Skip to content
GitLab
Menu
Projects
Groups
Snippets
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Mirrors
biopet.biopet
Commits
a5f383c5
Commit
a5f383c5
authored
Jul 01, 2016
by
Peter van 't Hof
Browse files
Fixing failing tests
parent
431621b2
Changes
4
Hide whitespace changes
Inline
Side-by-side
carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala
View file @
a5f383c5
...
...
@@ -14,19 +14,19 @@
*/
package
nl.lumc.sasc.biopet.pipelines.carp
import
java.io.
{
File
,
FileOutputStream
}
import
java.io.
{
File
,
FileOutputStream
}
import
com.google.common.io.Files
import
nl.lumc.sasc.biopet.utils.config.Config
import
nl.lumc.sasc.biopet.extensions.bwa.BwaMem
import
nl.lumc.sasc.biopet.extensions.macs2.Macs2CallPeak
import
nl.lumc.sasc.biopet.extensions.picard.
{
MergeSamFiles
,
SortSam
}
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
nl.lumc.sasc.biopet.extensions.picard.
{
MergeSamFiles
,
SortSam
}
import
nl.lumc.sasc.biopet.utils.
{
ConfigUtils
,
Logging
}
import
org.apache.commons.io.FileUtils
import
org.broadinstitute.gatk.queue.QSettings
import
org.scalatest.Matchers
import
org.scalatest.testng.TestNGSuite
import
org.testng.annotations.
{
AfterClass
,
DataProvider
,
Test
}
import
org.testng.annotations.
{
AfterClass
,
DataProvider
,
Test
}
/**
* Test class for [[Carp]]
...
...
@@ -72,6 +72,7 @@ class CarpTest extends TestNGSuite with Matchers {
intercept
[
IllegalStateException
]
{
initPipeline
(
map
).
script
()
}
Logging
.
errors
.
clear
()
}
else
{
// When samples are correct
val
carp
=
initPipeline
(
map
)
carp
.
script
()
...
...
gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTest.scala
View file @
a5f383c5
...
...
@@ -72,7 +72,7 @@ abstract class GearsTest extends TestNGSuite with Matchers {
}
if
(!
sample1
&&
!
sample2
)
{
// When no samples
intercept
[
Illegal
Argument
Exception
]
{
intercept
[
Illegal
State
Exception
]
{
initPipeline
(
map
).
script
()
}
Logging
.
errors
.
clear
()
...
...
mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTest.scala
View file @
a5f383c5
...
...
@@ -14,17 +14,17 @@
*/
package
nl.lumc.sasc.biopet.pipelines.mapping
import
java.io.
{
File
,
FileOutputStream
}
import
java.io.
{
File
,
FileOutputStream
}
import
com.google.common.io.Files
import
nl.lumc.sasc.biopet.extensions.kraken.Kraken
import
nl.lumc.sasc.biopet.extensions.picard.
{
MarkDuplicates
,
MergeSamFiles
}
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
nl.lumc.sasc.biopet.extensions.picard.
{
MarkDuplicates
,
MergeSamFiles
}
import
nl.lumc.sasc.biopet.utils.
{
ConfigUtils
,
Logging
}
import
nl.lumc.sasc.biopet.utils.config.Config
import
org.broadinstitute.gatk.queue.QSettings
import
org.scalatest.Matchers
import
org.scalatest.testng.TestNGSuite
import
org.testng.annotations.
{
DataProvider
,
Test
}
import
org.testng.annotations.
{
DataProvider
,
Test
}
/**
* Created by pjvanthof on 15/05/16.
...
...
@@ -72,9 +72,10 @@ trait MultisampleMappingTestTrait extends TestNGSuite with Matchers {
}
if
(!
sample1
&&
!
sample2
&&
!
sample3
&&
!
sample4
)
{
// When no samples
intercept
[
Illegal
Argument
Exception
]
{
intercept
[
Illegal
State
Exception
]
{
initPipeline
(
map
).
script
()
}
Logging
.
errors
.
clear
()
}
else
if
(
sample4
&&
!
bamToFastq
&&
!
correctReadgroups
)
{
intercept
[
IllegalStateException
]
{
initPipeline
(
map
).
script
()
...
...
shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
View file @
a5f383c5
...
...
@@ -14,18 +14,18 @@
*/
package
nl.lumc.sasc.biopet.pipelines.shiva
import
java.io.
{
File
,
FileOutputStream
}
import
java.io.
{
File
,
FileOutputStream
}
import
com.google.common.io.Files
import
nl.lumc.sasc.biopet.extensions.gatk.
{
BaseRecalibrator
,
IndelRealigner
,
PrintReads
,
RealignerTargetCreator
}
import
nl.lumc.sasc.biopet.extensions.gatk.
{
BaseRecalibrator
,
IndelRealigner
,
PrintReads
,
RealignerTargetCreator
}
import
nl.lumc.sasc.biopet.extensions.picard.MarkDuplicates
import
nl.lumc.sasc.biopet.extensions.tools.VcfStats
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
nl.lumc.sasc.biopet.utils.
{
ConfigUtils
,
Logging
}
import
nl.lumc.sasc.biopet.utils.config.Config
import
org.broadinstitute.gatk.queue.QSettings
import
org.scalatest.Matchers
import
org.scalatest.testng.TestNGSuite
import
org.testng.annotations.
{
DataProvider
,
Test
}
import
org.testng.annotations.
{
DataProvider
,
Test
}
/**
* Class for testing shiva
...
...
@@ -86,6 +86,7 @@ trait ShivaTestTrait extends TestNGSuite with Matchers {
intercept
[
IllegalArgumentException
]
{
initPipeline
(
map
).
script
()
}
Logging
.
errors
.
clear
()
}
else
{
val
pipeline
=
initPipeline
(
map
)
pipeline
.
script
()
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment