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biopet.biopet
Commits
9ca759c7
Commit
9ca759c7
authored
Jul 13, 2017
by
Peter van 't Hof
Browse files
Style issues
parent
385c71e9
Changes
6
Hide whitespace changes
Inline
Side-by-side
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
View file @
9ca759c7
...
...
@@ -30,7 +30,8 @@ trait PipelineCommand extends MainCommand with GatkLogging with ImplicitConversi
* Gets location of compiled class of pipeline
* @return path from classPath to class file
*/
def
pipeline
:
String
=
"/"
+
getClass
.
getName
.
takeWhile
(
_
!=
'$'
).
replaceAll
(
"\\."
,
"/"
)
+
".class"
def
pipeline
:
String
=
"/"
+
getClass
.
getName
.
takeWhile
(
_
!=
'$'
).
replaceAll
(
"\\."
,
"/"
)
+
".class"
def
pipelineName
:
String
=
getClass
.
getName
.
takeWhile
(
_
!=
'$'
).
split
(
"\\."
).
last
.
toLowerCase
...
...
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
View file @
9ca759c7
...
...
@@ -64,27 +64,27 @@ class WriteSummary(val parent: SummaryQScript) extends InProcessFunction with Co
qscript
match
{
case
s
:
MultiSampleQScript
=>
s
.
initSummaryDb
()
case
t
:
SampleLibraryTag
=>
t
.
sampleId
.
foreach
{
sampleName
=>
val
sampleId
=
Await
.
result
(
db
.
getSamples
(
name
=
Some
(
sampleName
),
runId
=
Some
(
qscript
.
summaryRunId
))
.
map
(
_
.
headOption
.
map
(
_
.
id
)),
Duration
.
Inf
)
.
getOrElse
{
Await
.
result
(
db
.
createOrUpdateSample
(
sampleName
,
qscript
.
summaryRunId
),
Duration
.
Inf
)
}
t
.
libId
.
foreach
{
libName
=>
Await
.
result
(
db
.
getSamples
(
name
=
Some
(
libName
),
runId
=
Some
(
qscript
.
summaryRunId
),
sampleId
=
Some
(
sampleId
))
.
map
(
_
.
headOption
.
map
(
_
.
id
)),
Duration
.
Inf
)
.
getOrElse
{
Await
.
result
(
db
.
createOrUpdateLibrary
(
libName
,
qscript
.
summaryRunId
,
sampleId
),
t
.
sampleId
.
foreach
{
sampleName
=>
val
sampleId
=
Await
.
result
(
db
.
getSamples
(
name
=
Some
(
sampleName
),
runId
=
Some
(
qscript
.
summaryRunId
))
.
map
(
_
.
headOption
.
map
(
_
.
id
)),
Duration
.
Inf
)
}
.
getOrElse
{
Await
.
result
(
db
.
createOrUpdateSample
(
sampleName
,
qscript
.
summaryRunId
),
Duration
.
Inf
)
}
t
.
libId
.
foreach
{
libName
=>
Await
.
result
(
db
.
getSamples
(
name
=
Some
(
libName
),
runId
=
Some
(
qscript
.
summaryRunId
),
sampleId
=
Some
(
sampleId
))
.
map
(
_
.
headOption
.
map
(
_
.
id
)),
Duration
.
Inf
)
.
getOrElse
{
Await
.
result
(
db
.
createOrUpdateLibrary
(
libName
,
qscript
.
summaryRunId
,
sampleId
),
Duration
.
Inf
)
}
}
}
case
_
=>
qscript
.
summaryRunId
}
...
...
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/MultiSampleQScriptTest.scala
View file @
9ca759c7
...
...
@@ -210,7 +210,8 @@ object MultiSampleQScriptTest {
)
)
def
apply
(
configs
:
List
[
Map
[
String
,
Any
]],
only
:
List
[
String
]
=
Nil
)
:
QScript
with
MultiSampleQScript
{
def
apply
(
configs
:
List
[
Map
[
String
,
Any
]],
only
:
List
[
String
]
=
Nil
)
:
QScript
with
MultiSampleQScript
{
def
init
()
:
Unit
def
getLastLogMessage:
String
...
...
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/PedigreeQScriptTest.scala
View file @
9ca759c7
...
...
@@ -171,7 +171,8 @@ object PedigreeQScriptTest {
val
trioPed
=
Map
(
"ped_file"
->
resourcePath
(
"/trio.ped"
))
def
apply
(
configs
:
List
[
Map
[
String
,
Any
]],
only
:
List
[
String
]
=
Nil
)
:
QScript
with
PedigreeQscript
{
def
apply
(
configs
:
List
[
Map
[
String
,
Any
]],
only
:
List
[
String
]
=
Nil
)
:
QScript
with
PedigreeQscript
{
def
init
()
:
Unit
def
biopetScript
()
:
Unit
...
...
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/WriteDependenciesTest.scala
View file @
9ca759c7
...
...
@@ -33,8 +33,10 @@ class WriteDependenciesTest extends TestNGSuite with Matchers {
case
class
Qfunc
(
in
:
Seq
[
File
],
out
:
Seq
[
File
])
extends
QFunction
{
override
def
inputs
:
Seq
[
File
]
=
in
override
def
outputs
:
Seq
[
File
]
=
out
override
def
doneOutputs
:
Seq
[
File
]
=
out
.
map
(
x
=>
new
File
(
x
.
getParentFile
,
s
".${x.getName}.done"
))
override
def
failOutputs
:
Seq
[
File
]
=
out
.
map
(
x
=>
new
File
(
x
.
getParentFile
,
s
".${x.getName}.fail"
))
override
def
doneOutputs
:
Seq
[
File
]
=
out
.
map
(
x
=>
new
File
(
x
.
getParentFile
,
s
".${x.getName}.done"
))
override
def
failOutputs
:
Seq
[
File
]
=
out
.
map
(
x
=>
new
File
(
x
.
getParentFile
,
s
".${x.getName}.fail"
))
jobOutputFile
=
new
File
(
out
.
head
+
".out"
)
}
...
...
biopet-core/src/test/scala/nl/lumc/sasc/biopet/extensions/tools/VcfFilterTest.scala
View file @
9ca759c7
...
...
@@ -65,7 +65,8 @@ class VcfFilterTest extends TestNGSuite with Matchers {
@Test
def
testMinQualScore
()
:
Unit
=
testCommand
(
minQualScore
=
Some
(
50.0
))
@Test
def
testFilterHetVarToHomVar
()
:
Unit
=
testCommand
(
filterHetVarToHomVar
=
List
(
"dummy"
))
@Test
def
testId
()
:
Unit
=
testCommand
(
id
=
List
(
"rs01"
,
"rs02"
))
@Test
def
testIdFile
()
:
Unit
=
testCommand
(
idFile
=
Some
(
File
.
createTempFile
(
"vcfFilter"
,
".txt"
)))
@Test
def
testIdFile
()
:
Unit
=
testCommand
(
idFile
=
Some
(
File
.
createTempFile
(
"vcfFilter"
,
".txt"
)))
protected
def
testCommand
(
minSampleDepth
:
Option
[
Int
]
=
None
,
minTotalDepth
:
Option
[
Int
]
=
None
,
...
...
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