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biopet.biopet
Commits
69a3c90f
Commit
69a3c90f
authored
Aug 01, 2015
by
Peter van 't Hof
Browse files
Name fix
parent
2fe05703
Changes
1
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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
View file @
69a3c90f
...
...
@@ -28,7 +28,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class
VariantEffectPredictor
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
with
Reference
{
executable
=
config
(
"exe"
,
submodule
=
"perl"
,
default
=
"perl"
)
var
vep
_s
cript
:
String
=
config
(
"vep_script"
)
var
vep
S
cript
:
String
=
config
(
"vep_script"
)
@Input
(
doc
=
"input VCF"
,
required
=
true
)
var
input
:
File
=
null
...
...
@@ -37,7 +37,7 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
var
output
:
File
=
null
override
def
versionRegex
=
"""version (\d*)"""
.
r
override
def
versionCommand
=
executable
+
" "
+
vep
_s
cript
+
" --help"
override
def
versionCommand
=
executable
+
" "
+
vep
S
cript
+
" --help"
//Boolean vars
var
v
:
Boolean
=
config
(
"v"
,
default
=
true
)
...
...
@@ -152,7 +152,7 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
/** Returns command to execute */
def
cmdLine
=
required
(
executable
)
+
required
(
vep
_s
cript
)
+
required
(
vep
S
cript
)
+
required
(
"-i"
,
input
)
+
required
(
"-o"
,
output
)
+
conditional
(
v
,
"-v"
)
+
...
...
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