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biopet.biopet
Commits
02b8fdad
Commit
02b8fdad
authored
Mar 09, 2017
by
Peter van 't Hof
Browse files
Fix code warnings
parent
d16c8ad1
Changes
1
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Inline
Side-by-side
flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
View file @
02b8fdad
...
...
@@ -43,7 +43,7 @@ class FlexiprepTest extends TestNGSuite with Matchers {
}
@DataProvider
(
name
=
"flexiprepOptions"
)
def
flexiprepOptions
=
{
def
flexiprepOptions
:
Array
[
Array
[
Any
]]
=
{
val
paired
=
Array
(
true
,
false
)
val
skipTrims
=
Array
(
true
,
false
)
val
skipClips
=
Array
(
true
,
false
)
...
...
@@ -66,7 +66,7 @@ class FlexiprepTest extends TestNGSuite with Matchers {
skipTrim
:
Boolean
,
skipClip
:
Boolean
,
zipped
:
Boolean
,
abortOnCorruptFastq
:
Boolean
)
=
{
abortOnCorruptFastq
:
Boolean
)
:
Unit
=
{
val
outputDir
=
FlexiprepTest
.
outputDir
dirs
:+=
outputDir
val
map
=
ConfigUtils
.
mergeMaps
(
Map
(
"output_dir"
->
outputDir
,
...
...
@@ -76,8 +76,8 @@ class FlexiprepTest extends TestNGSuite with Matchers {
),
Map
(
FlexiprepTest
.
executables
.
toSeq
:
_
*
))
val
flexiprep
:
Flexiprep
=
initPipeline
(
map
)
flexiprep
.
inputR1
=
(
if
(
zipped
)
FlexiprepTest
.
r1Zipped
else
FlexiprepTest
.
r1
)
if
(
paired
)
flexiprep
.
inputR2
=
Some
(
(
if
(
zipped
)
FlexiprepTest
.
r2Zipped
else
FlexiprepTest
.
r2
)
)
flexiprep
.
inputR1
=
if
(
zipped
)
FlexiprepTest
.
r1Zipped
else
FlexiprepTest
.
r1
if
(
paired
)
flexiprep
.
inputR2
=
Some
(
if
(
zipped
)
FlexiprepTest
.
r2Zipped
else
FlexiprepTest
.
r2
)
flexiprep
.
sampleId
=
Some
(
"1"
)
flexiprep
.
libId
=
Some
(
"1"
)
flexiprep
.
script
()
...
...
@@ -91,7 +91,7 @@ class FlexiprepTest extends TestNGSuite with Matchers {
}
@Test
def
testNoSample
:
Unit
=
{
def
testNoSample
()
:
Unit
=
{
val
outputDir
=
FlexiprepTest
.
outputDir
dirs
:+=
outputDir
val
map
=
ConfigUtils
.
mergeMaps
(
Map
(
...
...
@@ -105,15 +105,15 @@ class FlexiprepTest extends TestNGSuite with Matchers {
}
// remove temporary run directory all tests in the class have been run
@AfterClass
def
removeTempOutputDir
()
=
{
@AfterClass
def
removeTempOutputDir
()
:
Unit
=
{
dirs
.
foreach
(
FileUtils
.
deleteDirectory
)
}
}
object
FlexiprepTest
{
def
outputDir
=
Files
.
createTempDir
()
def
outputDir
:
File
=
Files
.
createTempDir
()
val
inputDir
=
Files
.
createTempDir
()
val
inputDir
:
File
=
Files
.
createTempDir
()
val
r1
=
new
File
(
inputDir
,
"R1.fq"
)
Files
.
touch
(
r1
)
...
...
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