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biopet.biopet
Commits
4143a145
Commit
4143a145
authored
Jan 06, 2016
by
Peter van 't Hof
Browse files
Moved summaryFile
parent
6e4327e7
Changes
3
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public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
View file @
4143a145
...
...
@@ -52,7 +52,7 @@ class Carp(val root: Configurable) extends QScript with MultisampleMappingTrait
)
)
override
def
summaryFile
=
new
File
(
outputDir
,
"Carp.summary.json"
)
def
summaryFile
=
new
File
(
outputDir
,
"Carp.summary.json"
)
override
def
makeSample
(
id
:
String
)
=
new
Sample
(
id
)
class
Sample
(
sampleId
:
String
)
extends
super
.
Sample
(
sampleId
)
{
...
...
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTrait.scala
View file @
4143a145
...
...
@@ -41,8 +41,6 @@ trait MultisampleMappingTrait extends MultiSampleQScript
// this code will be executed after all code of all samples is executed
}
def
summaryFile
:
File
=
new
File
(
outputDir
,
"MultisamplePipeline.summary.json"
)
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
(
"referenceFasta"
->
referenceFasta
())
def
summarySettings
:
Map
[
String
,
Any
]
=
Map
(
...
...
@@ -199,6 +197,8 @@ trait MultisampleMappingTrait extends MultiSampleQScript
class
MultisampleMapping
(
val
root
:
Configurable
)
extends
QScript
with
MultisampleMappingTrait
{
def
this
()
=
this
(
null
)
def
summaryFile
:
File
=
new
File
(
outputDir
,
"MultisamplePipeline.summary.json"
)
}
object
MultisampleMapping
extends
PipelineCommand
{
...
...
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
View file @
4143a145
...
...
@@ -154,7 +154,7 @@ trait ShivaTrait extends MultisampleMappingTrait with Reference with TargetRegio
}
/** Location of summary file */
override
def
summaryFile
=
new
File
(
outputDir
,
"Shiva.summary.json"
)
def
summaryFile
=
new
File
(
outputDir
,
"Shiva.summary.json"
)
/** Settings of pipeline for summary */
override
def
summarySettings
=
super
.
summarySettings
++
Map
(
...
...
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