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biopet.biopet
Commits
a3009b39
Commit
a3009b39
authored
Jan 15, 2016
by
bow
Browse files
Unify output bam names
parent
9e62862f
Changes
2
Hide whitespace changes
Inline
Side-by-side
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
a3009b39
...
...
@@ -107,7 +107,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
)
/** File to add to the summary */
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
(
"output_bam
file
"
->
finalBamFile
,
"input_R1"
->
input_R1
,
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
(
"output_bam"
->
finalBamFile
,
"input_R1"
->
input_R1
,
"reference"
->
referenceFasta
())
++
(
if
(
input_R2
.
isDefined
)
Map
(
"input_R2"
->
input_R2
.
get
)
else
Map
())
...
...
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTrait.scala
View file @
a3009b39
...
...
@@ -62,7 +62,7 @@ trait MultisampleMappingTrait extends MultiSampleQScript
class
Library
(
libId
:
String
)
extends
AbstractLibrary
(
libId
)
{
def
summaryFiles
:
Map
[
String
,
File
]
=
(
inputR1
.
map
(
"input_R1"
->
_
)
::
inputR2
.
map
(
"input_R2"
->
_
)
::
inputBam
.
map
(
"input_bam"
->
_
)
::
bamFile
.
map
(
"output_bam"
->
_
)
::
preProcessBam
.
map
(
"output_pre
P
rocess
Bam
"
->
_
)
::
Nil
).
flatten
.
toMap
preProcessBam
.
map
(
"output_
bam_
pre
p
rocess"
->
_
)
::
Nil
).
flatten
.
toMap
def
summaryStats
:
Map
[
String
,
Any
]
=
Map
()
...
...
@@ -159,7 +159,7 @@ trait MultisampleMappingTrait extends MultiSampleQScript
}
def
summaryFiles
:
Map
[
String
,
File
]
=
(
bamFile
.
map
(
"output_bam"
->
_
)
::
preProcessBam
.
map
(
"output_pre
P
rocess
Bam
"
->
_
)
::
Nil
).
flatten
.
toMap
preProcessBam
.
map
(
"output_
bam_
pre
p
rocess"
->
_
)
::
Nil
).
flatten
.
toMap
def
summaryStats
:
Map
[
String
,
Any
]
=
Map
()
...
...
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