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biopet.biopet
Commits
a9eae104
Commit
a9eae104
authored
Apr 10, 2017
by
Peter van 't Hof
Browse files
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Switching to Future.successful
parent
dcb9fd03
Changes
4
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4 changed files
with
29 additions
and
28 deletions
+29
-28
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
...ala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
+17
-17
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleReport.scala
.../lumc/sasc/biopet/pipelines/gears/GearsSingleReport.scala
+1
-0
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingReport.scala
...nl/lumc/sasc/biopet/pipelines/mapping/MappingReport.scala
+1
-1
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
...c/biopet/pipelines/mapping/MultisampleMappingReport.scala
+10
-10
No files found.
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
View file @
a9eae104
...
...
@@ -51,8 +51,8 @@ object GearsReport extends MultisampleReportBuilder {
val
qiimeClosesOtuTable
=
summary
.
getFile
(
runId
,
"gears"
,
key
=
"qiime_closed_otu_table"
)
val
qiimeOpenOtuTable
=
summary
.
getFile
(
runId
,
"gears"
,
key
=
"qiime_open_otu_table"
)
val
centrifugePage
=
(
if
(
centrifugeExecuted
)
Some
(
"Centriguge analysis"
->
Future
(
ReportPage
(
List
(
"Non-unique"
->
Future
(
ReportPage
(
List
(),
List
(
"All mappings"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
,
val
centrifugePage
=
(
if
(
centrifugeExecuted
)
Some
(
"Centriguge analysis"
->
Future
.
successful
(
ReportPage
(
List
(
"Non-unique"
->
Future
.
successful
(
ReportPage
(
List
(),
List
(
"All mappings"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
,
Map
(
"summaryStatsTag"
->
"centrifuge_report"
)
)),
Map
()))),
List
(
"Unique mappings"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
,
...
...
@@ -60,17 +60,17 @@ object GearsReport extends MultisampleReportBuilder {
)),
Map
(
"summaryModuleTag"
->
"gearscentrifuge"
,
"centrifugeTag"
->
Some
(
"centrifuge"
)))))
else
None
)
val
krakenPage
=
(
if
(
krakenExecuted
)
Some
(
"Kraken analysis"
->
Future
(
ReportPage
(
List
(),
List
(
"Krona plot"
->
Future
(
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
val
krakenPage
=
(
if
(
krakenExecuted
)
Some
(
"Kraken analysis"
->
Future
.
successful
(
ReportPage
(
List
(),
List
(
"Krona plot"
->
Future
.
successful
(
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
))),
Map
())))
else
None
)
val
qiimeClosedPage
=
(
if
(
qiimeClosesOtuTable
.
isDefined
)
Some
(
"Qiime closed reference analysis"
->
Future
(
ReportPage
(
List
(),
List
(
"Krona plot"
->
Future
(
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp"
val
qiimeClosedPage
=
(
if
(
qiimeClosesOtuTable
.
isDefined
)
Some
(
"Qiime closed reference analysis"
->
Future
.
successful
(
ReportPage
(
List
(),
List
(
"Krona plot"
->
Future
.
successful
(
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp"
))),
Map
(
"biomFile"
->
new
File
(
run
.
outputDir
+
File
.
separator
+
qiimeClosesOtuTable
.
get
.
path
)))))
else
None
)
val
qiimeOpenPage
=
(
if
(
qiimeOpenOtuTable
.
isDefined
)
Some
(
"Qiime open reference analysis"
->
Future
(
ReportPage
(
List
(),
List
(
val
qiimeOpenPage
=
(
if
(
qiimeOpenOtuTable
.
isDefined
)
Some
(
"Qiime open reference analysis"
->
Future
.
successful
(
ReportPage
(
List
(),
List
(
"Krona plot"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp"
)),
Map
(
"biomFile"
->
new
File
(
run
.
outputDir
+
File
.
separator
+
qiimeOpenOtuTable
.
get
.
path
)))))
else
None
)
...
...
@@ -99,20 +99,20 @@ object GearsReport extends MultisampleReportBuilder {
val
qiimeClosesOtuTable
=
Await
.
result
(
summary
.
getFile
(
runId
,
"gearssingle"
,
NoModule
,
sampleId
,
NoLibrary
,
"qiime_closed_otu_table"
),
Duration
.
