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biopet.biopet
Commits
1c158133
Commit
1c158133
authored
Apr 06, 2015
by
Peter van 't Hof
Browse files
Refactor output dir
parent
fdf13694
Changes
1
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Inline
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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
View file @
1c158133
...
...
@@ -37,10 +37,8 @@ trait BiopetQScript extends Configurable with GatkLogging {
val
configValues
:
List
[
String
]
=
Nil
var
outputDir
:
File
=
{
Config
.
getValueFromMap
(
globalConfig
.
map
,
ConfigValueIndex
(
this
.
configName
,
configPath
,
"output_dir"
))
match
{
case
Some
(
value
)
=>
new
File
(
value
.
asString
).
getAbsoluteFile
case
_
=>
new
File
(
"."
)
}
if
(
config
.
contains
(
"output_dir"
,
path
=
Nil
))
config
(
"output_dir"
,
path
=
Nil
).
asFile
else
new
File
(
"."
)
}
@Argument
(
doc
=
"Disable all scatters"
,
shortName
=
"DSC"
,
required
=
false
)
...
...
@@ -64,11 +62,8 @@ trait BiopetQScript extends Configurable with GatkLogging {
* Script from queue itself, final to force some checks for each pipeline and write report
*/
final
def
script
()
{
if
(
config
.
contains
(
"output_dir"
))
outputDir
=
config
(
"output_dir"
).
asFile
.
getAbsoluteFile
else
{
outputDir
=
new
File
(
"."
).
getAbsoluteFile
BiopetQScript
.
addError
(
"No output_dir defined in config"
)
}
outputDir
=
config
(
"output_dir"
)
outputDir
=
outputDir
.
getAbsoluteFile
init
biopetScript
...
...
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