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biopet.biopet
Commits
3c8c6fa3
Commit
3c8c6fa3
authored
Jul 27, 2015
by
Peter van 't Hof
Browse files
Fix config error
parent
2d4ea4b7
Changes
1
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public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala
View file @
3c8c6fa3
...
...
@@ -64,7 +64,7 @@ class ShivaSvCalling(val root: Configurable) extends QScript with SummaryQScript
}
/** Variantcallers requested by the config */
protected
val
configCallers
:
Set
[
String
]
=
config
(
"sv_callers"
)
protected
val
configCallers
:
Set
[
String
]
=
config
(
"sv_callers"
,
default
=
Set
(
"breakdancer"
,
"clever"
,
"delly"
)
)
/** This will add jobs for this pipeline */
def
biopetScript
()
:
Unit
=
{
...
...
@@ -148,7 +148,7 @@ class ShivaSvCalling(val root: Configurable) extends QScript with SummaryQScript
/** Files for the summary */
def
summaryFiles
:
Map
[
String
,
File
]
=
{
val
callers
:
Set
[
String
]
=
config
(
"sv_c
allers
"
)
val
callers
:
Set
[
String
]
=
config
C
allers
//callersList.filter(x => callers.contains(x.name)).map(x => x.name -> x.outputFile).toMap + ("final" -> finalFile)
Map
()
}
...
...
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