Skip to content
GitLab
Projects
Groups
Snippets
Help
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
B
biopet.biopet
Project overview
Project overview
Details
Activity
Releases
Repository
Repository
Files
Commits
Branches
Tags
Contributors
Graph
Compare
CI / CD
CI / CD
Pipelines
Jobs
Schedules
Operations
Operations
Environments
Analytics
Analytics
CI / CD
Repository
Value Stream
Members
Members
Collapse sidebar
Close sidebar
Activity
Graph
Jobs
Commits
Open sidebar
Mirrors
biopet.biopet
Commits
89bc7d9a
Commit
89bc7d9a
authored
Nov 02, 2015
by
Peter van 't Hof
Browse files
Options
Browse Files
Download
Email Patches
Plain Diff
Added sunburst plot to mapping and shiva
parent
9ac622a9
Changes
4
Hide whitespace changes
Inline
Side-by-side
Showing
4 changed files
with
22 additions
and
7 deletions
+22
-7
public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsSunburst.ssp
...ces/nl/lumc/sasc/biopet/pipelines/gears/gearsSunburst.ssp
+2
-2
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
...ala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
+0
-2
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingReport.scala
...nl/lumc/sasc/biopet/pipelines/mapping/MappingReport.scala
+11
-2
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
...ala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
+9
-1
No files found.
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"
)
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment