Skip to content
GitLab
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
86ad2593
Commit
86ad2593
authored
Jan 19, 2016
by
Sander van der Zeeuw
Browse files
add varscan test to shiva variantcalling test
parent
ca40d875
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
View file @
86ad2593
...
...
@@ -53,28 +53,31 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
bams
<-
0
to
3
;
raw
<-
bool
;
bcftools
<-
bool
;
bcftools_singlesample
<-
bool
;
freebayes
<-
bool
)
yield
Array
(
bams
,
raw
,
bcftools
,
bcftools_singlesample
,
freebayes
)).
toArray
bcftoolsSinglesample
<-
bool
;
freebayes
<-
bool
;
varscanCnsSinglesample
<-
bool
)
yield
Array
(
bams
,
raw
,
bcftools
,
bcftoolsSinglesample
,
freebayes
,
varscanCnsSinglesample
)).
toArray
}
@Test
(
dataProvider
=
"shivaVariantcallingOptions"
)
def
testShivaVariantcalling
(
bams
:
Int
,
raw
:
Boolean
,
bcftools
:
Boolean
,
bcftools_singlesample
:
Boolean
,
freebayes
:
Boolean
)
=
{
bcftoolsSinglesample
:
Boolean
,
freebayes
:
Boolean
,
varscanCnsSinglesample
:
Boolean
)
=
{
val
callers
:
ListBuffer
[
String
]
=
ListBuffer
()
if
(
raw
)
callers
.
append
(
"raw"
)
if
(
bcftools
)
callers
.
append
(
"bcftools"
)
if
(
bcftools
_s
inglesample
)
callers
.
append
(
"bcftools_singlesample"
)
if
(
bcftools
S
inglesample
)
callers
.
append
(
"bcftools_singlesample"
)
if
(
freebayes
)
callers
.
append
(
"freebayes"
)
if
(
varscanCnsSinglesample
)
callers
.
append
(
"varscan_cns_singlesample"
)
val
map
=
Map
(
"variantcallers"
->
callers
.
toList
)
val
pipeline
=
initPipeline
(
map
)
pipeline
.
inputBams
=
(
for
(
n
<-
1
to
bams
)
yield
n
.
toString
->
ShivaVariantcallingTest
.
inputTouch
(
"bam_"
+
n
+
".bam"
)).
toMap
val
illegalArgumentException
=
pipeline
.
inputBams
.
isEmpty
||
(!
raw
&&
!
bcftools
&&
!
bcftools
_s
inglesample
&&
!
freebayes
)
val
illegalArgumentException
=
pipeline
.
inputBams
.
isEmpty
||
(!
raw
&&
!
bcftools
&&
!
bcftools
S
inglesample
&&
!
freebayes
)
if
(
illegalArgumentException
)
intercept
[
IllegalArgumentException
]
{
pipeline
.
script
()
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new 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