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biopet.biopet
Commits
f3343df9
Commit
f3343df9
authored
Sep 13, 2015
by
Peter van 't Hof
Browse files
Fix pipeline without framework
parent
3bf08752
Changes
47
Hide whitespace changes
Inline
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protected/biopet-gatk-extensions/pom.xml
View file @
f3343df9
...
...
@@ -25,7 +25,7 @@
<dependencies>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Biopet
Framework
</artifactId>
<artifactId>
Biopet
Core
</artifactId>
<version>
${project.version}
</version>
</dependency>
<dependency>
...
...
protected/biopet-gatk-pipelines/pom.xml
View file @
f3343df9
...
...
@@ -25,7 +25,7 @@
<dependencies>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Biopet
Framework
</artifactId>
<artifactId>
Biopet
Core
</artifactId>
<version>
${project.version}
</version>
</dependency>
<dependency>
...
...
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
View file @
f3343df9
...
...
@@ -12,7 +12,7 @@ import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
import
nl.lumc.sasc.biopet.extensions.Ln
import
nl.lumc.sasc.biopet.extensions.gatk.broad._
import
nl.lumc.sasc.biopet.extensions.picard.MarkDuplicates
import
nl.lumc.sasc.biopet.tools.
{
MergeAlleles
,
MpileupToVcf
,
VcfFilter
,
VcfStats
}
import
nl.lumc.sasc.biopet.
extensions.
tools.
{
MergeAlleles
,
MpileupToVcf
,
VcfFilter
,
VcfStats
}
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
org.broadinstitute.gatk.queue.QScript
import
org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
...
...
protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala
View file @
f3343df9
...
...
@@ -12,7 +12,7 @@ import nl.lumc.sasc.biopet.utils.config.Config
import
nl.lumc.sasc.biopet.extensions.bwa.BwaMem
import
nl.lumc.sasc.biopet.extensions.gatk.broad._
import
nl.lumc.sasc.biopet.extensions.picard.
{
MarkDuplicates
,
SortSam
}
import
nl.lumc.sasc.biopet.tools.VcfStats
import
nl.lumc.sasc.biopet.
extensions.
tools.VcfStats
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
org.broadinstitute.gatk.queue.QSettings
import
org.scalatest.Matchers
...
...
protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala
View file @
f3343df9
...
...
@@ -11,7 +11,7 @@ import com.google.common.io.Files
import
nl.lumc.sasc.biopet.utils.config.Config
import
nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
import
nl.lumc.sasc.biopet.extensions.gatk.broad.
{
HaplotypeCaller
,
UnifiedGenotyper
}
import
nl.lumc.sasc.biopet.tools.
{
MpileupToVcf
,
VcfFilter
,
VcfStats
}
import
nl.lumc.sasc.biopet.
extensions.
tools.
{
MpileupToVcf
,
VcfFilter
,
VcfStats
}
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
org.apache.commons.io.FileUtils
import
org.broadinstitute.gatk.queue.QSettings
...
...
protected/biopet-protected-package/pom.xml
View file @
f3343df9
...
...
@@ -30,7 +30,7 @@
<dependencies>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Biopet
Framework
</artifactId>
<artifactId>
Biopet
Core
</artifactId>
<version>
${project.version}
</version>
</dependency>
<dependency>
...
...
protected/biopet-protected-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutableProtected.scala
View file @
f3343df9
...
...
@@ -5,7 +5,8 @@
*/
package
nl.lumc.sasc.biopet
import
nl.lumc.sasc.biopet.core.
{
BiopetExecutable
,
MainCommand
}
import
nl.lumc.sasc.biopet.core.BiopetExecutable
import
nl.lumc.sasc.biopet.utils.MainCommand
object
BiopetExecutableProtected
extends
BiopetExecutable
{
def
pipelines
:
List
[
MainCommand
]
=
BiopetExecutablePublic
.
pipelines
:::
List
(
...
...
public/bam2wig/pom.xml
View file @
f3343df9
...
...
@@ -37,7 +37,7 @@
<dependencies>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Biopet
Framework
</artifactId>
<artifactId>
Biopet
Core
</artifactId>
<version>
${project.version}
</version>
</dependency>
</dependencies>
...
...
public/bammetrics/pom.xml
View file @
f3343df9
...
...
@@ -35,7 +35,12 @@
<dependencies>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
BiopetFramework
</artifactId>
<artifactId>
BiopetCore
</artifactId>
<version>
${project.version}
</version>
</dependency>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
BiopetToolsExtensions
</artifactId>
<version>
${project.version}
</version>
</dependency>
<dependency>
...
...
public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
View file @
f3343df9
...
...
