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biopet.biopet
Commits
a90b06da
Commit
a90b06da
authored
Jul 29, 2014
by
bow
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Update base BiopetQScript command line argument names
parent
c0598153
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-2
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
...c/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+3
-2
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biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
View file @
a90b06da
...
...
@@ -8,10 +8,11 @@ import org.broadinstitute.gatk.queue.QSettings
import
org.broadinstitute.gatk.queue.function.QFunction
trait
BiopetQScript
extends
Configurable
{
@Argument
(
doc
=
"Config Json file"
,
shortName
=
"config"
,
required
=
false
)
@Argument
(
doc
=
"JSON config file(s)"
,
fullName
=
"config_file"
,
shortName
=
"conf"
,
required
=
false
)
val
configfiles
:
List
[
File
]
=
Nil
@Argument
(
doc
=
"Output directory"
,
shortName
=
"outp
utDir"
,
required
=
true
)
@Argument
(
doc
=
"Output directory"
,
fullName
=
"output_directory"
,
shortName
=
"o
utDir"
,
required
=
true
)
var
outputDir
:
String
=
_
var
outputFiles
:
Map
[
String
,
File
]
=
Map
()
...
...
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