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biopet.biopet
Commits
1b5553ec
Commit
1b5553ec
authored
Dec 10, 2015
by
Peter van 't Hof
Browse files
Added multisample gears report
parent
8427c6a6
Changes
5
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public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsFront.ssp
View file @
1b5553ec
...
...
@@ -2,8 +2,6 @@
#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>
...
...
@@ -11,8 +9,6 @@
<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>${libId}</td></tr> #end
</tbody>
</table>
<br/>
...
...
public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsSingleFront.ssp
0 → 100644
View file @
1b5553ec
#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
<%@ var summary: Summary %>
<%@ var rootPath: String %>
<%@ var sampleId: Option[String] = None %>
<%@ var libId: Option[String] = None %>
<table class="table">
<tbody>
<tr><th>Pipeline</th><td>Gears</td></tr>
<tr><th>Version</th><td>${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>
#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/>
<div class="row">
<div class="col-md-1"></div>
<div class="col-md-6">
<p>\
In this web document you can find your <em>Gears</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
public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsSunburst.ssp
View file @
1b5553ec
...
...
@@ -54,7 +54,7 @@
<script type="application/ecmascript">
#{
val rawreport = Map("kraken" -> summary.getValue(sampleId, libId, "gears", "stats", "krakenreport"))
val rawreport = Map("kraken" -> summary.getValue(sampleId, libId, "gears
kraken
", "stats", "krakenreport"))
val jsonReport = ConfigUtils.mapToJson(rawreport)
}#
...
...
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
0 → 100644
View file @
1b5553ec
package
nl.lumc.sasc.biopet.pipelines.gears
import
nl.lumc.sasc.biopet.core.report.
{
ReportSection
,
ReportPage
,
MultisampleReportBuilder
,
ReportBuilderExtension
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
/**
* Created by pjvan_thof on 12/10/15.
*/
class
GearsReport
(
val
root
:
Configurable
)
extends
ReportBuilderExtension
{
def
builder
=
GearsReport
}
object
GearsReport
extends
MultisampleReportBuilder
{
def
reportName
=
"Gears Report"
override
def
extFiles
=
super
.
extFiles
++
List
(
"js/gears.js"
)
.
map
(
x
=>
ExtFile
(
"/nl/lumc/sasc/biopet/pipelines/gears/report/ext/"
+
x
,
x
))
def
indexPage
=
{
ReportPage
(
List
(
"Samples"
->
generateSamplesPage
(
pageArgs
))
++
Map
(
"Versions"
->
ReportPage
(
List
(),
List
(
"Executables"
->
ReportSection
(
"/nl/lumc/sasc/biopet/core/report/executables.ssp"
)
),
Map
())
),
List
(
"Report"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/gearsFront.ssp"
))
++
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
)
}
/** Single sample page */
def
samplePage
(
sampleId
:
String
,
args
:
Map
[
String
,
Any
])
:
ReportPage
=
{
ReportPage
(
List
(
"Libraries"
->
generateLibraryPage
(
args
)
),
List
(
"QC reads"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"
),
"QC bases"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp"
)
),
args
)
}
/** Library page */
def
libraryPage
(
sampleId
:
String
,
libId
:
String
,
args
:
Map
[
String
,
Any
])
:
ReportPage
=
{
val
krakenExecuted
=
summary
.
getValue
(
Some
(
sampleId
),
Some
(
libId
),
"gearskraken"
,
"stats"
,
"krakenreport"
).
isDefined
ReportPage
(
(
if
(
krakenExecuted
)
List
(
"Gears - Metagenomics"
->
ReportPage
(
List
(),
List
(
"Sunburst analysis"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/gearsSunburst.ssp"
)),
Map
()))
else
Nil
),
List
(
"QC reads"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"
),
"QC bases"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp"
)
),
args
)
}
}
\ No newline at end of file
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleReport.scala
View file @
1b5553ec
...
...
@@ -38,7 +38,7 @@ object GearsSingleReport extends ReportBuilder {
))),
Map
())
),
List
(
"Gears intro"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/gearsFront.ssp"
),
"Gears intro"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/gears
Single
Front.ssp"
),
"Sunburst analysis"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/gearsSunburst.ssp"
)
),
pageArgs
...
...
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