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biopet.biopet
Commits
2387d560
Commit
2387d560
authored
Sep 23, 2015
by
Peter van 't Hof
Browse files
Remove intermediate
parent
e40baa30
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
2387d560
...
...
@@ -333,7 +333,6 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
if
(
paired
)
bwaCommand
.
R2
=
R2
.
get
bwaCommand
.
deps
=
deps
bwaCommand
.
R
=
Some
(
getReadGroupBwa
)
bwaCommand
.
isIntermediate
=
true
val
sortSam
=
new
SortSam
(
this
)
sortSam
.
output
=
output
add
(
bwaCommand
|
sortSam
,
chunking
||
!
skipMarkduplicates
)
...
...
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