Inf
)
val
qiimeOpenOtuTable
=
Await
.
result
(
summary
.
getFile
(
runId
,
"gearssingle"
,
NoModule
,
sampleId
,
NoLibrary
,
"qiime_open_otu_table"
),
Duration
.
Inf
)
ReportPage
((
if
(
centrifugeExecuted
)
List
(
"Centriguge analysis"
->
Future
(
ReportPage
(
List
(
"Non-unique"
->
Future
(
ReportPage
(
List
(),
List
(
"All mappings"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
,
ReportPage
((
if
(
centrifugeExecuted
)
List
(
"Centriguge analysis"
->
Future
.
successful
(
ReportPage
(
List
(
"Non-unique"
->
Future
.
successful
(
ReportPage
(
List
(),
List
(
"All mappings"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
,
Map
(
"summaryStatsTag"
->
"centrifuge_report"
)
)),
Map
()))),
List
(
"Unique mappings"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
,
Map
(
"summaryStatsTag"
->
"centrifuge_unique_report"
)
)),
Map
(
"summaryModuleTag"
->
"gearscentrifuge"
,
"centrifugeTag"
->
Some
(
"centrifuge"
)))))
else
Nil
)
:::
(
if
(
krakenExecuted
)
List
(
"Kraken analysis"
->
Future
(
ReportPage
(
List
(),
List
(
else
Nil
)
:::
(
if
(
krakenExecuted
)
List
(
"Kraken analysis"
->
Future
.
successful
(
ReportPage
(
List
(),
List
(
"Krona plot"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
)),
Map
())))
else
Nil
)
:::
(
if
(
qiimeClosesOtuTable
.
isDefined
)
List
(
"Qiime closed reference analysis"
->
Future
(
ReportPage
(
List
(),
List
(
else
Nil
)
:::
(
if
(
qiimeClosesOtuTable
.
isDefined
)
List
(
"Qiime closed reference analysis"
->
Future
.
successful
(
ReportPage
(
List
(),
List
(
"Krona plot"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp"
)),
Map
(
"biomFile"
->
new
File
(
run
.
outputDir
+
File
.
separator
+
qiimeClosesOtuTable
.
get
.
path
)))))
else
Nil
)
:::
(
if
(
qiimeOpenOtuTable
.
isDefined
)
List
(
"Qiime open reference analysis"
->
Future
(
ReportPage
(
List
(),
List
(
else
Nil
)
:::
(
if
(
qiimeOpenOtuTable
.
isDefined
)
List
(
"Qiime open reference analysis"
->
Future
.
successful
(
ReportPage
(
List
(),
List
(
"Krona plot"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp"
)),
Map
(
"biomFile"
->
new
File
(
run
.
outputDir
+
File
.
separator
+
qiimeOpenOtuTable
.
get
.
path
)))))
else
Nil
)
:::
List
(
...
...
@@ -136,20 +136,20 @@ object GearsReport extends MultisampleReportBuilder {
ReportPage
(
(
if
(
flexiprepExecuted
)
List
(
"QC"
->
FlexiprepReport
.
flexiprepPage
)
else
Nil
)
:::
(
if
(
centrifugeExecuted
)
List
(
"Centriguge analysis"
->
Future
(
ReportPage
(
List
(
"Non-unique"
->
Future
(
ReportPage
(
List
(),
List
(
"All mappings"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
,
)
:::
(
if
(
centrifugeExecuted
)
List
(
"Centriguge analysis"
->
Future
.
successful
(
ReportPage
(
List
(
"Non-unique"
->
Future
.
successful
(
ReportPage
(
List
(),
List
(
"All mappings"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
,
Map
(
"summaryStatsTag"
->
"centrifuge_report"
)
)),
Map
()))),
List
(
"Unique mappings"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
,
Map
(
"summaryStatsTag"
->
"centrifuge_unique_report"
)
)),
Map
(
"summaryModuleTag"
->
"gearscentrifuge"
,
"centrifugeTag"
->
Some
(
"centrifuge"
)))))
else
Nil
)
:::
(
if
(
krakenExecuted
)
List
(
"Kraken analysis"
->
Future
(
ReportPage
(
List
(),
List
(
else
Nil
)
:::
(
if
(
krakenExecuted
)
List
(
"Kraken analysis"
->
Future
.
