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biopet.biopet
Commits
bb2dac47
Commit
bb2dac47
authored
Feb 04, 2016
by
Wai Yi Leung
Browse files
TinyCap report base
parent
574ccefb
Changes
4
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public/TinyCap/src/main/resources/nl/lumc/sasc/biopet/pipleines/tinycap/tinycapFront.ssp
0 → 100644
View file @
bb2dac47
#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
<%@ var summary: Summary %>
<%@ var rootPath: String %>
<%@ var pipeline: String %>
<table class="table">
<tbody>
<tr><th>Pipeline</th><td>${pipeline}</td></tr>
<tr><th>Version</th><td>${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>
<tr><th>Reference</th><td>${summary.getValue(pipeline, "settings", "reference", "species")} - ${summary.getValue(pipeline, "settings", "reference", "name")}</td></tr>
<tr><th>Number of samples</th><td>${summary.samples.size}</td></tr>
</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>${pipeline}</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/TinyCap/src/main/scala/nl/lumc/sasc/biopet/pipelines/tinycap/TinyCap.scala
View file @
bb2dac47
package
nl.lumc.sasc.biopet.pipelines.tinycap
import
nl.lumc.sasc.biopet.core.
{
PipelineCommand
,
Reference
}
import
nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
import
nl.lumc.sasc.biopet.core.
{
PipelineCommand
,
Reference
}
import
nl.lumc.sasc.biopet.extensions.HtseqCount
import
nl.lumc.sasc.biopet.pipelines.mapping.MultisampleMappingTrait
import
nl.lumc.sasc.biopet.utils.config.Configurable
...
...
@@ -85,6 +86,13 @@ class TinyCap(val root: Configurable) extends QScript with MultisampleMappingTra
"annotationGff"
->
annotationGff
)
override
def
reportClass
:
Option
[
ReportBuilderExtension
]
=
{
val
report
=
new
TinyCapReport
(
this
)
report
.
outputDir
=
new
File
(
outputDir
,
"report"
)
report
.
summaryFile
=
summaryFile
Some
(
report
)
}
override
def
addMultiSampleJobs
=
{
super
.
addMultiSampleJobs
}
...
...
public/TinyCap/src/main/scala/nl/lumc/sasc/biopet/pipelines/tinycap/TinyCapReport.scala
0 → 100644
View file @
bb2dac47
package
nl.lumc.sasc.biopet.pipelines.tinycap
import
nl.lumc.sasc.biopet.core.report.
{
ReportPage
,
ReportSection
,
ReportBuilderExtension
}
import
nl.lumc.sasc.biopet.pipelines.mapping.MultisampleMappingReportTrait
import
nl.lumc.sasc.biopet.utils.config.Configurable
/**
* Created by wyleung on 4-2-16.
*/
class
TinyCapReport
(
val
root
:
Configurable
)
extends
ReportBuilderExtension
{
def
builder
=
TinyCapReport
}
object
TinyCapReport
extends
MultisampleMappingReportTrait
{
/** Name of the report */
def
reportName
=
"TinyCap Report"
/** Front section for the report */
override
def
frontSection
:
ReportSection
=
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/tinycap/tinycapFront.ssp"
)
override
def
pipelineName
=
"tinycap"
/** Root page for the carp report */
override
def
indexPage
=
{
val
wgsExecuted
=
summary
.
getSampleValues
(
"bammetrics"
,
"stats"
,
"wgs"
).
values
.
exists
(
_
.
isDefined
)
val
rnaExecuted
=
summary
.
getSampleValues
(
"bammetrics"
,
"stats"
,
"rna"
).
values
.
exists
(
_
.
isDefined
)
ReportPage
(
List
(
"Samples"
->
generateSamplesPage
(
pageArgs
))
++
Map
(
"Reference"
->
ReportPage
(
List
(),
List
(
"Reference"
->
ReportSection
(
"/nl/lumc/sasc/biopet/core/report/reference.ssp"
,
Map
(
"pipeline"
->
pipelineName
))
),
Map
()),
"Files"
->
filesPage
,
"Versions"
->
ReportPage
(
List
(),
List
(
"Executables"
->
ReportSection
(
"/nl/lumc/sasc/biopet/core/report/executables.ssp"
)),
Map
())
),
List
(
"Report"
->
frontSection
,
"Alignment"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"
,
Map
(
"sampleLevel"
->
true
,
"showPlot"
->
true
,
"showTable"
->
false
)
))
++
(
if
(
wgsExecuted
)
List
(
"Whole genome coverage"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp"
,
Map
(
"sampleLevel"
->
true
,
"showPlot"
->
true
,
"showTable"
->
false
)))
else
Nil
)
++
(
if
(
rnaExecuted
)
List
(
"Rna coverage"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp"
,
Map
(
"sampleLevel"
->
true
,
"showPlot"
->
true
,
"showTable"
->
false
)))
else
Nil
)
++
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
++
Map
(
"pipeline"
->
pipelineName
)
)
}
}
public/mapping/src/main/resources/nl/lumc/sasc/biopet/pipelines/mapping/multisampleMappingFront.ssp
View file @
bb2dac47
...
...
@@ -6,7 +6,7 @@
<table class="table">
<tbody>
<tr><th>Pipeline</th><td>
Shiva
</td></tr>
<tr><th>Pipeline</th><td>
${pipeline}
</td></tr>
<tr><th>Version</th><td>${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>
...
...
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