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biopet.biopet
Commits
05096c7d
Commit
05096c7d
authored
Oct 03, 2016
by
Peter van 't Hof
Browse files
Format fix
parent
9ec465f6
Changes
1
Hide whitespace changes
Inline
Side-by-side
sage/src/test/scala/nl/lumc/sasc/biopet/pipelines/sage/SageTest.scala
View file @
05096c7d
package
nl.lumc.sasc.biopet.pipelines.sage
import
java.io.
{
File
,
FileOutputStream
}
import
java.io.
{
File
,
FileOutputStream
}
import
com.google.common.io.Files
import
nl.lumc.sasc.biopet.utils.
{
ConfigUtils
,
Logging
}
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 28/09/16.
*/
* Created by pjvanthof on 28/09/16.
*/
class
SageTest
extends
TestNGSuite
with
Matchers
{
def
initPipeline
(
map
:
Map
[
String
,
Any
])
:
Sage
=
{
new
Sage
()
{
...
...
@@ -71,15 +71,17 @@ class SageTest extends TestNGSuite with Matchers {
pipeline
.
summaryFiles
shouldBe
Map
()
pipeline
.
summarySettings
shouldBe
Map
()
pipeline
.
samples
.
foreach
{
case
(
sampleId
,
sample
)
=>
sample
.
summaryFiles
shouldBe
Map
()
sample
.
summaryStats
shouldBe
Map
()
sample
.
summarySettings
shouldBe
Map
()
sample
.
libraries
.
foreach
{
case
(
libId
,
lib
)
=>
lib
.
summaryFiles
shouldBe
Map
()
lib
.
summaryStats
shouldBe
Map
()
lib
.
summarySettings
shouldBe
Map
()
}
pipeline
.
samples
.
foreach
{
case
(
sampleId
,
sample
)
=>
sample
.
summaryFiles
shouldBe
Map
()
sample
.
summaryStats
shouldBe
Map
()
sample
.
summarySettings
shouldBe
Map
()
sample
.
libraries
.
foreach
{
case
(
libId
,
lib
)
=>
lib
.
summaryFiles
shouldBe
Map
()
lib
.
summaryStats
shouldBe
Map
()
lib
.
summarySettings
shouldBe
Map
()
}
}
}
...
...
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