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biopet.biopet
Commits
a4292fbc
Commit
a4292fbc
authored
Nov 25, 2016
by
Peter van 't Hof
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parent
90b5c62d
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3 additions
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3 deletions
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-3
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
...c/biopet/pipelines/mapping/MultisampleMappingReport.scala
+3
-3
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mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
View file @
a4292fbc
...
...
@@ -46,7 +46,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
def
indexPage
=
{
val
krakenExecuted
=
summary
.
getSampleValues
(
"gearskraken"
,
"stats"
,
"krakenreport"
).
values
.
forall
(
_
.
isDefined
)
val
centrifugeExecuted
=
summary
.
getSampleValues
(
"gears
kraken
"
,
"stats"
,
"centrifuge_report"
).
values
.
forall
(
_
.
isDefined
)
val
centrifugeExecuted
=
summary
.
getSampleValues
(
"gears
centrifuge
"
,
"stats"
,
"centrifuge_report"
).
values
.
forall
(
_
.
isDefined
)
val
wgsExecuted
=
summary
.
getSampleValues
(
"bammetrics"
,
"stats"
,
"wgs"
).
values
.
exists
(
_
.
isDefined
)
val
rnaExecuted
=
summary
.
getSampleValues
(
"bammetrics"
,
"stats"
,
"rna"
).
values
.
exists
(
_
.
isDefined
)
val
insertsizeExecuted
=
summary
.
getSampleValues
(
"bammetrics"
,
"stats"
,
"CollectInsertSizeMetrics"
,
"metrics"
).
values
.
exists
(
_
!=
Some
(
None
))
...
...
@@ -116,7 +116,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
/** Single sample page */
def
samplePage
(
sampleId
:
String
,
args
:
Map
[
String
,
Any
])
:
ReportPage
=
{
val
krakenExecuted
=
summary
.
getValue
(
Some
(
sampleId
),
None
,
"gearskraken"
,
"stats"
,
"krakenreport"
).
isDefined
val
centrifugeExecuted
=
summary
.
getValue
(
Some
(
sampleId
),
None
,
"gears
kraken
"
,
"stats"
,
"centrifuge_report"
).
isDefined
val
centrifugeExecuted
=
summary
.
getValue
(
Some
(
sampleId
),
None
,
"gears
centrifuge
"
,
"stats"
,
"centrifuge_report"
).
isDefined
val
flexiprepExecuted
=
summary
.
getLibraryValues
(
"flexiprep"
)
.
exists
{
case
((
sample
,
lib
),
value
)
=>
sample
==
sampleId
&&
value
.
isDefined
}
...
...
@@ -147,7 +147,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
/** Library page */
def
libraryPage
(
sampleId
:
String
,
libId
:
String
,
args
:
Map
[
String
,
Any
])
:
ReportPage
=
{
val
krakenExecuted
=
summary
.
getValue
(
Some
(
sampleId
),
Some
(
libId
),
"gearskraken"
,
"stats"
,
"krakenreport"
).
isDefined
val
centrifugeExecuted
=
summary
.
getValue
(
Some
(
sampleId
),
Some
(
libId
),
"gears
kraken
"
,
"stats"
,
"centrifuge_report"
).
isDefined
val
centrifugeExecuted
=
summary
.
getValue
(
Some
(
sampleId
),
Some
(
libId
),
"gears
centrifuge
"
,
"stats"
,
"centrifuge_report"
).
isDefined
val
flexiprepExecuted
=
summary
.
getValue
(
Some
(
sampleId
),
Some
(
libId
),
"flexiprep"
).
isDefined
ReportPage
(
...
...
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