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
21e0eede
Commit
21e0eede
authored
Aug 01, 2017
by
Ruben Vorderman
Browse files
Options
Browse Files
Download
Email Patches
Plain Diff
Defutured multi and single page
parent
6c753678
Changes
1
Hide whitespace changes
Inline
Side-by-side
Showing
1 changed file
with
151 additions
and
134 deletions
+151
-134
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
...c/biopet/pipelines/mapping/MultisampleMappingReport.scala
+151
-134
No files found.
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
View file @
21e0eede
...
...
@@ -14,14 +14,9 @@
*/
package
nl.lumc.sasc.biopet.pipelines.mapping
import
nl.lumc.sasc.biopet.core.report.
{
MultisampleReportBuilder
,
ReportBuilderExtension
,
ReportPage
,
ReportSection
}
import
nl.lumc.sasc.biopet.core.report.
{
MultisampleReportBuilder
,
ReportBuilderExtension
,
ReportPage
,
ReportSection
}
import
nl.lumc.sasc.biopet.pipelines.bammetrics.
{
BammetricsReport
,
BammetricsReportPage
}
import
nl.lumc.sasc.biopet.pipelines.flexiprep.
FlexiprepReport
import
nl.lumc.sasc.biopet.pipelines.flexiprep.
{
FlexiprepReadSummary
,
FlexiprepBaseSummary
,
FlexiprepReport
}
import
nl.lumc.sasc.biopet.pipelines.gears.GearsKronaPlot
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._
...
...
@@ -142,6 +137,16 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
sampleLevel
=
true
,
showPlot
=
true
,
showTable
=
false
)
val
clippingReportValues
=
BammetricsReportPage
.
clippingValues
(
summary
,
runId
,
samples
,
libraries
,
sampleId
,
libId
,
sampleLevel
=
true
,
showPlot
=
true
,
showTable
=
false
)
val
insertSizeReportValues
=
BammetricsReportPage
.
insertSizeValues
(
summary
,
runId
,
samples
,
libraries
,
sampleId
,
libId
,
sampleLevel
=
true
,
showPlot
=
true
,
showTable
=
false
)
val
wgsHistogramReportValues
=
BammetricsReportPage
.
wgsHistogramValues
(
summary
,
runId
,
samples
,
libraries
,
sampleId
,
libId
,
sampleLevel
=
true
,
showPlot
=
true
,
showTable
=
false
)
val
rnaHistogramReportValues
=
BammetricsReportPage
.
rnaHistogramValues
(
summary
,
runId
,
samples
,
libraries
,
sampleId
,
libId
,
sampleLevel
=
true
,
showPlot
=
true
,
showTable
=
false
)
val
flexiprepReadSummary
=
FlexiprepReadSummary
.
values
(
summary
,
runId
,
samples
,
libraries
,
sampleId
,
libId
,
showPlot
=
true
,
showTable
=
false
)
val
flexiprepBaseSummary
=
FlexiprepBaseSummary
.
values
(
summary
,
runId
,
samples
,
libraries
,
sampleId
,
libId
,
showPlot
=
true
,
showTable
=
false
)
Future
{
ReportPage
(
List
(
"Samples"
->
generateSamplesPage
(
pageArgs
))
++
...
...
