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biopet.biopet
Commits
8215133a
Commit
8215133a
authored
Feb 12, 2016
by
Peter van 't Hof
Browse files
Simplyfy additional sections
parent
27775a71
Changes
2
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Inline
Side-by-side
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
View file @
8215133a
...
...
@@ -21,6 +21,8 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
/** Front section for the report */
def
frontSection
:
ReportSection
=
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/mapping/multisampleMappingFront.ssp"
)
def
additionalSections
:
List
[(
String
,
ReportSection
)]
=
Nil
def
pipelineName
=
"multisamplemapping"
/** Root page for the carp report */
...
...
@@ -42,8 +44,9 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
)),
Map
())
),
List
(
"Report"
->
frontSection
,
"Alignment"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"
,
"Report"
->
frontSection
)
++
additionalSections
++
List
(
"Alignment"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"
,
Map
(
"sampleLevel"
->
true
,
"showPlot"
->
true
,
"showTable"
->
false
)
))
++
(
if
(
insertsizeExecuted
)
List
(
"Insert Size"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp"
,
...
...
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
View file @
8215133a
...
...
@@ -47,16 +47,16 @@ object ShivaReport extends MultisampleMappingReportTrait {
override
def
extFiles
=
super
.
extFiles
++
List
(
"js/gears.js"
)
.
map
(
x
=>
ExtFile
(
"/nl/lumc/sasc/biopet/pipelines/gears/report/ext/"
+
x
,
x
))
override
def
additionalSections
=
super
.
additionalSections
++
(
if
(
variantcallingExecuted
)
List
(
"Variantcalling"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp"
,
Map
(
"showPlot"
->
true
,
"showTable"
->
false
)))
else
Nil
)
/** Root page for the shiva report */
override
def
indexPage
=
{
val
variantcallingSection
=
(
if
(
variantcallingExecuted
)
List
(
"Variantcalling"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp"
,
Map
(
"showPlot"
->
true
,
"showTable"
->
false
)))
else
Nil
)
val
regions
=
regionsPage
val
oldPage
=
super
.
indexPage
oldPage
.
copy
(
sections
=
oldPage
.
sections
.
head
::
variantcallingSection
:::
oldPage
.
sections
.
tail
,
subPages
=
oldPage
.
subPages
++
regionsPage
)
oldPage
.
copy
(
subPages
=
oldPage
.
subPages
++
regionsPage
)
}
/** Generate a page with all target coverage stats */
...
...
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