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biopet.biopet
Commits
65897482
Commit
65897482
authored
Apr 25, 2017
by
pjvan_thof
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parent
c7e64e0c
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-5
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
...ala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
+9
-5
No files found.
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
View file @
65897482
...
...
@@ -24,7 +24,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
import
org.broadinstitute.gatk.queue.QScript
import
scala.concurrent.
Await
import
scala.concurrent.
{
Await
,
Future
}
import
scala.concurrent.duration.Duration
import
scala.concurrent.ExecutionContext.Implicits.global
...
...
@@ -62,10 +62,14 @@ class GearsSingle(val parent: Configurable) extends QScript with SummaryQScript
if
(!
skipFlexiprep
)
{
val
db
=
SummaryDb
.
openSqliteSummary
(
summaryDbFile
)
val
sample
=
Await
.
result
(
db
.
getSamples
(
runId
=
summaryRunId
,
name
=
sampleId
).
map
(
_
.
headOption
),
Duration
.
Inf
)
val
sId
=
sample
.
map
(
_
.
id
).
getOrElse
(
Await
.
result
(
db
.
createSample
(
sampleId
.
getOrElse
(
"noSampleName"
),
summaryRunId
),
Duration
.
Inf
))
val
library
=
Await
.
result
(
db
.
getLibraries
(
runId
=
summaryRunId
,
name
=
libId
,
sampleId
=
Some
(
sId
)).
map
(
_
.
headOption
),
Duration
.
Inf
)
val
lId
=
library
.
map
(
_
.
id
).
getOrElse
(
Await
.
result
(
db
.
createLibrary
(
libId
.
getOrElse
(
"noLibName"
),
summaryRunId
,
sId
),
Duration
.
Inf
))
Await
.
result
(
for
{
sample
<-
db
.
getSamples
(
runId
=
summaryRunId
,
name
=
sampleId
).
map
(
_
.
headOption
)
sId
<-
sample
.
map
(
s
=>
Future
.
successful
(
s
.
id
))
.
getOrElse
(
db
.
createSample
(
sampleId
.
getOrElse
(
"noSampleName"
),
summaryRunId
))
library
<-
db
.
getLibraries
(
runId
=
summaryRunId
,
name
=
libId
,
sampleId
=
Some
(
sId
)).
map
(
_
.
headOption
)
lId
<-
library
.
map
(
l
=>
Future
.
successful
(
l
.
id
))
.
getOrElse
(
db
.
createLibrary
(
libId
.
getOrElse
(
"noLibName"
),
summaryRunId
,
sId
))
}
yield
lId
,
Duration
.
Inf
)
}
if
(
outputName
==
null
)
{
outputName
=
sampleId
.
getOrElse
(
"noName"
)
+
libId
.
map
(
"-"
+
_
).
getOrElse
(
""
)
...
...
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