@@ -189,36 +194,34 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
"/nl/lumc/sasc/biopet/pipelines/bammetrics/mappingQuality.ssp"
,
mappingQualityReportValues
),
"Clipping"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/clipping.ssp"
,
Map
(
"sampleLevel"
->
true
,
"showPlot"
->
true
,
"showTable"
->
false
))
clippingReportValues
)
)
++
(
if
(
pairedFound
&&
insertsizeExecuted
)
List
(
"Insert Size"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp"
,
Map
(
"sampleLevel"
->
true
,
"showPlot"
->
true
,
"showTable"
->
false
)
))
insertSizeReportValues
))
else
Nil
)
++
(
if
(
wgsExecuted
)
List
(
"Whole genome coverage"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp"
,
Map
(
"sampleLevel"
->
true
,
"showPlot"
->
true
,
"showTable"
->
false
)
))
wgsHistogramReportValues
))
else
Nil
)
++
(
if
(
rnaExecuted
)
List
(
"Rna coverage"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp"
,
Map
(
"sampleLevel"
->
true
,
"showPlot"
->
true
,
"showTable"
->
false
)
))
rnaHistogramReportValues
))
else
Nil
)
++
(
if
(
flexiprepExecuted
)
List
(
"QC reads"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"
,
Map
(
"showPlot"
->
true
,
"showTable"
->
false
)
),
flexiprepReadSummary
),
"QC bases"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp"
,
Map
(
"showPlot"
->
true
,
"showTable"
->
false
)
)
flexiprepBaseSummary
)
)
else
Nil
),
pageArgs
++
Map
(
"pipeline"
->
pipelineName
)
...
...
@@ -227,131 +230,145 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
}
/** Single sample page */
def
samplePage
(
sampleId
:
Int
,
args
:
Map
[
String
,
Any
])
:
Future
[
ReportPage
]
=
Future
{
def
samplePage
(
sampleId
:
Int
,
args
:
Map
[
String
,
Any
])
:
Future
[
ReportPage
]
=
{
val
krakenExecuted
=
Await
.
result
(
summary
.
getStatsSize
(
runId
,
"gearskraken"
,
"krakenreport"
,
library
=
NoLibrary
,
sample
=
sampleId
),
Duration
.
Inf
)
>=
1
"gearskraken"
,
"krakenreport"
,
library
=
NoLibrary
,
sample
=
sampleId
),
Duration
.
Inf
)
>=
1
val
centrifugeExecuted
=
Await
.
result
(
summary
.
getStatsSize
(
runId
,
"gearscentrifuge"
,
"centrifuge_report"
,
library
=
NoLibrary
,
sample
=
sampleId
,
mustHaveSample
=
true
),
Duration
.
Inf
)
>=
1
"gearscentrifuge"
,
"centrifuge_report"
,
library
=
NoLibrary
,
sample
=
sampleId
,
mustHaveSample
=
true
),
Duration
.
Inf
)
>=
1
val
flexiprepExecuted
=
Await
.
result
(
summary
.
getStatsSize
(
runId
,
"flexiprep"
,
sample
=
sampleId
,
mustHaveLibrary
=
true
),
Duration
.
Inf
)
>=
1
ReportPage
(
List
(
"Libraries"
->
generateLibraryPage
(
args
),
"Alignment"
->
BammetricsReport
.
bamMetricsPage
(
summary
,
Some
(
sampleId
),
None
))
++
(
if
(
centrifugeExecuted
)
List
(
"Centrifuge analysis"
->
Future
.
successful
(
ReportPage
(
List
(
"Non-unique"
->
Future
.
successful
(
ReportPage
(
List
(),
List
(
"All mappings"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
,
Map
(
"summaryStatsTag"
->
"centrifuge_report"
,
"centrifugeTag"
->
Some
(
"centrifuge"
)))),
Map
()
))),
List
(
"Unique mappings"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
,
Map
(
"summaryStatsTag"
->
"centrifuge_unique_report"
))),
Map
(
"summaryModuleTag"
->
"gearscentrifuge"
)
)))
else
Nil
)
:::
(
if
(
krakenExecuted
)
List
(
"Dustbin analysis"
->
Future
.
successful
(
ReportPage
(
List
(),
List
(
"Krona Plot"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
)),
Map
())))
else
Nil
),
List
(
"Alignment"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"
,
Map
(
"showPlot"
->
true
)),
"Preprocessing"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"
,
Map
(
"sampleLevel"
->
true
))
)
++
(
if
(
flexiprepExecuted
)
List
(
"QC reads"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"
),
"QC bases"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp"
)
)
else
Nil
),
args
)
}
val
centrifugeAllMappingsReportValues
=
GearsKronaPlot
.