successful
(
ReportPage
(
List
(),
List
(
"Krona plot"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
)),
Map
())))
else
Nil
)
:::
(
if
(
qiimeClosesOtuTable
.
isDefined
)
List
(
"Qiime closed reference analysis"
->
Future
(
ReportPage
(
List
(),
List
(
else
Nil
)
:::
(
if
(
qiimeClosesOtuTable
.
isDefined
)
List
(
"Qiime closed reference analysis"
->
Future
.
successful
(
ReportPage
(
List
(),
List
(
"Krona plot"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp"
)),
Map
(
"biomFile"
->
new
File
(
qiimeClosesOtuTable
.
get
.
path
)))))
else
Nil
)
:::
(
if
(
qiimeOpenOtuTable
.
isDefined
)
List
(
"Qiime open reference analysis"
->
Future
(
ReportPage
(
List
(),
List
(
else
Nil
)
:::
(
if
(
qiimeOpenOtuTable
.
isDefined
)
List
(
"Qiime open reference analysis"
->
Future
.
successful
(
ReportPage
(
List
(),
List
(
"Krona plot"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp"
)),
Map
(
"biomFile"
->
new
File
(
qiimeOpenOtuTable
.
get
.
path
)))))
else
Nil
),
List
(
...
...
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleReport.scala
View file @
a9eae104
...
...
@@ -34,6 +34,7 @@ object GearsSingleReport extends ReportBuilder {
.
map
(
x
=>
ExtFile
(
"/nl/lumc/sasc/biopet/pipelines/gears/report/ext/"
+
x
,
x
))
def
indexPage
:
Future
[
ReportPage
]
=
Future
{
sampleId
.
map
val
sampleName
=
sampleId
.
flatMap
(
x
=>
Await
.
result
(
summary
.
getSampleName
(
x
),
Duration
.
Inf
))
val
libraryName
=
libId
.
flatMap
(
x
=>
Await
.
result
(
summary
.
getLibraryName
(
x
),
Duration
.
Inf
))
...
...
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingReport.scala
View file @
a9eae104
...
...
@@ -56,7 +56,7 @@ object MappingReport extends ReportBuilder {
}
else
None
ReportPage
((
if
(
skipFlexiprep
)
Nil
else
List
(
"QC"
->
FlexiprepReport
.
flexiprepPage
))
:::
bamMetricsPage
.
map
(
_
.
subPages
).
getOrElse
(
Nil
)
:::
(
if
(
krakenExecuted
)
List
(
"Gears - Metagenomics"
->
Future
(
ReportPage
(
List
(),
List
(
(
if
(
krakenExecuted
)
List
(
"Gears - Metagenomics"
->
Future
.
successful
(
ReportPage
(
List
(),
List
(
"Sunburst analysis"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/gearsSunburst.ssp"
)),
Map
())))
else
Nil
),
List
(
...
...
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
View file @
a9eae104
...
...
@@ -66,18 +66,18 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
ReportPage
(
List
(
"Samples"
->
generateSamplesPage
(
pageArgs
))
++
(
if
(
krakenExecuted
)
List
(
"Dustbin analysis - Kraken"
->
Future
(
ReportPage
(
List
(),
List
(
(
if
(
krakenExecuted
)
List
(
"Dustbin analysis - Kraken"
->
Future
.
successful
(
ReportPage
(
List
(),
List
(
"Krona plot"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
)),
Map
())))
else
Nil
)
++
(
if
(
centrifugeExecuted
)
List
(
"Centriguge analysis"
->
Future
(
ReportPage
(
List
(
"Non-unique"
->
Future
(
ReportPage
(
List
(),
List
(
"All mappings"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
,
else
Nil
)
++
(
if
(
centrifugeExecuted
)
List
(
"Centriguge analysis"
->
Future
.
successful
(
ReportPage
(
List
(
"Non-unique"
->
Future
.
