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biopet.biopet
Commits
9d0b9d7e
Commit
9d0b9d7e
authored
Jan 04, 2017
by
Peter van 't Hof
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Fix format
parent
b632a8b4
Changes
3
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3 changed files
with
10 additions
and
10 deletions
+10
-10
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/TemplateTool.scala
...rc/main/scala/nl/lumc/sasc/biopet/core/TemplateTool.scala
+3
-4
biopet-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutableMain.scala
...main/scala/nl/lumc/sasc/biopet/BiopetExecutableMain.scala
+2
-1
gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/template/Gentrap.scala
...lumc/sasc/biopet/pipelines/gentrap/template/Gentrap.scala
+5
-5
No files found.
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/TemplateTool.scala
View file @
9d0b9d7e
package
nl.lumc.sasc.biopet.core
import
java.io.
{
File
,
PrintWriter
}
import
java.io.
{
File
,
PrintWriter
}
import
nl.lumc.sasc.biopet.utils.config.Config
import
nl.lumc.sasc.biopet.utils.summary.Summary
import
nl.lumc.sasc.biopet.utils.
{
ConfigUtils
,
Question
,
ToolCommand
}
import
nl.lumc.sasc.biopet.utils.
{
ConfigUtils
,
Question
,
ToolCommand
}
import
scala.io.Source
...
...
@@ -58,7 +57,7 @@ trait TemplateTool extends ToolCommand {
case
Some
(
f
)
=>
f
case
_
=>
sys
.
env
.
get
(
"BIOPET_SCRIPT_TEMPLATE"
)
match
{
case
Some
(
file
)
=>
new
File
(
file
)
case
_
=>
throw
new
IllegalArgumentException
(
"No template found on argument or 'BIOPET_SCRIPT_TEMPLATE'"
)
case
_
=>
throw
new
IllegalArgumentException
(
"No template found on argument or 'BIOPET_SCRIPT_TEMPLATE'"
)
}
}
...
...
biopet-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutableMain.scala
View file @
9d0b9d7e
...
...
@@ -46,6 +46,7 @@ object BiopetExecutableMain extends BiopetExecutable {
def
templates
:
List
[
MainCommand
]
=
List
(
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
mapping
.
template
.
MultiSampleMapping
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
shiva
.
template
.
Shiva
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
shiva
.
template
.
Shiva
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
gentrap
.
template
.
Gentrap
)
}
gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/template/Gentrap.scala
View file @
9d0b9d7e
...
...
@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.pipelines.gentrap.template
import
java.io.File
import
nl.lumc.sasc.biopet.core.TemplateTool
import
nl.lumc.sasc.biopet.pipelines.gentrap.Gentrap.
{
ExpMeasures
,
StrandProtocol
}
import
nl.lumc.sasc.biopet.pipelines.gentrap.Gentrap.
{
ExpMeasures
,
StrandProtocol
}
import
nl.lumc.sasc.biopet.pipelines.mapping.template.MultiSampleMapping
import
nl.lumc.sasc.biopet.pipelines.shiva.template.Shiva
import
nl.lumc.sasc.biopet.utils._
...
...
@@ -43,10 +43,10 @@ object Gentrap extends TemplateTool {
"strand_protocol"
->
strandProtocol
,
"annotation_refflat"
->
annotationRefFlat
)
++
(
if
(
Question
.
boolean
(
"Call variants"
))
{
val
variantCallers
=
Question
.
list
(
"Variantcallers"
,
posibleValues
=
Shiva
.
possibleVariantcallers
,
default
=
Some
(
List
(
"varscan_cns_singlesample"
)))
val
variantCallers
=
Question
.
list
(
"Variantcallers"
,
posibleValues
=
Shiva
.
possibleVariantcallers
,
default
=
Some
(
List
(
"varscan_cns_singlesample"
)))
Map
(
"call_variants"
->
true
,
"variantcallers"
->
variantCallers
)
}
else
Map
(
"call_variants"
->
false
))
Map
(
"call_variants"
->
true
,
"variantcallers"
->
variantCallers
)
}
else
Map
(
"call_variants"
->
false
))
}
}
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