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biopet.biopet
Commits
aeb3c024
Commit
aeb3c024
authored
Jan 27, 2015
by
Peter van 't Hof
Browse files
Remove outputDir from arguments
parent
c05ab685
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
View file @
aeb3c024
...
...
@@ -29,11 +29,10 @@ trait BiopetQScript extends Configurable with GatkLogging {
@Argument
(
doc
=
"JSON config file(s)"
,
fullName
=
"config_file"
,
shortName
=
"config"
,
required
=
false
)
val
configfiles
:
List
[
File
]
=
Nil
@Argument
(
doc
=
"Output directory"
,
fullName
=
"output_directory"
,
shortName
=
"outDir"
,
required
=
true
)
var
outputDir
:
String
=
_
@Argument
(
doc
=
"Disable all scatters"
,
shortName
=
"DSC"
,
required
=
false
)
var
disableScatter
Default
:
Boolean
=
false
var
disableScatter
:
Boolean
=
false
var
outputFiles
:
Map
[
String
,
File
]
=
Map
()
...
...
@@ -45,11 +44,12 @@ trait BiopetQScript extends Configurable with GatkLogging {
var
functions
:
Seq
[
QFunction
]
final
def
script
()
{
outputDir
=
config
(
"output_dir"
,
required
=
true
)
if
(!
outputDir
.
endsWith
(
"/"
))
outputDir
+=
"/"
init
biopetScript
if
(
disableScatter
Default
)
for
(
function
<-
functions
)
function
match
{
if
(
disableScatter
)
for
(
function
<-
functions
)
function
match
{
case
f
:
ScatterGatherableFunction
=>
f
.
scatterCount
=
1
case
_
=>
}
...
...
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