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biopet.biopet
Commits
7d530c20
Commit
7d530c20
authored
Dec 06, 2016
by
Peter van 't Hof
Browse files
Fixed compile error
parent
bff12a5f
Changes
2
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biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
View file @
7d530c20
...
...
@@ -16,14 +16,14 @@ package nl.lumc.sasc.biopet.core
import
java.io.File
import
nl.lumc.sasc.biopet.core.summary.
{
SummaryQScript
,
WriteSummary
}
import
nl.lumc.sasc.biopet.core.summary.
{
SummaryQScript
,
WriteSummary
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
import
nl.lumc.sasc.biopet.core.workaround.BiopetQCommandLine
import
nl.lumc.sasc.biopet.utils.Logging
import
org.broadinstitute.gatk.queue.
{
QScript
,
QSettings
}
import
org.broadinstitute.gatk.queue.
{
QScript
,
QSettings
}
import
org.broadinstitute.gatk.queue.function.QFunction
import
org.broadinstitute.gatk.queue.util.
{
Logging
=>
GatkLogging
}
import
org.broadinstitute.gatk.queue.util.
{
Logging
=>
GatkLogging
}
/** Base for biopet pipeline */
trait
BiopetQScript
extends
Configurable
with
GatkLogging
{
qscript
:
QScript
=>
...
...
@@ -177,5 +177,4 @@ object BiopetQScript {
require
(
outputDir
.
getAbsoluteFile
.
canWrite
,
s
"No premision to write outputdir: $outputDir"
)
}
}
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/WriteDependenciesTest.scala
View file @
7d530c20
...
...
@@ -39,15 +39,14 @@ class WriteDependenciesTest extends TestNGSuite with Matchers {
}
@Test
def
testDeps
:
Unit
=
{
def
testDeps
()
:
Unit
=
{
val
tempDir
=
Files
.
createTempDir
()
tempDir
.
deleteOnExit
()
val
prefix
=
"test"
val
outputFile
=
new
File
(
tempDir
,
s
"$prefix.deps.json"
)
val
outputFile
=
new
File
(
tempDir
,
s
"deps.json"
)
outputFile
.
deleteOnExit
()
val
func1
=
Qfunc
(
file1
::
Nil
,
file2
::
Nil
)
val
func2
=
Qfunc
(
file2
::
Nil
,
file3
::
Nil
)
WriteDependencies
.
writeDependencies
(
func1
::
func2
::
Nil
,
tempDir
,
prefix
)
WriteDependencies
.
writeDependencies
(
func1
::
func2
::
Nil
,
tempDir
)
val
deps
=
ConfigUtils
.
fileToConfigMap
(
outputFile
)
deps
(
"jobs"
)
shouldBe
a
[
Map
[
_
,
_
]]
val
jobs
=
deps
(
"jobs"
).
asInstanceOf
[
Map
[
String
,
Map
[
String
,
Any
]]]
...
...
@@ -55,7 +54,7 @@ class WriteDependenciesTest extends TestNGSuite with Matchers {
deps
(
"files"
)
shouldBe
a
[
List
[
_
]]
val
files
=
deps
(
"files"
).
asInstanceOf
[
List
[
Map
[
String
,
Any
]]]
val
paths
=
files
.
m
ap
(
x
=>
x
.
get
(
"path"
))
.
flatten
val
paths
=
files
.
flatM
ap
(
x
=>
x
.
get
(
"path"
))
assert
(
paths
.
contains
(
file1
.
toString
))
assert
(
paths
.
contains
(
file2
.
toString
))
assert
(
paths
.
contains
(
file3
.
toString
))
...
...
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