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biopet.biopet
Commits
be30372c
Commit
be30372c
authored
Jun 06, 2015
by
Peter van 't Hof
Browse files
Added bam and vcf files to report of Shiva
parent
6b6ea1fe
Changes
6
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Inline
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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
()
}
}
...
...
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