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biopet.biopet
Commits
c4c8292b
Commit
c4c8292b
authored
Sep 13, 2015
by
Peter van 't Hof
Browse files
Move abstract commandlines function for Rscript and Python
parent
806133cd
Changes
8
Hide whitespace changes
Inline
Side-by-side
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/PythonCommandLineFunction.scala
→
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/
core/
extensions/PythonCommandLineFunction.scala
View file @
c4c8292b
...
...
@@ -13,9 +13,9 @@
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package
nl.lumc.sasc.biopet.extensions
package
nl.lumc.sasc.biopet.
core.
extensions
import
java.io.
{
File
,
FileOutputStream
}
import
java.io.
{
File
,
FileOutputStream
}
import
nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import
org.broadinstitute.gatk.utils.commandline.Input
...
...
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/RscriptCommandLineFunction.scala
→
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/
core/
extensions/RscriptCommandLineFunction.scala
View file @
c4c8292b
...
...
@@ -13,9 +13,9 @@
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package
nl.lumc.sasc.biopet.extensions
package
nl.lumc.sasc.biopet.
core.
extensions
import
java.io.
{
File
,
FileOutputStream
}
import
java.io.
{
File
,
FileOutputStream
}
import
nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
...
...
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala
View file @
c4c8292b
...
...
@@ -17,8 +17,8 @@ package nl.lumc.sasc.biopet.extensions.breakdancer
import
java.io.File
import
nl.lumc.sasc.biopet.core.extensions.PythonCommandLineFunction
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.extensions.PythonCommandLineFunction
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
class
BreakdancerVCF
(
val
root
:
Configurable
)
extends
PythonCommandLineFunction
{
...
...
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala
View file @
c4c8292b
...
...
@@ -15,7 +15,7 @@
*/
package
nl.lumc.sasc.biopet.extensions.conifer
import
nl.lumc.sasc.biopet.extensions.PythonCommandLineFunction
import
nl.lumc.sasc.biopet.
core.
extensions.PythonCommandLineFunction
abstract
class
Conifer
extends
PythonCommandLineFunction
{
override
def
subPath
=
"conifer"
::
super
.
subPath
...
...
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/LinePlot.scala
View file @
c4c8292b
...
...
@@ -17,8 +17,8 @@ package nl.lumc.sasc.biopet.extensions.rscript
import
java.io.File
import
nl.lumc.sasc.biopet.core.extensions.RscriptCommandLineFunction
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.extensions.RscriptCommandLineFunction
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
/**
...
...
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/ScatterPlot.scala
View file @
c4c8292b
...
...
@@ -17,8 +17,8 @@ package nl.lumc.sasc.biopet.extensions.rscript
import
java.io.File
import
nl.lumc.sasc.biopet.core.extensions.RscriptCommandLineFunction
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.extensions.RscriptCommandLineFunction
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
/**
...
...
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/StackedBarPlot.scala
View file @
c4c8292b
...
...
@@ -17,8 +17,8 @@ package nl.lumc.sasc.biopet.extensions.rscript
import
java.io.File
import
nl.lumc.sasc.biopet.core.extensions.RscriptCommandLineFunction
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.extensions.RscriptCommandLineFunction
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
/**
...
...
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/scripts/CoverageStats.scala
View file @
c4c8292b
...
...
@@ -17,9 +17,9 @@ package nl.lumc.sasc.biopet.scripts
import
java.io.File
import
nl.lumc.sasc.biopet.core.extensions.PythonCommandLineFunction
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.core.summary.Summarizable
import
nl.lumc.sasc.biopet.extensions.PythonCommandLineFunction
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
...
...
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