successful
(
ReportPage
(
List
(),
List
(
"All mappings"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
,
Map
(
"summaryStatsTag"
->
"centrifuge_report"
)
)),
Map
()))),
List
(
"Unique mappings"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
,
Map
(
"summaryStatsTag"
->
"centrifuge_unique_report"
)
)),
Map
(
"summaryModuleTag"
->
"gearscentrifuge"
,
"centrifugeTag"
->
Some
(
"centrifuge"
)))))
else
Nil
)
++
List
(
"Reference"
->
Future
(
ReportPage
(
List
(),
List
(
List
(
"Reference"
->
Future
.
successful
(
ReportPage
(
List
(),
List
(
"Reference"
->
ReportSection
(
"/nl/lumc/sasc/biopet/core/report/reference.ssp"
,
Map
(
"pipeline"
->
pipelineName
))
),
Map
()))
),
...
...
@@ -122,14 +122,14 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
ReportPage
(
List
(
"Libraries"
->
generateLibraryPage
(
args
),
"Alignment"
->
BammetricsReport
.
bamMetricsPage
(
summary
,
Some
(
sampleId
),
None
))
++
(
if
(
centrifugeExecuted
)
List
(
"Centriguge analysis"
->
Future
(
ReportPage
(
List
(
"Non-unique"
->
Future
(
ReportPage
(
List
(),
List
(
"All mappings"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
,
(
if
(
centrifugeExecuted
)
List
(
"Centriguge analysis"
->
Future
.
successful
(
ReportPage
(
List
(
"Non-unique"
->
Future
.
successful
(
ReportPage
(
List
(),
List
(
"All mappings"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
,
Map
(
"summaryStatsTag"
->
"centrifuge_report"
,
"centrifugeTag"
->
Some
(
"centrifuge"
))
)),
Map
()))),
List
(
"Unique mappings"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
,
Map
(
"summaryStatsTag"
->
"centrifuge_unique_report"
)
)),
Map
(
"summaryModuleTag"
->
"gearscentrifuge"
))))
else
Nil
)
:::
(
if
(
krakenExecuted
)
List
(
"Dustbin analysis"
->
Future
(
ReportPage
(
List
(),
List
(
else
Nil
)
:::
(
if
(
krakenExecuted
)
List
(
"Dustbin analysis"
->
Future
.
successful
(
ReportPage
(
List
(),
List
(
"Krona Plot"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
)),
Map
())))
else
Nil
),
List
(
...
...
@@ -154,14 +154,14 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
ReportPage
(
(
"Alignment"
->
BammetricsReport
.
bamMetricsPage
(
summary
,
Some
(
sampleId
),
Some
(
libId
)))
::
(
if
(
flexiprepExecuted
)
List
(
"QC"
->
FlexiprepReport
.
flexiprepPage
)
else
Nil
)
:::
(
if
(
centrifugeExecuted
)
List
(
"Centriguge analysis"
->
Future
(
ReportPage
(
List
(
"Non-unique"
->
Future
(
ReportPage
(
List
(),
List
(
"All mappings"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
,
(
if
(
centrifugeExecuted
)
List
(
"Centriguge analysis"
->
Future
.
successful
(
ReportPage
(
List
(
"Non-unique"
->
Future
.
successful
(
ReportPage
(
List
(),
List
(
"All mappings"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
,
Map
(
"summaryStatsTag"
->
"centrifuge_report"
)
)),
Map
()))),
List
(
"Unique mappings"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
,
Map
(
"summaryStatsTag"
->
"centrifuge_unique_report"
)
)),
Map
(
"summaryModuleTag"
->
"gearscentrifuge"
,
"centrifugeTag"
->
Some
(
"centrifuge"
)))))
else
Nil
)
:::
(
if
(
krakenExecuted
)
List
(
"Dustbin analysis"
->
Future
(
ReportPage
(
List
(),
List
(
else
Nil
)
:::
(
if
(
krakenExecuted
)
List
(
"Dustbin analysis"
->
Future
.
successful
(
ReportPage
(
List
(),
List
(
"Krona Plot"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
)),
Map
())))
else
Nil
),
...
...
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