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biopet.biopet
Commits
14d93e73
Commit
14d93e73
authored
Mar 02, 2015
by
Peter van 't Hof
Browse files
Added place holders for summary
parent
4dd8d4f0
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
View file @
14d93e73
...
...
@@ -40,10 +40,23 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
def
makeSample
(
id
:
String
)
=
new
Sample
(
id
)
class
Sample
(
sampleId
:
String
)
extends
AbstractSample
(
sampleId
)
{
//TODO: Add summary
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
()
//TODO: Add summary
def
summaryStats
:
Map
[
String
,
Any
]
=
Map
()
def
makeLibrary
(
id
:
String
)
=
new
Library
(
id
)
class
Library
(
libId
:
String
)
extends
AbstractLibrary
(
libId
)
{
//TODO: Add summary
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
()
//TODO: Add summary
def
summaryStats
:
Map
[
String
,
Any
]
=
Map
()
def
preProcess
(
input
:
File
)
:
Option
[
File
]
=
None
def
makeMapping
=
{
...
...
@@ -168,7 +181,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
md
.
outputMetrics
=
new
File
(
sampleDir
,
sampleId
+
".dedup.bam"
)
md
.
isIntermediate
=
isIntermediate
add
(
md
)
addSummarizable
(
md
,
"mark_duplicates"
,
Some
(
sampleId
)
)
addSummarizable
(
md
,
"mark_duplicates"
)
Some
(
md
.
output
)
}
}
...
...
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