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biopet.biopet
Commits
66e90444
Commit
66e90444
authored
Nov 08, 2016
by
Peter van 't Hof
Browse files
Fixed unit tests
parent
a4553c54
Changes
3
Hide whitespace changes
Inline
Side-by-side
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/centrifuge/Centrifuge.scala
View file @
66e90444
...
...
@@ -27,19 +27,19 @@ class Centrifuge(val root: Configurable) extends BiopetCommandLineFunction with
var
report
:
Option
[
File
]
=
None
@Output
(
required
=
false
)
var
un
:
Option
[
File
]
=
_
var
un
:
Option
[
File
]
=
None
@Output
(
required
=
false
)
var
al
:
Option
[
File
]
=
_
var
al
:
Option
[
File
]
=
None
@Output
(
required
=
false
)
var
unConc
:
Option
[
File
]
=
_
var
unConc
:
Option
[
File
]
=
None
@Output
(
required
=
false
)
var
alConc
:
Option
[
File
]
=
_
var
alConc
:
Option
[
File
]
=
None
@Output
(
required
=
false
)
var
metFile
:
Option
[
File
]
=
_
var
metFile
:
Option
[
File
]
=
None
// Input args
var
q
:
Boolean
=
config
(
"q"
,
default
=
false
)
...
...
gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleTest.scala
View file @
66e90444
...
...
@@ -108,12 +108,12 @@ abstract class TestGearsSingle extends TestNGSuite with Matchers {
val
pipesJobs
=
gears
.
functions
.
filter
(
_
.
isInstanceOf
[
BiopetPipe
]).
flatMap
(
_
.
asInstanceOf
[
BiopetPipe
].
pipesJobs
)
gears
.
summarySettings
(
"gears_use_kraken"
)
shouldBe
kraken
.
getOrElse
(
tru
e
)
gears
.
summarySettings
(
"gears_use_kraken"
)
shouldBe
kraken
.
getOrElse
(
fals
e
)
gears
.
summarySettings
(
"gear_use_qiime_rtax"
)
shouldBe
qiimeRtax
gears
.
summarySettings
(
"gear_use_qiime_closed"
)
shouldBe
qiimeClosed
gears
.
summarySettings
(
"gear_use_qiime_open"
)
shouldBe
qiimeOpen
gears
.
krakenScript
.
isDefined
shouldBe
kraken
.
getOrElse
(
tru
e
)
gears
.
krakenScript
.
isDefined
shouldBe
kraken
.
getOrElse
(
fals
e
)
gears
.
centrifugeScript
.
isDefined
shouldBe
centrifuge
gears
.
qiimeClosed
.
isDefined
shouldBe
qiimeClosed
gears
.
qiimeOpen
.
isDefined
shouldBe
qiimeOpen
...
...
@@ -124,10 +124,10 @@ abstract class TestGearsSingle extends TestNGSuite with Matchers {
gears
.
functions
.
count
(
_
.
isInstanceOf
[
SamtoolsView
])
shouldBe
(
if
(
inputMode
==
Some
(
"bam"
))
1
else
0
)
gears
.
functions
.
count
(
_
.
isInstanceOf
[
SamToFastq
])
shouldBe
(
if
(
inputMode
==
Some
(
"bam"
))
1
else
0
)
gears
.
functions
.
count
(
_
.
isInstanceOf
[
Kraken
])
shouldBe
(
if
(
kraken
.
getOrElse
(
tru
e
))
1
else
0
)
gears
.
functions
.
count
(
_
.
isInstanceOf
[
KrakenReport
])
shouldBe
(
if
(
kraken
.
getOrElse
(
tru
e
))
1
else
0
)
gears
.
functions
.
count
(
_
.
isInstanceOf
[
Kraken
])
shouldBe
(
if
(
kraken
.
getOrElse
(
fals
e
))
1
else
0
)
gears
.
functions
.
count
(
_
.
isInstanceOf
[
KrakenReport
])
shouldBe
(
if
(
kraken
.
getOrElse
(
fals
e
))
1
else
0
)
gears
.
functions
.
count
(
_
.
isInstanceOf
[
KrakenReportToJson
])
shouldBe
((
if
(
kraken
.
getOrElse
(
tru
e
))
1
else
0
)
+
(
if
(
centrifuge
)
2
else
0
))
((
if
(
kraken
.
getOrElse
(
fals
e
))
1
else
0
)
+
(
if
(
centrifuge
)
2
else
0
))
gears
.
functions
.
count
(
_
.
isInstanceOf
[
Centrifuge
])
shouldBe
(
if
(
centrifuge
)
1
else
0
)
gears
.
functions
.
count
(
_
.
isInstanceOf
[
CentrifugeKreport
])
shouldBe
(
if
(
centrifuge
)
2
else
0
)
...
...
gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTest.scala
View file @
66e90444
...
...
@@ -130,7 +130,10 @@ object GearsTest {
"seqtk"
->
Map
(
"exe"
->
"test"
),
"sickle"
->
Map
(
"exe"
->
"test"
),
"cutadapt"
->
Map
(
"exe"
->
"test"
),
"pickopenreferenceotus"
->
Map
(
"exe"
->
"test"
)
"centrifuge"
->
Map
(
"exe"
->
"test"
),
"centrifuge_index"
->
"test"
,
"pickopenreferenceotus"
->
Map
(
"exe"
->
"test"
),
"centrifugekreport"
->
Map
(
"exe"
->
"test"
)
)
val
sample1
=
Map
(
...
...
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