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biopet.biopet
Commits
a10b5ec5
Commit
a10b5ec5
authored
Mar 04, 2016
by
Peter van 't Hof
Browse files
Added kraken plots to report
parent
3fb5cf10
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
View file @
a10b5ec5
...
...
@@ -28,6 +28,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
/** Root page for the carp report */
def
indexPage
=
{
val
krakenExecuted
=
summary
.
getSampleValues
(
"gearskraken"
,
"stats"
,
"krakenreport"
).
values
.
forall
(
_
.
isDefined
)
val
wgsExecuted
=
summary
.
getSampleValues
(
"bammetrics"
,
"stats"
,
"wgs"
).
values
.
exists
(
_
.
isDefined
)
val
rnaExecuted
=
summary
.
getSampleValues
(
"bammetrics"
,
"stats"
,
"rna"
).
values
.
exists
(
_
.
isDefined
)
val
insertsizeExecuted
=
summary
.
getSampleValues
(
"bammetrics"
,
"stats"
,
"CollectInsertSizeMetrics"
,
"metrics"
).
values
.
exists
(
_
!=
Some
(
None
))
...
...
@@ -36,7 +37,11 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
ReportPage
(
List
(
"Samples"
->
generateSamplesPage
(
pageArgs
))
++
Map
(
"Reference"
->
ReportPage
(
List
(),
List
(
(
if
(
krakenExecuted
)
List
(
"Dustbin analysis"
->
ReportPage
(
List
(),
List
(
"Krona plot"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
)),
Map
()))
else
Nil
)
++
List
(
"Reference"
->
ReportPage
(
List
(),
List
(
"Reference"
->
ReportSection
(
"/nl/lumc/sasc/biopet/core/report/reference.ssp"
,
Map
(
"pipeline"
->
pipelineName
))
),
Map
()),
"Files"
->
filesPage
,
...
...
@@ -84,13 +89,18 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
/** Single sample page */
def
samplePage
(
sampleId
:
String
,
args
:
Map
[
String
,
Any
])
:
ReportPage
=
{
val
krakenExecuted
=
summary
.
getValue
(
Some
(
sampleId
),
None
,
"gearskraken"
,
"stats"
,
"krakenreport"
).
isDefined
val
flexiprepExecuted
=
summary
.
getLibraryValues
(
"flexiprep"
)
.
exists
{
case
((
sample
,
lib
),
value
)
=>
sample
==
sampleId
&&
value
.
isDefined
}
ReportPage
(
List
(
"Libraries"
->
generateLibraryPage
(
args
),
"Alignment"
->
BammetricsReport
.
bamMetricsPage
(
summary
,
Some
(
sampleId
),
None
),
"Files"
->
filesPage
"Alignment"
->
BammetricsReport
.
bamMetricsPage
(
summary
,
Some
(
sampleId
),
None
))
++
(
if
(
krakenExecuted
)
List
(
"Kraken"
->
ReportPage
(
List
(),
List
(
"Kraken analysis"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
)),
Map
()))
else
Nil
)
++
List
(
"Files"
->
filesPage
),
List
(
"Alignment"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"
,
Map
(
"showPlot"
->
true
)),
...
...
@@ -103,11 +113,16 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
/** Library page */
def
libraryPage
(
sampleId
:
String
,
libId
:
String
,
args
:
Map
[
String
,
Any
])
:
ReportPage
=
{
val
krakenExecuted
=
summary
.
getValue
(
Some
(
sampleId
),
Some
(
libId
),
"gearskraken"
,
"stats"
,
"krakenreport"
).
isDefined
val
flexiprepExecuted
=
summary
.
getValue
(
Some
(
sampleId
),
Some
(
libId
),
"flexiprep"
).
isDefined
ReportPage
(
(
"Alignment"
->
BammetricsReport
.
bamMetricsPage
(
summary
,
Some
(
sampleId
),
Some
(
libId
)))
::
(
if
(
flexiprepExecuted
)
List
(
"QC"
->
FlexiprepReport
.
flexiprepPage
)
else
Nil
),
(
if
(
flexiprepExecuted
)
List
(
"QC"
->
FlexiprepReport
.
flexiprepPage
)
else
Nil
)
:::
(
if
(
krakenExecuted
)
List
(
"Kraken"
->
ReportPage
(
List
(),
List
(
"Kraken analysis"
->
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"
))
...
...
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