Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Mirrors
biopet.biopet
Commits
73995acb
Commit
73995acb
authored
Feb 26, 2015
by
Peter van 't Hof
Browse files
Updated Executable
parent
51f729f1
Changes
4
Hide whitespace changes
Inline
Side-by-side
protected/biopet-protected-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutableProtected.scala
View file @
73995acb
...
...
@@ -7,12 +7,12 @@ package nl.lumc.sasc.biopet.core
object
BiopetExecutableProtected
extends
BiopetExecutable
{
def
pipelines
:
List
[
MainCommand
]
=
BiopetExecutablePublic
.
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
.
ShivaGatk
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
gatk
.
ShivaVariantcallingGatk
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
basty
.
Basty
)
def
tools
=
BiopetExecutablePublic
.
tools
...
...
public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutablePublic.scala
View file @
73995acb
...
...
@@ -27,7 +27,8 @@ object BiopetExecutablePublic extends BiopetExecutable {
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
kopisu
.
ConiferPipeline
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
carp
.
Carp
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
toucan
.
Toucan
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
shiva
.
Shiva
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
shiva
.
Shiva
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
shiva
.
ShivaVariantcalling
)
def
tools
:
List
[
MainCommand
]
=
List
(
...
...
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
View file @
73995acb
...
...
@@ -193,7 +193,6 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
addAll
(
bamMetrics
.
functions
)
addSummaryQScript
(
bamMetrics
)
if
(
config
(
"single_sample_variantcalling"
,
default
=
false
).
asBoolean
)
{
val
vc
=
makeVariantcalling
(
multisample
=
false
)
vc
.
sampleId
=
Some
(
sampleId
)
...
...
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
View file @
73995acb
...
...
@@ -5,7 +5,7 @@ import java.io.File
import
nl.lumc.sasc.biopet.core.
{
PipelineCommand
,
SampleLibraryTag
}
import
nl.lumc.sasc.biopet.core.summary.SummaryQScript
import
nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
import
nl.lumc.sasc.biopet.tools.
{
VcfStats
,
VcfFilter
,
MpileupToVcf
}
import
nl.lumc.sasc.biopet.tools.
{
VcfStats
,
VcfFilter
,
MpileupToVcf
}
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
org.broadinstitute.gatk.utils.commandline.Input
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment