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biopet.biopet
Commits
3835e14b
Commit
3835e14b
authored
Jul 18, 2017
by
pjvan_thof
Browse files
Fix compile errors
parent
8f9236a6
Changes
4
Hide whitespace changes
Inline
Side-by-side
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/TemplateTool.scala
View file @
3835e14b
...
...
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.core
import
java.io.
{
File
,
PrintWriter
}
import
nl.lumc.sasc.biopet.utils.summary.Summary
import
nl.lumc.sasc.biopet.utils.
{
ConfigUtils
,
Question
,
ToolCommand
}
import
nl.lumc.sasc.biopet.utils.
{
AbstractOptParser
,
ConfigUtils
,
Question
,
ToolCommand
}
import
scala.io.Source
...
...
@@ -30,9 +30,8 @@ trait TemplateTool extends ToolCommand {
runScript
:
Option
[
File
]
=
None
,
expert
:
Boolean
=
false
,
template
:
Option
[
File
]
=
None
)
extends
AbstractArgs
class
OptParser
extends
AbstractOptParser
{
class
OptParser
extends
AbstractOptParser
[
Args
](
commandName
)
{
opt
[
File
](
'o'
,
"outputConfig"
)
required
()
valueName
"<file>"
action
{
(
x
,
c
)
=>
c
.
copy
(
outputConfig
=
x
)
}
text
"Path to output config"
...
...
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/pipelinestatus/PipelineStatus.scala
View file @
3835e14b
...
...
@@ -20,7 +20,7 @@ import akka.actor.ActorSystem
import
akka.stream.ActorMaterializer
import
nl.lumc.sasc.biopet.utils.pim._
import
nl.lumc.sasc.biopet.utils.pim.
{
Job
=>
PimJob
}
import
nl.lumc.sasc.biopet.utils.
{
ConfigUtils
,
ToolCommand
}
import
nl.lumc.sasc.biopet.utils.
{
AbstractOptParser
,
ConfigUtils
,
ToolCommand
}
import
play.api.libs.ws.ahc.AhcWSClient
import
scala.concurrent.ExecutionContext.Implicits.global
...
...
@@ -41,9 +41,8 @@ object PipelineStatus extends ToolCommand {
compressPlots
:
Boolean
=
true
,
pimHost
:
Option
[
String
]
=
None
,
pimRunId
:
Option
[
String
]
=
None
)
extends
AbstractArgs
class
OptParser
extends
AbstractOptParser
{
class
OptParser
extends
AbstractOptParser
[
Args
](
commandName
)
{
opt
[
File
](
'd'
,
"pipelineDir"
)
required
()
maxOccurs
1
valueName
"<file>"
action
{
(
x
,
c
)
=>
c
.
copy
(
pipelineDir
=
x
)
}
text
"Output directory of the pipeline"
...
...
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
View file @
3835e14b
...
...
@@ -17,10 +17,10 @@ package nl.lumc.sasc.biopet.core.report
import
java.io._
import
nl.lumc.sasc.biopet.core.ToolCommandFunction
import
nl.lumc.sasc.biopet.utils.summary.db.Schema.
{
Library
,
Module
,
Pipeline
,
Sample
,
Run
}
import
nl.lumc.sasc.biopet.utils.summary.db.Schema.
{
Library
,
Module
,
Pipeline
,
Run
,
Sample
}
import
nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
import
nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.
{
LibraryId
,
SampleId
}
import
nl.lumc.sasc.biopet.utils.
{
IoUtils
,
Logging
,
ToolCommand
}
import
nl.lumc.sasc.biopet.utils.
{
AbstractOptParser
,
IoUtils
,
Logging
,
ToolCommand
}
import
org.broadinstitute.gatk.utils.commandline.Input
import
org.fusesource.scalate.TemplateEngine
...
...
@@ -82,9 +82,8 @@ trait ReportBuilder extends ToolCommand {
outputDir
:
File
=
null
,
runId
:
Int
=
0
,
pageArgs
:
mutable.Map
[
String
,
Any
]
=
mutable
.
Map
())
extends
AbstractArgs
class
OptParser
extends
AbstractOptParser
{
class
OptParser
extends
AbstractOptParser
[
Args
](
commandName
)
{
head
(
s
"""
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/VcfStatsOptParser.scala
View file @
3835e14b
...
...
@@ -2,7 +2,12 @@ package nl.lumc.sasc.biopet.tools.vcfstats
import
java.io.File
import
nl.lumc.sasc.biopet.tools.vcfstats.VcfStats.
{
defaultGenotypeFields
,
defaultInfoFields
,
generalWiggleOptions
,
genotypeWiggleOptions
}
import
nl.lumc.sasc.biopet.tools.vcfstats.VcfStats.
{
defaultGenotypeFields
,
defaultInfoFields
,
generalWiggleOptions
,
genotypeWiggleOptions
}
import
nl.lumc.sasc.biopet.utils.AbstractOptParser
/**
...
...
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