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biopet.biopet
Commits
e3df8cc5
Commit
e3df8cc5
authored
Nov 18, 2014
by
Peter van 't Hof
Browse files
Remove BIOPET_CONFIG_SCATTER env value, change flag to disable scatters
parent
85885148
Changes
2
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biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
View file @
e3df8cc5
...
...
@@ -6,6 +6,7 @@ import nl.lumc.sasc.biopet.core.config.{ Config, Configurable }
import
org.broadinstitute.gatk.utils.commandline.Argument
import
org.broadinstitute.gatk.queue.QSettings
import
org.broadinstitute.gatk.queue.function.QFunction
import
org.broadinstitute.gatk.queue.function.scattergather.ScatterGatherableFunction
trait
BiopetQScript
extends
Configurable
{
...
...
@@ -15,8 +16,8 @@ trait BiopetQScript extends Configurable {
@Argument
(
doc
=
"Output directory"
,
fullName
=
"output_directory"
,
shortName
=
"outDir"
,
required
=
true
)
var
outputDir
:
String
=
_
@Argument
(
doc
=
"
Use scatter defaults, env value BIOPET_CONFIG_SCATTER
"
,
shortName
=
"SC"
,
required
=
false
)
var
us
eScatterDefault
:
Boolean
=
false
@Argument
(
doc
=
"
Disable all scatters
"
,
shortName
=
"
D
SC"
,
required
=
false
)
var
disabl
eScatterDefault
:
Boolean
=
false
var
outputFiles
:
Map
[
String
,
File
]
=
Map
()
...
...
@@ -28,10 +29,14 @@ trait BiopetQScript extends Configurable {
var
functions
:
Seq
[
QFunction
]
final
def
script
()
{
if
(
useScatterDefault
)
Config
.
global
.
loadDefaultScatterConfig
if
(!
outputDir
.
endsWith
(
"/"
))
outputDir
+=
"/"
init
biopetScript
if
(
disableScatterDefault
)
for
(
function
<-
functions
)
function
match
{
case
f
:
ScatterGatherableFunction
=>
f
.
scatterCount
=
1
case
_
=>
}
for
(
function
<-
functions
)
function
match
{
case
f
:
BiopetCommandLineFunctionTrait
=>
f
.
afterGraph
case
_
=>
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
View file @
e3df8cc5
...
...
@@ -28,10 +28,6 @@ class Config(var map: Map[String, Any]) extends Logging {
loadConfigEnv
(
"BIOPET_CONFIG"
)
}
def
loadDefaultScatterConfig
()
{
loadConfigEnv
(
"BIOPET_CONFIG_SCATTER"
)
}
def
loadConfigFile
(
configFile
:
File
)
{
logger
.
debug
(
"Jsonfile: "
+
configFile
)
val
jsonText
=
scala
.
io
.
Source
.
fromFile
(
configFile
).
mkString
...
...
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