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biopet.biopet
Commits
d9e3b6d1
Commit
d9e3b6d1
authored
Mar 02, 2017
by
Peter van 't Hof
Browse files
Fixed last unit tests
parent
f7166e18
Changes
2
Hide whitespace changes
Inline
Side-by-side
generate-indexes/src/test/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/DownloadGenomesTest.scala
View file @
d9e3b6d1
...
...
@@ -29,10 +29,10 @@ import org.testng.annotations.{ AfterClass, Test }
* Created by pjvan_thof on 13-5-16.
*/
class
DownloadGenomesTest
extends
TestNGSuite
with
Matchers
{
def
initPipeline
(
map
:
Map
[
String
,
Any
],
outputD
ir
:
File
)
:
DownloadGenomes
=
{
def
initPipeline
(
map
:
Map
[
String
,
Any
],
d
ir
:
File
)
:
DownloadGenomes
=
{
new
DownloadGenomes
()
{
override
def
configNamespace
=
"generateindexes"
override
def
globalConfig
=
new
Config
(
ConfigUtils
.
mergeMaps
(
map
,
DownloadGenomesTest
.
config
(
outputD
ir
)))
override
def
globalConfig
=
new
Config
(
ConfigUtils
.
mergeMaps
(
map
,
DownloadGenomesTest
.
config
(
d
ir
)))
qSettings
=
new
QSettings
qSettings
.
runName
=
"test"
}
...
...
tinycap/src/test/scala/nl/lumc/sasc/biopet/pipelines/tinycap/TinyCapTest.scala
View file @
d9e3b6d1
...
...
@@ -102,9 +102,9 @@ object TinyCapTest {
def
outputDir
=
Files
.
createTempDir
()
val
inputDir
=
Files
.
createTempDir
()
val
r1
=
new
File
(
inputDir
,
"input"
+
File
.
separator
+
"R1.fq.gz"
)
val
r1
=
new
File
(
inputDir
,
"R1.fq.gz"
)
Files
.
touch
(
r1
)
val
bam
=
new
File
(
inputDir
,
"input"
+
File
.
separator
+
"bamfile.bam"
)
val
bam
=
new
File
(
inputDir
,
"bamfile.bam"
)
Files
.
touch
(
bam
)
val
referenceFasta
=
new
File
(
inputDir
,
"ref.fa"
)
...
...
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