@ -69,6 +69,8 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript with Sam
val
gears
=
new
GearsReport
(
this
)
gears
.
outputDir
=
new
File
(
outputDir
,
"report"
)
gears
.
summaryFile
=
summaryFile
sampleId
.
foreach
(
gears
.
args
+=
"sampleId"
->
_
)
libId
.
foreach
(
gears
.
args
+=
"libId"
->
_
)
Some
(
gears
)
}
...
...
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