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biopet.biopet
Commits
e671341e
Commit
e671341e
authored
Nov 22, 2014
by
Peter van 't Hof
Browse files
Protected copy content from public
parent
5a474415
Changes
4
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protected/biopet-protected-package/pom.xml
View file @
e671341e
...
...
@@ -25,6 +25,11 @@
<artifactId>
BiopetFramework
</artifactId>
<version>
0.2.0-DEV
</version>
</dependency>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
BiopetPublicPackage
</artifactId>
<version>
0.2.0-DEV
</version>
</dependency>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
BiopetGatkPipelines
</artifactId>
...
...
protected/biopet-protected-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutableProtected.scala
View file @
e671341e
package
nl.lumc.sasc.biopet.core
object
BiopetExecutableProtected
extends
BiopetExecutable
{
lazy
val
pipelines
:
List
[
MainCommand
]
=
List
(
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
flexiprep
.
Flexiprep
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
mapping
.
Mapping
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
gentrap
.
Gentrap
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
bammetrics
.
BamMetrics
,
trait
BiopetExecutableProtected
extends
BiopetExecutablePublic
{
override
def
pipelines
:
List
[
MainCommand
]
=
super
.
pipelines
:::
List
(
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
gatk
.
GatkBenchmarkGenotyping
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
gatk
.
GatkGenotyping
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
gatk
.
GatkVariantcalling
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
gatk
.
GatkPipeline
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
gatk
.
GatkVariantRecalibration
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
gatk
.
GatkVcfSampleCompare
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
sage
.
Sage
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
basty
.
Basty
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
yamsvp
.
Yamsvp
)
lazy
val
tools
:
List
[
MainCommand
]
=
List
(
nl
.
lumc
.
sasc
.
biopet
.
tools
.
WipeReads
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
ExtractAlignedFastq
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
BiopetFlagstat
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
CheckAllelesVcfInBam
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
VcfToTsv
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
VcfFilter
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
FindRepeatsPacBio
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
BedToInterval
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
MpileupToVcf
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
FastqSplitter
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
BedtoolsCoverageToCounts
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
SageCountFastq
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
SageCreateLibrary
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
SageCreateTagCounts
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
BastyGenerateFasta
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
MergeAlleles
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
SamplesTsvToJson
)
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
basty
.
Basty
)
}
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala
View file @
e671341e
...
...
@@ -5,9 +5,9 @@ import org.apache.log4j.Logger
trait
BiopetExecutable
extends
Logging
{
val
pipelines
:
List
[
MainCommand
]
def
pipelines
:
List
[
MainCommand
]
val
tools
:
List
[
MainCommand
]
def
tools
:
List
[
MainCommand
]
val
modules
:
Map
[
String
,
List
[
MainCommand
]]
=
Map
(
"pipeline"
->
pipelines
,
...
...
public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutablePublic.scala
View file @
e671341e
package
nl.lumc.sasc.biopet.core
objec
t
BiopetExecutablePublic
extends
BiopetExecutable
{
lazy
val
pipelines
:
List
[
MainCommand
]
=
List
(
trai
t
BiopetExecutablePublic
extends
BiopetExecutable
{
def
pipelines
:
List
[
MainCommand
]
=
List
(
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
flexiprep
.
Flexiprep
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
mapping
.
Mapping
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
gentrap
.
Gentrap
,
...
...
@@ -9,7 +9,7 @@ object BiopetExecutablePublic extends BiopetExecutable {
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
sage
.
Sage
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
yamsvp
.
Yamsvp
)
lazy
val
tools
:
List
[
MainCommand
]
=
List
(
def
tools
:
List
[
MainCommand
]
=
List
(
nl
.
lumc
.
sasc
.
biopet
.
tools
.
WipeReads
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
ExtractAlignedFastq
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
BiopetFlagstat
,
...
...
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