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biopet.biopet
Commits
fa4b60f8
Commit
fa4b60f8
authored
Jan 06, 2016
by
Peter van 't Hof
Browse files
Fixed typo
parent
4143a145
Changes
1
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Inline
Side-by-side
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTrait.scala
View file @
fa4b60f8
...
...
@@ -58,9 +58,9 @@ trait MultisampleMappingTrait extends MultiSampleQScript
def
summaryStats
:
Map
[
String
,
Any
]
=
Map
()
lazy
val
inputR1
:
Option
[
File
]
=
MultisampleMapping
.
fileMustBeAbs
u
lute
(
config
(
"R1"
))
lazy
val
inputR2
:
Option
[
File
]
=
MultisampleMapping
.
fileMustBeAbs
u
lute
(
config
(
"R2"
))
lazy
val
inputBam
:
Option
[
File
]
=
MultisampleMapping
.
fileMustBeAbs
u
lute
(
if
(
inputR1
.
isEmpty
)
config
(
"bam"
)
else
None
)
lazy
val
inputR1
:
Option
[
File
]
=
MultisampleMapping
.
fileMustBeAbs
o
lute
(
config
(
"R1"
))
lazy
val
inputR2
:
Option
[
File
]
=
MultisampleMapping
.
fileMustBeAbs
o
lute
(
config
(
"R2"
))
lazy
val
inputBam
:
Option
[
File
]
=
MultisampleMapping
.
fileMustBeAbs
o
lute
(
if
(
inputR1
.
isEmpty
)
config
(
"bam"
)
else
None
)
lazy
val
bamToFastq
:
Boolean
=
config
(
"bam_to_fastq"
,
default
=
false
)
lazy
val
correctReadgroups
:
Boolean
=
config
(
"correct_readgroups"
,
default
=
false
)
...
...
@@ -207,7 +207,7 @@ object MultisampleMapping extends PipelineCommand {
val
None
,
MergeSam
,
MarkDuplicates
,
PreProcessMergeSam
,
PreProcessMarkDuplicates
=
Value
}
def
fileMustBeAbs
u
lute
(
file
:
Option
[
File
])
:
Option
[
File
]
=
{
def
fileMustBeAbs
o
lute
(
file
:
Option
[
File
])
:
Option
[
File
]
=
{
if
(
file
.
forall
(
_
.
isAbsolute
))
file
else
{
Logging
.
addError
(
s
"$file should be a absolute file path"
)
...
...
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