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biopet.biopet
Commits
c0f8f2a3
Commit
c0f8f2a3
authored
Sep 19, 2016
by
Peter van 't Hof
Browse files
Added executables to testing
parent
7e6ef439
Changes
3
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/centrifuge/Centrifuge.scala
View file @
c0f8f2a3
...
...
@@ -19,7 +19,7 @@ class Centrifuge(val root: Configurable) extends BiopetCommandLineFunction with
var
inputR2
:
Option
[
File
]
=
None
@Input
(
doc
=
"Centrifuge index prefix"
,
required
=
true
)
var
index
:
File
=
config
(
"centrif
i
ge_index"
)
var
index
:
File
=
config
(
"centrif
u
ge_index"
)
@Output
(
doc
=
"Output with hits per sequence"
)
var
output
:
File
=
_
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/centrifuge/CentrifugeKreport.scala
View file @
c0f8f2a3
...
...
@@ -17,7 +17,7 @@ class CentrifugeKreport(val root: Configurable) extends BiopetCommandLineFunctio
var
output
:
File
=
_
@Input
(
doc
=
"Centrifuge index prefix"
,
required
=
true
)
var
index
:
File
=
config
(
"centrif
i
ge_index"
,
namespace
=
"centrifuge"
)
var
index
:
File
=
config
(
"centrif
u
ge_index"
,
namespace
=
"centrifuge"
)
executable
=
config
(
"exe"
,
default
=
"centrifuge-kreport"
,
freeVar
=
false
)
...
...
gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleTest.scala
View file @
c0f8f2a3
...
...
@@ -231,6 +231,8 @@ object TestGearsSingle {
val
executables
=
Map
(
"kraken"
->
Map
(
"exe"
->
"test"
,
"db"
->
"test"
),
"centrifuge"
->
Map
(
"exe"
->
"test"
,
"centrifuge_index"
->
"test"
),
"centrifugekreport"
->
Map
(
"exe"
->
"test"
),
"krakenreport"
->
Map
(
"exe"
->
"test"
,
"db"
->
"test"
),
"sambamba"
->
Map
(
"exe"
->
"test"
),
"samtools"
->
Map
(
"exe"
->
"test"
),
...
...
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