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biopet.biopet
Commits
3f5dd689
Commit
3f5dd689
authored
Nov 23, 2016
by
Sander Bollen
Browse files
xhmm discover wrapper
parent
6b51387d
Changes
1
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmDiscover.scala
0 → 100644
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3f5dd689
package
nl.lumc.sasc.biopet.extensions.xhmm
import
java.io.File
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Input
,
Output
}
/**
* Created by Sander Bollen on 23-11-16.
*/
class
XhmmDiscover
(
val
root
:
Configurable
)
extends
Xhmm
{
@Input
var
inputMatrix
:
File
=
_
@Output
var
outputXcnv
:
File
=
_
@Input
var
r
:
File
=
_
@Argument
var
discoverParamsFile
:
File
=
config
(
"discover_params"
,
namespace
=
"xhmm"
)
private
lazy
val
outputXcnvAuxFile
:
File
=
{
new
File
(
outputXcnv
.
getAbsolutePath
+
".aux"
)
}
@Argument
var
xhmmAnalysisName
:
String
=
_
def
cmdLine
=
{
executable
+
required
(
"--discover"
)
+
required
(
"-r"
,
inputMatrix
)
+
required
(
"-R"
,
r
)
+
required
(
"-c"
,
outputXcnv
)
+
required
(
"-a"
,
outputXcnvAuxFile
)
+
required
(
"-s"
,
xhmmAnalysisName
)
}
}
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