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biopet.biopet
Commits
2c5d1151
Commit
2c5d1151
authored
Oct 08, 2014
by
Peter van 't Hof
Browse files
Automatic class name conversion
parent
16182a89
Changes
13
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biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
View file @
2c5d1151
...
...
@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.core
trait
PipelineCommand
extends
MainCommand
{
val
pipeline
=
""
def
pipeline
=
"
/"
+
getClass
.
getName
.
stripSuffix
(
"$"
).
replaceAll
(
"\\."
,
"/"
)
+
".class
"
def
main
(
args
:
Array
[
String
])
:
Unit
=
{
var
argv
:
Array
[
String
]
=
Array
()
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
View file @
2c5d1151
...
...
@@ -73,8 +73,6 @@ class BamMetrics(val root: Configurable) extends QScript with BiopetQScript {
}
object
BamMetrics
extends
PipelineCommand
{
override
val
pipeline
=
"/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.class"
def
apply
(
root
:
Configurable
,
bamFile
:
File
,
outputDir
:
String
)
:
BamMetrics
=
{
val
bamMetrics
=
new
BamMetrics
(
root
)
bamMetrics
.
inputBam
=
bamFile
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
View file @
2c5d1151
...
...
@@ -55,6 +55,4 @@ class Basty (val root: Configurable) extends QScript with MultiSampleQScript {
}
}
object
Basty
extends
PipelineCommand
{
override
val
pipeline
=
"/nl/lumc/sasc/biopet/pipelines/basty/Basty.class"
}
object
Basty
extends
PipelineCommand
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
View file @
2c5d1151
...
...
@@ -272,6 +272,4 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
}
}
object
Flexiprep
extends
PipelineCommand
{
override
val
pipeline
=
"/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.class"
}
object
Flexiprep
extends
PipelineCommand
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.scala
View file @
2c5d1151
...
...
@@ -58,6 +58,4 @@ class GatkBenchmarkGenotyping(val root: Configurable) extends QScript with Biope
}
}
object
GatkBenchmarkGenotyping
extends
PipelineCommand
{
override
val
pipeline
=
"/nl/lumc/sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.class"
}
object
GatkBenchmarkGenotyping
extends
PipelineCommand
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala
View file @
2c5d1151
...
...
@@ -57,6 +57,4 @@ class GatkGenotyping(val root: Configurable) extends QScript with BiopetQScript
}
}
object
GatkGenotyping
extends
PipelineCommand
{
override
val
pipeline
=
"/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.class"
}
object
GatkGenotyping
extends
PipelineCommand
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
View file @
2c5d1151
...
...
@@ -214,6 +214,4 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
}
}
object
GatkPipeline
extends
PipelineCommand
{
override
val
pipeline
=
"/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.class"
}
object
GatkPipeline
extends
PipelineCommand
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantRecalibration.scala
View file @
2c5d1151
...
...
@@ -73,6 +73,4 @@ class GatkVariantRecalibration(val root: Configurable) extends QScript with Biop
}
}
object
GatkVariantRecalibration
extends
PipelineCommand
{
override
val
pipeline
=
"/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantRecalibration.class"
}
object
GatkVariantRecalibration
extends
PipelineCommand
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
View file @
2c5d1151
...
...
@@ -221,8 +221,6 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
}
object
GatkVariantcalling
extends
PipelineCommand
{
override
val
pipeline
=
"/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.class"
class
ScriptOutput
{
var
bamFiles
:
List
[
File
]
=
_
var
gvcfFile
:
File
=
_
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVcfSampleCompare.scala
View file @
2c5d1151
...
...
@@ -87,6 +87,4 @@ class GatkVcfSampleCompare(val root: Configurable) extends QScript with BiopetQS
}
}
object
GatkVcfSampleCompare
extends
PipelineCommand
{
override
val
pipeline
=
"/nl/lumc/sasc/biopet/pipelines/gatk/GatkVcfSampleCompare.class"
}
object
GatkVcfSampleCompare
extends
PipelineCommand
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
View file @
2c5d1151
...
...
@@ -76,6 +76,4 @@ class Gentrap(val root: Configurable) extends QScript with BiopetQScript {
}
}
object
Gentrap
extends
PipelineCommand
{
override
val
pipeline
=
"/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.class"
}
object
Gentrap
extends
PipelineCommand
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
2c5d1151
...
...
@@ -278,8 +278,6 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
}
object
Mapping
extends
PipelineCommand
{
override
val
pipeline
=
"/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.class"
def
loadFromLibraryConfig
(
root
:
Configurable
,
runConfig
:
Map
[
String
,
Any
],
sampleConfig
:
Map
[
String
,
Any
],
runDir
:
String
)
:
Mapping
=
{
val
mapping
=
new
Mapping
(
root
)
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
View file @
2c5d1151
...
...
@@ -197,6 +197,4 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
}
}
object
Sage
extends
PipelineCommand
{
override
val
pipeline
=
"/nl/lumc/sasc/biopet/pipelines/sage/Sage.class"
}
object
Sage
extends
PipelineCommand
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