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biopet.biopet
Commits
89bc7d9a
Commit
89bc7d9a
authored
Nov 02, 2015
by
Peter van 't Hof
Browse files
Added sunburst plot to mapping and shiva
parent
9ac622a9
Changes
4
Hide whitespace changes
Inline
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public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsSunburst.ssp
View file @
89bc7d9a
...
...
@@ -57,10 +57,10 @@
#{
val rawreport = Map("kraken" -> summary.getValue(sampleId, libId, "gears", "stats", "krakenreport"))
val
bla
= ConfigUtils.mapToJson(rawreport)
val
jsonReport
= ConfigUtils.mapToJson(rawreport)
}#
var krakenresult = JSON.parse('<%= unescape(
bla
) %>');
var krakenresult = JSON.parse('<%= unescape(
jsonReport
) %>');
loadGears(krakenresult.kraken.classified);
</script>
...
...
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
View file @
89bc7d9a
...
...
@@ -9,8 +9,6 @@ class GearsReport(val root: Configurable) extends ReportBuilderExtension {
object
GearsReport
extends
ReportBuilder
{
// FIXME: Not yet finished
// TODO: Sample specific: Add summary (sunflare plot)
// TODO: Add dustbin analysis (aggregated)
// TODO: Add alignment stats per sample for the dustbin analysis
...
...
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingReport.scala
View file @
89bc7d9a
...
...
@@ -16,7 +16,7 @@
package
nl.lumc.sasc.biopet.pipelines.mapping
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.core.report.
{
ReportBuilderExtension
,
ReportSection
,
ReportPage
,
ReportBuilder
}
import
nl.lumc.sasc.biopet.core.report.
_
import
nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport
import
nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
...
...
@@ -33,6 +33,11 @@ object MappingReport extends ReportBuilder {
/** Name of report */
val
reportName
=
"Mapping Report"
override
def
extFiles
=
super
.
extFiles
++
List
(
"js/gears.js"
)
.
map
(
x
=>
ExtFile
(
"/nl/lumc/sasc/biopet/pipelines/gears/report/ext/"
+
x
,
x
))
def
krakenExecuted
=
summary
.
getValue
(
sampleId
,
libId
,
"gears"
,
"stats"
,
"krakenreport"
).
isDefined
/** Root page for single BamMetrcis report */
def
indexPage
=
{
val
skipFlexiprep
=
summary
.
getValue
(
sampleId
,
libId
,
"mapping"
,
"settings"
,
"skip_flexiprep"
).
getOrElse
(
false
)
==
true
...
...
@@ -48,7 +53,11 @@ object MappingReport extends ReportBuilder {
"After QC fastq files"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepOutputfiles.ssp"
)))
:::
List
(
"Bam files per lib"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp"
,
Map
(
"sampleLevel"
->
false
))
),
Map
())
),
List
(
)
:::
(
if
(
krakenExecuted
)
List
(
"Gears - Metagenomics"
->
ReportPage
(
List
(),
List
(
"Sunburst analysis"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/gearsSunburst.ssp"
)),
Map
()))
else
Nil
),
List
(
"Report"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/mapping/mappingFront.ssp"
)
)
:::
bamMetricsPage
.
map
(
_
.
sections
).
getOrElse
(
Nil
),
Map
()
...
...
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
View file @
89bc7d9a
...
...
@@ -36,6 +36,9 @@ class ShivaReport(val root: Configurable) extends ReportBuilderExtension {
/** Object for report generation for Shiva pipeline */
object
ShivaReport
extends
MultisampleReportBuilder
{
override
def
extFiles
=
super
.
extFiles
++
List
(
"js/gears.js"
)
.
map
(
x
=>
ExtFile
(
"/nl/lumc/sasc/biopet/pipelines/gears/report/ext/"
+
x
,
x
))
/** Root page for the shiva report */
def
indexPage
=
{
val
regions
=
regionsPage
...
...
@@ -136,10 +139,15 @@ object ShivaReport extends MultisampleReportBuilder {
/** Library page */
def
libraryPage
(
sampleId
:
String
,
libId
:
String
,
args
:
Map
[
String
,
Any
])
:
ReportPage
=
{
def
krakenExecuted
=
summary
.
getValue
(
Some
(
sampleId
),
Some
(
libId
),
"gears"
,
"stats"
,
"krakenreport"
).
isDefined
ReportPage
(
List
(
"Alignment"
->
BammetricsReport
.
bamMetricsPage
(
summary
,
Some
(
sampleId
),
Some
(
libId
)),
"QC"
->
FlexiprepReport
.
flexiprepPage
),
List
(
)
:::
(
if
(
krakenExecuted
)
List
(
"Gears - Metagenomics"
->
ReportPage
(
List
(),
List
(
"Sunburst analysis"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/gearsSunburst.ssp"
)),
Map
()))
else
Nil
),
List
(
"Alignment"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"
),
"QC reads"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"
),
"QC bases"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp"
)
...
...
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