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biopet.biopet
Commits
c7e64e0c
Commit
c7e64e0c
authored
Apr 25, 2017
by
pjvan_thof
Browse files
Fixing names
parent
7e69b265
Changes
1
Hide whitespace changes
Inline
Side-by-side
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
View file @
c7e64e0c
...
...
@@ -63,9 +63,9 @@ 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
(
"noSample"
),
summaryRunId
),
Duration
.
Inf
))
val
sId
=
sample
.
map
(
_
.
id
).
getOrElse
(
Await
.
result
(
db
.
createSample
(
sampleId
.
getOrElse
(
"noSample
Name
"
),
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
(
"noLib"
),
summaryRunId
,
sId
),
Duration
.
Inf
))
val
lId
=
library
.
map
(
_
.
id
).
getOrElse
(
Await
.
result
(
db
.
createLibrary
(
libId
.
getOrElse
(
"noLib
Name
"
),
summaryRunId
,
sId
),
Duration
.
Inf
))
}
if
(
outputName
==
null
)
{
outputName
=
sampleId
.
getOrElse
(
"noName"
)
+
libId
.
map
(
"-"
+
_
).
getOrElse
(
""
)
...
...
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