values
(
summary
,
runId
,
"gearscentrifuge"
,
"centrifuge_report"
,
samples
,
libraries
,
sampleId
,
libId
,
Some
(
"centrifuge"
))
val
centrifugeUniqueMappingsReportValues
=
GearsKronaPlot
.
values
(
summary
,
runId
,
"gearscentrifuge"
,
"centrifuge_unique_report"
,
samples
,
libraries
,
sampleId
,
libId
)
val
dustbinAnalysisReportValues
=
GearsKronaPlot
.
values
(
summary
,
runId
,
"gearskraken"
,
"krakenreport"
,
samples
,
libraries
,
sampleId
,
libId
)
val
alignmentSummaryReportValues
=
BammetricsReportPage
.
alignmentSummaryValues
(
summary
,
runId
,
samples
,
libraries
,
sampleId
,
libId
,
showPlot
=
true
)
val
preprocessingReportValues
=
BammetricsReportPage
.
alignmentSummaryValues
(
summary
,
runId
,
samples
,
libraries
,
sampleId
,
libId
,
sampleLevel
=
true
)
val
flexiprepReadSummary
=
FlexiprepReadSummary
.
values
(
summary
,
runId
,
samples
,
libraries
,
sampleId
,
libId
)
val
flexiprepBaseSummary
=
FlexiprepBaseSummary
.
values
(
summary
,
runId
,
samples
,
libraries
,
sampleId
,
libId
)
/** Library page */
def
libraryPage
(
sampleId
:
Int
,
libId
:
Int
,
args
:
Map
[
String
,
Any
])
:
Future
[
ReportPage
]
=
Future
{
val
krakenExecuted
=
Await
.
result
(
summary
.
getStatsSize
(
runId
,
"gearskraken"
,
"krakenreport"
,
library
=
libId
,
sample
=
sampleId
),
Duration
.
Inf
)
>=
1
val
centrifugeExecuted
=
Await
.
result
(
summary
.
getStatsSize
(
runId
,
"gearscentrifuge"
,
"centrifuge_report"
,
library
=
libId
,
sample
=
sampleId
,
mustHaveSample
=
true
),
Duration
.
Inf
)
>=
1
val
flexiprepExecuted
=
Await
.
result
(
summary
.
getStatsSize
(
runId
,
"flexiprep"
,
library
=
libId
,
sample
=
sampleId
,
mustHaveLibrary
=
true
),
Duration
.
Inf
)
>=
1
Future
{
ReportPage
(
List
(
"Libraries"
->
generateLibraryPage
(
args
),
"Alignment"
->
BammetricsReport
.
bamMetricsPage
(
summary
,
Some
(
sampleId
),
None
))
++
(
if
(
centrifugeExecuted
)
List
(
"Centrifuge analysis"
->
Future
.
successful
(
ReportPage
(
List
(
"Non-unique"
->
Future
.
successful
(
ReportPage
(
List
(),
List
(
"All mappings"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
,
centrifugeAllMappingsReportValues
)),
Map
()
))),
List
(
"Unique mappings"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
,
centrifugeUniqueMappingsReportValues
)),
Map
(
"summaryPipelineName"
->
"gearscentrifuge"
)
)))
else
Nil
)
:::
(
if
(
krakenExecuted
)
List
(
"Dustbin analysis"
->
Future
.
successful
(
ReportPage
(
List
(),
List
(
"Krona Plot"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
,
dustbinAnalysisReportValues
)),
Map
())))
else
Nil
),
List
(
"Alignment"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"
,
alignmentSummaryReportValues
),
"Preprocessing"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"
,
preprocessingReportValues
)
)
++
(
if
(
flexiprepExecuted
)
List
(
"QC reads"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"
,
flexiprepReadSummary
),
"QC bases"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp"
,
flexiprepBaseSummary
)
)
else
Nil
),
args
)
}
/** Library page */
def
libraryPage
(
sampleId
:
Int
,
libId
:
Int
,
args
:
Map
[
String
,
Any
])
:
Future
[
ReportPage
]
=
Future
{
val
krakenExecuted
=
Await
.
result
(
summary
.
getStatsSize
(
runId
,
"gearskraken"
,
"krakenreport"
,
library
=
libId
,
sample
=
sampleId
),
Duration
.
