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biopet.biopet
Commits
e2e3d2a5
Commit
e2e3d2a5
authored
Aug 01, 2017
by
rhpvorderman
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Defuture flexiprepPage method
parent
1a7a8908
Changes
3
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3 changed files
with
179 additions
and
169 deletions
+179
-169
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
...umc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
+13
-10
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
...ala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
+4
-1
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
...c/biopet/pipelines/mapping/MultisampleMappingReport.scala
+162
-158
No files found.
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
View file @
e2e3d2a5
...
...
@@ -51,15 +51,18 @@ object FlexiprepReport extends ReportBuilder {
override
def
pageArgs
=
Map
(
"multisample"
->
false
)
/** Index page for a flexiprep report */
def
indexPage
:
Future
[
ReportPage
]
=
this
.
flexiprepPage
(
summary
,
sampleId
.
get
,
libId
.
get
).
map
{
page
=>
ReportPage
(
Nil
,
List
(
"Report"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFront.ssp"
)
)
:::
page
.
sections
,
Map
())
}
def
indexPage
:
Future
[
ReportPage
]
=
{
val
flexiprepPageSummaries
=
this
.
flexiprepPageSummaries
(
summary
,
sampleId
.
get
,
libId
.
get
)
this
.
flexiprepPage
(
flexiprepPageSummaries
).
map
{
page
=>
ReportPage
(
Nil
,
List
(
"Report"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFront.ssp"
)
)
:::
page
.
sections
,
Map
())
}}
/** Generate a QC report page for 1 single library, sampleId and libId must be defined in the arguments */
def
flexiprepPageSummaries
(
summary
:
SummaryDb
,
sampleId
:
Int
,
libId
:
Int
)
:
Map
[
String
,
Map
[
String
,
Any
]]
=
{
...
...
@@ -81,7 +84,7 @@ object FlexiprepReport extends ReportBuilder {
"flexiprepBaseSummary"
->
flexiprepBaseSummary
)
}
/** Generate a QC report page for 1 single library, sampleId and libId must be defined in the arguments */
def
flexiprepPage
(
summaries
:
Map
[
String
,
Map
[
String
,
Any
]])
:
Future
[
ReportPage
]
=
{
val
flexiprepBaseSummary
=
summaries
(
"flexiprepBaseSummary"
)
val
flexiprepReadSummary
=
summaries
(
"flexiprepReadSummary"
)
...
...
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
View file @
e2e3d2a5
...
...
@@ -344,7 +344,10 @@ object GearsReport extends MultisampleReportBuilder {
Duration
.
Inf
)
val
flexiprepReportPage
=
if
(
flexiprepExecuted
)
Some
(
"QC"
->
FlexiprepReport
.
flexiprepPage
(
summary
,
sampleId
,
libId
))
if
(
flexiprepExecuted
)
{
val
flexiprepPageSummaries
=
FlexiprepReport
.
flexiprepPageSummaries
(
summary
,
sampleId
,
libId
)
Some
(
"QC"
->
FlexiprepReport
.
flexiprepPage
(
flexiprepPageSummaries
))
}
else
None
val
centrifugePageAllMappingsKronaPlot
=
GearsKronaPlot
.
values
(
summary
,
...
...
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
View file @
e2e3d2a5
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