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biopet.biopet
Commits
0c858996
Commit
0c858996
authored
Aug 26, 2014
by
Peter van 't Hof
Browse files
Replace SortSam to AddOrReplaceReadGroups for Bowtie
parent
337ef542
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
0c858996
...
...
@@ -214,30 +214,26 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
def
addBwa
(
R1
:
File
,
R2
:
File
,
output
:
File
,
deps
:
List
[
File
])
:
File
=
{
val
bwaCommand
=
new
Bwa
(
this
)
bwaCommand
.
R1
=
R1
if
(
paired
)
bwaCommand
.
R2
=
R2
bwaCommand
.
deps
=
deps
bwaCommand
.
R
=
getReadGroup
bwaCommand
.
output
=
this
.
swapExt
(
output
.
getParent
,
output
,
".bam"
,
".sam"
)
add
(
bwaCommand
,
isIntermediate
=
true
)
val
sortSam
=
SortSam
(
this
,
bwaCommand
.
output
,
output
)
if
(
chunking
||
!
skipMarkduplicates
)
sortSam
.
isIntermediate
=
true
add
(
sortSam
)
return
sortSam
.
output
bwaCommand
.
R1
=
R1
if
(
paired
)
bwaCommand
.
R2
=
R2
bwaCommand
.
deps
=
deps
bwaCommand
.
R
=
getReadGroup
bwaCommand
.
output
=
this
.
swapExt
(
output
.
getParent
,
output
,
".bam"
,
".sam"
)
add
(
bwaCommand
,
isIntermediate
=
true
)
val
sortSam
=
SortSam
(
this
,
bwaCommand
.
output
,
output
)
if
(
chunking
||
!
skipMarkduplicates
)
sortSam
.
isIntermediate
=
true
add
(
sortSam
)
return
sortSam
.
output
}
def
addBowtie
(
R1
:
File
,
R2
:
File
,
output
:
File
,
deps
:
List
[
File
])
:
File
=
{
val
bowtie
=
new
Bowtie
(
this
)
bowtie
.
R1
=
R1
if
(
paired
)
bowtie
.
R2
=
R2
bowtie
.
deps
=
deps
bowtie
.
sam_RG
=
getReadGroup
bowtie
.
output
=
this
.
swapExt
(
output
.
getParent
,
output
,
".bam"
,
".sam"
)
add
(
bowtie
,
isIntermediate
=
true
)
val
sortSam
=
SortSam
(
this
,
bowtie
.
output
,
output
)
if
(
chunking
||
!
skipMarkduplicates
)
sortSam
.
isIntermediate
=
true
add
(
sortSam
)
return
sortSam
.
output
bowtie
.
R1
=
R1
if
(
paired
)
bowtie
.
R2
=
R2
bowtie
.
deps
=
deps
bowtie
.
output
=
this
.
swapExt
(
output
.
getParent
,
output
,
".bam"
,
".sam"
)
add
(
bowtie
,
isIntermediate
=
true
)
return
addAddOrReplaceReadGroups
(
bowtie
.
output
,
output
)
}
def
addStar
(
R1
:
File
,
R2
:
File
,
output
:
File
,
deps
:
List
[
File
])
:
File
=
{
...
...
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