Inf
)
>=
1
val
centrifugeExecuted
=
Await
.
result
(
summary
.
getStatsSize
(
runId
,
"gearscentrifuge"
,
"centrifuge_report"
,
library
=
libId
,
sample
=
sampleId
,
mustHaveSample
=
true
),
Duration
.
Inf
)
>=
1
val
flexiprepExecuted
=
Await
.
result
(
summary
.
getStatsSize
(
runId
,
"flexiprep"
,
library
=
libId
,
sample
=
sampleId
,
mustHaveLibrary
=
true
),
Duration
.
Inf
)
>=
1
ReportPage
(
(
"Alignment"
->
BammetricsReport
.
bamMetricsPage
(
summary
,
Some
(
sampleId
),
Some
(
libId
)))
::
(
if
(
flexiprepExecuted
)
List
(
"QC"
->
FlexiprepReport
.
flexiprepPage
(
summary
,
sampleId
,
libId
))
else
Nil
)
:::
(
if
(
centrifugeExecuted
)
List
(
"Centrifuge analysis"
->
Future
.
successful
(
ReportPage
(
List
(
"Non-unique"
->
Future
.
successful
(
ReportPage
(
List
(),
List
(
"All mappings"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
,
Map
(
"summaryStatsTag"
->
"centrifuge_report"
))),
Map
()))),
List
(
"Unique mappings"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
,
Map
(
"summaryStatsTag"
->
"centrifuge_unique_report"
))),
Map
(
"summaryModuleTag"
->
"gearscentrifuge"
,
"centrifugeTag"
->
Some
(
"centrifuge"
))
)))
else
Nil
)
:::
(
if
(
krakenExecuted
)
List
(
"Dustbin analysis"
->
Future
.
successful
(
ReportPage
(
List
(),
List
(
"Krona Plot"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
)),
Map
())))
else
Nil
),
"Alignment"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"
)
::
(
if
(
flexiprepExecuted
)
List
(
"QC reads"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"
),
"QC bases"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp"
)
)
else
Nil
),
args
)
ReportPage
(
(
"Alignment"
->
BammetricsReport
.
bamMetricsPage
(
summary
,
Some
(
sampleId
),
Some
(
libId
)))
::
(
if
(
flexiprepExecuted
)
List
(
"QC"
->
FlexiprepReport
.
flexiprepPage
(
summary
,
sampleId
,
libId
))
else
Nil
)
:::
(
if
(
centrifugeExecuted
)
List
(
"Centrifuge analysis"
->
Future
.
successful
(
ReportPage
(
List
(
"Non-unique"
->
Future
.
successful
(
ReportPage
(
List
(),
List
(
"All mappings"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
,
Map
(
"summaryStatsTag"
->
"centrifuge_report"
))),
Map
()))),
List
(
"Unique mappings"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
,
Map
(
"summaryStatsTag"
->
"centrifuge_unique_report"
))),
Map
(
"summaryModuleTag"
->
"gearscentrifuge"
,
"centrifugeTag"
->
Some
(
"centrifuge"
))
)))
else
Nil
)
:::
(
if
(
krakenExecuted
)
List
(
"Dustbin analysis"
->
Future
.
successful
(
ReportPage
(
List
(),
List
(
"Krona Plot"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
)),
Map
())))
else
Nil
),
"Alignment"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"
)
::
(
if
(
flexiprepExecuted
)
List
(
"QC reads"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"
),
"QC bases"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp"
)
)
else
Nil
),
args
)
}
}
}
}
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