@@ -24,7 +24,7 @@ import nl.lumc.sasc.biopet.extensions.bedtools.{ BedtoolsCoverage, BedtoolsInter
import
nl.lumc.sasc.biopet.extensions.picard._
import
nl.lumc.sasc.biopet.extensions.samtools.SamtoolsFlagstat
import
nl.lumc.sasc.biopet.scripts.CoverageStats
import
nl.lumc.sasc.biopet.tools.BiopetFlagstat
import
nl.lumc.sasc.biopet.
extensions.
tools.BiopetFlagstat
import
org.broadinstitute.gatk.queue.QScript
class
BamMetrics
(
val
root
:
Configurable
)
extends
QScript
with
SummaryQScript
with
SampleLibraryTag
{
...
...
public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
View file @
f3343df9
...
...
@@ -19,7 +19,7 @@ import java.io.{ File, PrintWriter }
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.core.report.
{
ReportBuilderExtension
,
ReportBuilder
,
ReportPage
,
ReportSection
}
import
nl.lumc.sasc.biopet.
core
.summary.
{
Summary
,
SummaryValue
}
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
{
...
...
public/bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala
View file @
f3343df9
...
...
@@ -23,7 +23,7 @@ import nl.lumc.sasc.biopet.extensions.bedtools.{ BedtoolsCoverage, BedtoolsInter
import
nl.lumc.sasc.biopet.extensions.picard._
import
nl.lumc.sasc.biopet.extensions.samtools.SamtoolsFlagstat
import
nl.lumc.sasc.biopet.scripts.CoverageStats
import
nl.lumc.sasc.biopet.tools.BiopetFlagstat
import
nl.lumc.sasc.biopet.
extensions.
tools.BiopetFlagstat
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
org.apache.commons.io.FileUtils
import
org.broadinstitute.gatk.queue.QSettings
...
...
public/basty/pom.xml
View file @
f3343df9
...
...
@@ -42,7 +42,7 @@
<dependencies>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Biopet
Framework
</artifactId>
<artifactId>
Biopet
Core
</artifactId>
<version>
${project.version}
</version>
</dependency>
<dependency>
...
...
public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala
View file @
f3343df9
...
...
@@ -25,7 +25,7 @@ import java.io.File
import
nl.lumc.sasc.biopet.core.MultiSampleQScript
import
nl.lumc.sasc.biopet.extensions.
{
Cat
,
Raxml
,
RunGubbins
}
import
nl.lumc.sasc.biopet.pipelines.shiva.
{
Shiva
,
ShivaTrait
}
import
nl.lumc.sasc.biopet.tools.BastyGenerateFasta
import
nl.lumc.sasc.biopet.
extensions.
tools.BastyGenerateFasta
import
nl.lumc.sasc.biopet.utils.ConfigUtils
trait
BastyTrait
extends
MultiSampleQScript
{
...
...
public/biopet-core/pom.xml
View file @
f3343df9
...
...
@@ -41,6 +41,12 @@
<groupId>
org.broadinstitute.gatk
</groupId>
<artifactId>
gatk-queue
</artifactId>
<version>
3.4
</version>
<exclusions>
<exclusion>
<groupId>
org.broadinstitute.gatk
</groupId>
<artifactId>
gsalib
</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>
org.broadinstitute.gatk
</groupId>
...
...
public/biopet-public-package/pom.xml
View file @
f3343df9
...
...
@@ -41,7 +41,7 @@
<dependencies>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Biopet
Framework
</artifactId>
<artifactId>
Biopet
Core
</artifactId>
<version>
${project.version}
</version>
</dependency>
<dependency>
...
...
public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutablePublic.scala
View file @
f3343df9
...
...
@@ -15,7 +15,8 @@
*/
package
nl.lumc.sasc.biopet
import
nl.lumc.sasc.biopet.core.
{
BiopetExecutable
,
MainCommand
}
import
nl.lumc.sasc.biopet.core.BiopetExecutable
import
nl.lumc.sasc.biopet.utils.MainCommand
object
BiopetExecutablePublic
extends
BiopetExecutable
{
def
publicPipelines
:
List
[
MainCommand
]
=
List
(
...
...
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SeqStat.scala
View file @
f3343df9
...
...
@@ -47,7 +47,7 @@ class SeqStat(val root: Configurable) extends ToolCommandFuntion with Summarizab
}
}
object
Seq
s
tat
{
object
Seq
S
tat
{
def
apply
(
root
:
Configurable
,
input
:
File
,
output
:
File
)
:
SeqStat
=
{
val
seqstat
=
new
SeqStat
(
root
)
seqstat
.
input
=
input
...
...
public/carp/pom.xml
View file @
f3343df9
...
...
@@ -35,7 +35,7 @@
<dependencies>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Biopet
Framework
</artifactId>
<artifactId>
Biopet
Core
</artifactId>
<version>
${project.version}
</version>
</dependency>
<dependency>
...
...
public/flexiprep/pom.xml
View file @
f3343df9
...
...
@@ -35,7 +35,12 @@
<dependencies>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
BiopetFramework
</artifactId>
<artifactId>
BiopetCore
</artifactId>
<version>
${project.version}
</version>
</dependency>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
BiopetToolsExtensions
</artifactId>
<version>
${project.version}
</version>
</dependency>
<dependency>
...
...
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