Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Mirrors
biopet.biopet
Commits
607e9a1f
Commit
607e9a1f
authored
Nov 05, 2016
by
Peter van 't Hof
Browse files
Fix BIOPET-410
parent
204c72d0
Changes
1
Hide whitespace changes
Inline
Side-by-side
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleReport.scala
View file @
607e9a1f
...
...
@@ -23,23 +23,22 @@ class GearsSingleReport(val root: Configurable) extends ReportBuilderExtension {
object
GearsSingleReport
extends
ReportBuilder
{
// TODO: Add dustbin analysis (aggregated)
// TODO: Add alignment stats per sample for the dustbin analysis
override
def
extFiles
=
super
.
extFiles
++
List
(
"js/gears.js"
,
"js/krona-2.0.js"
,
"img/krona/loading.gif"
,
"img/krona/hidden.png"
,
"img/krona/favicon.ico"
)
.
map
(
x
=>
ExtFile
(
"/nl/lumc/sasc/biopet/pipelines/gears/report/ext/"
+
x
,
x
))
def
indexPage
=
{
val
krakenExecuted
=
summary
.
getValue
(
sampleId
,
libId
,
"gearskraken"
,
"stats"
,
"krakenreport"
).
isDefined
val
centrifugeExecuted
=
summary
.
getValue
(
sampleId
,
libId
,
"gearscentrifuge"
,
"stats"
,
"centrifuge_report"
).
isDefined
ReportPage
(
List
(
"Versions"
->
ReportPage
(
List
(),
List
((
"Executables"
->
ReportSection
(
"/nl/lumc/sasc/biopet/core/report/executables.ssp"
))),
Map
())
),
List
(
"Gears intro"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/gearsSingleFront.ssp"
),
"Kraken analysis"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
)
"Versions"
->
ReportPage
(
List
(),
List
((
"Executables"
->
ReportSection
(
"/nl/lumc/sasc/biopet/core/report/executables.ssp"
))),
Map
())
),
List
(
"Gears intro"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/gearsSingleFront.ssp"
))
++
(
if
(
krakenExecuted
)
List
(
"Kraken analysis"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
))
else
Nil
)
++
(
if
(
centrifugeExecuted
)
List
(
"Centrifuge analysis"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
,
Map
(
"summaryStatsTag"
->
"centrifuge_report"
)))
else
Nil
),
pageArgs
)
}
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new 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