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biopet.biopet
Commits
901b11d9
Commit
901b11d9
authored
Sep 19, 2016
by
Peter van 't Hof
Browse files
Added base version of centrifuge-kreport extension
parent
6bd92c80
Changes
2
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Inline
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/centrifuge/Centrifuge.scala
View file @
901b11d9
...
...
@@ -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
=
_
var
index
:
File
=
config
(
"centrifige_index"
)
@Output
(
doc
=
"Output with hits per sequence"
)
var
output
:
File
=
_
...
...
@@ -42,7 +42,7 @@ class Centrifuge(val root: Configurable) extends BiopetCommandLineFunction with
*
* @return Command to run
*/
protected
[
core
]
def
cmdLine
:
String
=
executable
+
def
cmdLine
:
String
=
executable
+
//TODO: Options
optional
(
"--threads"
,
threads
)
required
(
"-x"
,
index
)
+
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/centrifuge/CentrifugeKreport.scala
0 → 100644
View file @
901b11d9
package
nl.lumc.sasc.biopet.extensions.centrifuge
import
java.io.File
import
nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
/**
* Created by pjvanthof on 19/09/16.
*/
class
CentrifugeKreport
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
{
@Input
(
doc
=
"Output files centrifuge"
,
required
=
true
)
var
centrifugeOutputFiles
:
List
[
File
]
=
Nil
@Output
(
doc
=
"Output report"
)
var
output
:
File
=
_
@Input
(
doc
=
"Centrifuge index prefix"
,
required
=
true
)
var
index
:
File
=
config
(
"centrifige_index"
,
namespace
=
"centrifuge"
)
executable
=
config
(
"exe"
,
default
=
"centrifuge-kreport"
,
freeVar
=
false
)
def
cmdLine
=
executable
+
//TODO: Options
required
(
"-x"
,
index
)
+
repeat
(
centrifugeOutputFiles
)
}
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