Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Mirrors
biopet.biopet
Commits
9d0b9d7e
Commit
9d0b9d7e
authored
Jan 04, 2017
by
Peter van 't Hof
Browse files
Fix format
parent
b632a8b4
Changes
3
Hide whitespace changes
Inline
Side-by-side
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
))
}
}
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment