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biopet.biopet
Commits
bcbb2916
Commit
bcbb2916
authored
Apr 04, 2017
by
Peter van 't Hof
Browse files
Style fixes
parent
10248b22
Changes
3
Hide whitespace changes
Inline
Side-by-side
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
View file @
bcbb2916
...
...
@@ -17,10 +17,10 @@ package nl.lumc.sasc.biopet.core.report
import
java.io._
import
nl.lumc.sasc.biopet.core.ToolCommandFunction
import
nl.lumc.sasc.biopet.utils.summary.db.Schema.
{
Library
,
Module
,
Pipeline
,
Sample
}
import
nl.lumc.sasc.biopet.utils.summary.db.Schema.
{
Library
,
Module
,
Pipeline
,
Sample
}
import
nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
import
nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.
{
LibraryId
,
SampleId
}
import
nl.lumc.sasc.biopet.utils.
{
IoUtils
,
Logging
,
ToolCommand
}
import
nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.
{
LibraryId
,
SampleId
}
import
nl.lumc.sasc.biopet.utils.
{
IoUtils
,
Logging
,
ToolCommand
}
import
org.broadinstitute.gatk.utils.commandline.Input
import
org.fusesource.scalate.TemplateEngine
...
...
@@ -204,7 +204,7 @@ trait ReportBuilder extends ToolCommand {
)
}
val
rootPage
=
indexPage
.
map
{
x
=>
x
.
copy
(
subPages
=
x
.
subPages
:::
generalPages
(
sampleId
,
libId
))}
val
rootPage
=
indexPage
.
map
{
x
=>
x
.
copy
(
subPages
=
x
.
subPages
:::
generalPages
(
sampleId
,
libId
))
}
// total = ReportBuilder.countPages(rootPage)
logger
.
info
(
total
+
" pages to be generated"
)
...
...
@@ -276,7 +276,7 @@ trait ReportBuilder extends ToolCommand {
}
def
pipelineName
def
pipelineName
:
String
/** Files page, can be used general or at sample level */
def
filesPage
(
sampleId
:
Option
[
Int
]
=
None
,
libraryId
:
Option
[
Int
]
=
None
)
:
Future
[
ReportPage
]
=
{
...
...
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
View file @
bcbb2916
...
...
@@ -78,7 +78,7 @@ object GearsReport extends MultisampleReportBuilder {
ReportPage
(
List
(
centrifugePage
,
krakenPage
,
qiimeClosedPage
,
qiimeOpenPage
).
flatten
:::
List
(
"Samples"
->
generateSamplesPage
(
pageArgs
)
),
),
List
(
"Report"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/gearsFront.ssp"
))
++
List
(
...
...
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingReport.scala
View file @
bcbb2916
...
...
@@ -56,10 +56,10 @@ object MappingReport extends ReportBuilder {
}
else
None
ReportPage
((
if
(
skipFlexiprep
)
Nil
else
List
(
"QC"
->
FlexiprepReport
.
flexiprepPage
))
:::
bamMetricsPage
.
map
(
_
.
subPages
).
getOrElse
(
Nil
)
:::
(
if
(
krakenExecuted
)
List
(
"Gears - Metagenomics"
->
Future
(
ReportPage
(
List
(),
List
(
"Sunburst analysis"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/gearsSunburst.ssp"
)),
Map
())))
else
Nil
),
List
(
(
if
(
krakenExecuted
)
List
(
"Gears - Metagenomics"
->
Future
(
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
()
...
...
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