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biopet.biopet
Commits
0477ae44
Commit
0477ae44
authored
Mar 14, 2016
by
Peter van 't Hof
Browse files
Added and remove tools from executable
parent
24aa443b
Changes
1
Hide whitespace changes
Inline
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public/biopet-tools-package/src/main/scala/nl/lumc/sasc/biopet/BiopetToolsExecutable.scala
View file @
0477ae44
...
...
@@ -22,30 +22,31 @@ object BiopetToolsExecutable extends BiopetExecutable {
def
pipelines
:
List
[
MainCommand
]
=
Nil
def
tools
:
List
[
MainCommand
]
=
List
(
nl
.
lumc
.
sasc
.
biopet
.
tools
.
MergeTables
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
WipeReads
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
ExtractAligned
Fast
q
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
FastqSync
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
AnnotateVcfWithBed
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
BaseCounter
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
BastyGenerate
Fast
a
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
BedtoolsCoverageToCounts
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
BiopetFlagstat
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
CheckAllelesVcfInBam
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
VcfToTsv
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
VcfFilter
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
VcfStats
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
BaseCounter
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
ExtractAlignedFastq
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
FastqSplitter
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
FastqSync
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
FindRepeatsPacBio
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
GvcfToBed
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
MergeAlleles
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
MergeTables
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
MpileupToVcf
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
FastqSplitter
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
BedtoolsCoverageToCounts
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
PrefixFastq
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
SageCountFastq
,
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
.
SamplesTsvToJson
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
SeqStat
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
VepNormalizer
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
AnnotateVcfWithBed
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
VcfWithVcf
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
SquishBed
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
SummaryToTsv
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
ValidateFastq
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
KrakenReportToJson
)
nl
.
lumc
.
sasc
.
biopet
.
tools
.
VcfFilter
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
VcfStats
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
VcfToTsv
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
VcfWithVcf
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
VepNormalizer
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
WipeReads
)
}
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