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biopet.biopet
Commits
b2156b2c
Commit
b2156b2c
authored
Jan 25, 2016
by
Peter van 't Hof
Browse files
Fixed bug in report
parent
88c9300a
Changes
1
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public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
View file @
b2156b2c
...
...
@@ -85,10 +85,11 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
/** Library page */
def
libraryPage
(
sampleId
:
String
,
libId
:
String
,
args
:
Map
[
String
,
Any
])
:
ReportPage
=
{
ReportPage
(
List
(
"Alignment"
->
BammetricsReport
.
bamMetricsPage
(
summary
,
Some
(
sampleId
),
Some
(
libId
)),
"QC"
->
FlexiprepReport
.
flexiprepPage
),
List
(
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
),
List
(
"Alignment"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"
),
"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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