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biopet.biopet
Commits
74efe128
Commit
74efe128
authored
Dec 09, 2014
by
Peter van 't Hof
Browse files
Unmask pipelines and tools
parent
1572cb02
Changes
2
Hide whitespace changes
Inline
Side-by-side
protected/biopet-protected-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutableProtected.scala
View file @
74efe128
...
...
@@ -7,7 +7,7 @@ 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
.
GatkBenchmarkGenotyping
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
gatk
.
GatkGenotyping
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
gatk
.
GatkVariantcalling
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
gatk
.
GatkPipeline
,
...
...
public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutablePublic.scala
View file @
74efe128
...
...
@@ -19,9 +19,9 @@ object 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,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
gentrap
.
Gentrap
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
bammetrics
.
BamMetrics
,
//
nl.lumc.sasc.biopet.pipelines.yamsvp.Yamsvp,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
yamsvp
.
Yamsvp
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
sage
.
Sage
)
...
...
@@ -41,6 +41,6 @@ object BiopetExecutablePublic extends BiopetExecutable {
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
.
MergeAlleles
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
SamplesTsvToJson
)
}
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