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biopet.biopet
Commits
31a835a1
Commit
31a835a1
authored
Dec 21, 2015
by
Peter van 't Hof
Browse files
Added files to summary
parent
7501f792
Changes
1
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public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMapping.scala
View file @
31a835a1
...
...
@@ -35,7 +35,7 @@ class MultisampleMapping(val root: Configurable) extends QScript
}
def
biopetScript
:
Unit
=
{
addSamplesJobs
()
// This executes jobs for all samples
addSamplesJobs
()
addSummaryJobs
()
}
...
...
@@ -47,14 +47,16 @@ class MultisampleMapping(val root: Configurable) extends QScript
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
()
def
summarySettings
:
Map
[
String
,
Any
]
=
Map
()
def
summarySettings
:
Map
[
String
,
Any
]
=
Map
(
"merge_strategy"
->
mergeStrategy
.
toString
)
def
makeSample
(
id
:
String
)
=
new
Sample
(
id
)
class
Sample
(
sampleId
:
String
)
extends
AbstractSample
(
sampleId
)
{
def
makeLibrary
(
id
:
String
)
=
new
Library
(
id
)
class
Library
(
libId
:
String
)
extends
AbstractLibrary
(
libId
)
{
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
()
def
summaryFiles
:
Map
[
String
,
File
]
=
(
inputR1
.
map
(
"input_R1"
->
_
)
::
inputR2
.
map
(
"input_R2"
->
_
)
::
inputBam
.
map
(
"input_bam"
->
_
)
::
bamFile
.
map
(
"output_bam"
->
_
)
::
preProcessBam
.
map
(
"output_preProcessBam"
->
_
)
::
Nil
).
flatten
.
toMap
def
summaryStats
:
Map
[
String
,
Any
]
=
Map
()
...
...
@@ -145,7 +147,8 @@ class MultisampleMapping(val root: Configurable) extends QScript
}
}
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
()
def
summaryFiles
:
Map
[
String
,
File
]
=
(
bamFile
.
map
(
"output_bam"
->
_
)
::
preProcessBam
.
map
(
"output_preProcessBam"
->
_
)
::
Nil
).
flatten
.
toMap
def
summaryStats
:
Map
[
String
,
Any
]
=
Map
()
...
...
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