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biopet.biopet
Commits
7f48f593
Commit
7f48f593
authored
Dec 10, 2015
by
Peter van 't Hof
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Fixed code warnings
parent
1b5553ec
Changes
1
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1 changed file
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4 additions
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2 deletions
+4
-2
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
...ala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
+4
-2
No files found.
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
View file @
7f48f593
...
...
@@ -4,6 +4,8 @@ import nl.lumc.sasc.biopet.core.report.{ ReportSection, ReportPage, MultisampleR
import
nl.lumc.sasc.biopet.utils.config.Configurable
/**
* Report for Gears
*
* Created by pjvan_thof on 12/10/15.
*/
class
GearsReport
(
val
root
:
Configurable
)
extends
ReportBuilderExtension
{
...
...
@@ -51,10 +53,10 @@ object GearsReport extends MultisampleReportBuilder {
val
krakenExecuted
=
summary
.
getValue
(
Some
(
sampleId
),
Some
(
libId
),
"gearskraken"
,
"stats"
,
"krakenreport"
).
isDefined
ReportPage
(
(
if
(
krakenExecuted
)
List
(
"Gears - Metagenomics"
->
ReportPage
(
List
(),
List
(
if
(
krakenExecuted
)
List
(
"Gears - Metagenomics"
->
ReportPage
(
List
(),
List
(
"Sunburst analysis"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/gearsSunburst.ssp"
)),
Map
()))
else
Nil
)
,
List
(
else
Nil
,
List
(
"QC reads"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"
),
"QC bases"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp"
)
),
args
)
...
...
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