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biopet.biopet
Commits
7f424eb9
Commit
7f424eb9
authored
Nov 19, 2015
by
Peter van 't Hof
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Fixed bug in loading the mainClass for biopet tools
parent
74f301a6
Changes
10
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10 changed files
with
11 additions
and
14 deletions
+11
-14
public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
...c/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
+1
-1
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommandFunction.scala
.../scala/nl/lumc/sasc/biopet/core/ToolCommandFunction.scala
+1
-4
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
...scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
+1
-1
public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/ToolCommandTest.scala
...test/scala/nl/lumc/sasc/biopet/core/ToolCommandTest.scala
+2
-2
public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpReport.scala
...scala/nl/lumc/sasc/biopet/pipelines/carp/CarpReport.scala
+1
-1
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
...umc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
+1
-1
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
...ala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
+1
-1
public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapReport.scala
...nl/lumc/sasc/biopet/pipelines/gentrap/GentrapReport.scala
+1
-1
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingReport.scala
...nl/lumc/sasc/biopet/pipelines/mapping/MappingReport.scala
+1
-1
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
...ala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
+1
-1
No files found.
public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
View file @
7f424eb9
...
...
@@ -23,7 +23,7 @@ import nl.lumc.sasc.biopet.utils.summary.{ Summary, SummaryValue }
import
nl.lumc.sasc.biopet.utils.rscript.
{
StackedBarPlot
,
LinePlot
}
class
BammetricsReport
(
val
root
:
Configurable
)
extends
ReportBuilderExtension
{
val
builder
=
BammetricsReport
def
builder
=
BammetricsReport
}
/**
...
...
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommandFunction.scala
View file @
7f424eb9
...
...
@@ -13,8 +13,5 @@ trait ToolCommandFunction extends BiopetJavaCommandLineFunction with Version {
override
def
getVersion
=
Some
(
"Biopet "
+
FullVersion
)
override
def
beforeGraph
()
:
Unit
=
{
javaMainClass
=
toolObject
.
getClass
.
getName
.
takeWhile
(
_
!=
'$'
)
super
.
beforeGraph
()
}
javaMainClass
=
toolObject
.
getClass
.
getName
.
takeWhile
(
_
!=
'$'
)
}
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
View file @
7f424eb9
...
...
@@ -33,7 +33,7 @@ import scala.collection.mutable
trait
ReportBuilderExtension
extends
ToolCommandFunction
{
/** Report builder object */
val
builder
:
ReportBuilder
def
builder
:
ReportBuilder
def
toolObject
=
builder
...
...
public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/ToolCommandTest.scala
View file @
7f424eb9
...
...
@@ -12,8 +12,8 @@ class ToolCommandTest extends TestNGSuite with Matchers {
@Test
def
testToolCommand
:
Unit
=
{
val
tool
=
new
ToolCommandFunction
{
val
root
=
null
val
toolObject
=
ToolCommandTest
def
root
=
null
def
toolObject
=
ToolCommandTest
}
tool
.
versionCommand
shouldBe
empty
...
...
public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpReport.scala
View file @
7f424eb9
...
...
@@ -26,7 +26,7 @@ import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
* Created by pjvanthof on 25/06/15.
*/
class
CarpReport
(
val
root
:
Configurable
)
extends
ReportBuilderExtension
{
val
builder
=
CarpReport
def
builder
=
CarpReport
}
object
CarpReport
extends
MultisampleReportBuilder
{
...
...
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
View file @
7f424eb9
...
...
@@ -23,7 +23,7 @@ import nl.lumc.sasc.biopet.utils.rscript.StackedBarPlot
import
nl.lumc.sasc.biopet.utils.summary.
{
Summary
,
SummaryValue
}
class
FlexiprepReport
(
val
root
:
Configurable
)
extends
ReportBuilderExtension
{
val
builder
=
FlexiprepReport
def
builder
=
FlexiprepReport
}
/**
...
...
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
View file @
7f424eb9
...
...
@@ -4,7 +4,7 @@ import nl.lumc.sasc.biopet.core.report._
import
nl.lumc.sasc.biopet.utils.config.Configurable
class
GearsReport
(
val
root
:
Configurable
)
extends
ReportBuilderExtension
{
val
builder
=
GearsReport
def
builder
=
GearsReport
}
object
GearsReport
extends
ReportBuilder
{
...
...
public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapReport.scala
View file @
7f424eb9
...
...
@@ -26,7 +26,7 @@ import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
* Created by pjvanthof on 25/06/15.
*/
class
GentrapReport
(
val
root
:
Configurable
)
extends
ReportBuilderExtension
{
val
builder
=
GentrapReport
def
builder
=
GentrapReport
}
object
GentrapReport
extends
MultisampleReportBuilder
{
...
...
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingReport.scala
View file @
7f424eb9
...
...
@@ -21,7 +21,7 @@ import nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport
import
nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
class
MappingReport
(
val
root
:
Configurable
)
extends
ReportBuilderExtension
{
val
builder
=
MappingReport
def
builder
=
MappingReport
}
/**
...
...
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
View file @
7f424eb9
...
...
@@ -30,7 +30,7 @@ import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
* Created by pjvan_thof on 3/30/15.
*/
class
ShivaReport
(
val
root
:
Configurable
)
extends
ReportBuilderExtension
{
val
builder
=
ShivaReport
def
builder
=
ShivaReport
}
/** Object for report generation for Shiva pipeline */
...
...
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