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biopet.biopet
Commits
53c4ba81
Commit
53c4ba81
authored
Feb 27, 2015
by
Peter van 't Hof
Browse files
Add default function to add summarizable
parent
21182480
Changes
1
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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
View file @
53c4ba81
...
...
@@ -49,12 +49,21 @@ trait MultiSampleQScript extends SummaryQScript {
/** Overrules config of qscript with default sample and default library */
val
config
=
new
ConfigFunctions
(
defaultSample
=
sampleId
,
defaultLibrary
=
libId
)
/**
* Name overules the one from qscript
* @param summarizable
* @param name
*/
def
addSummarizable
(
summarizable
:
Summarizable
,
name
:
String
)
:
Unit
=
{
qscript
.
addSummarizable
(
summarizable
,
name
,
Some
(
sampleId
),
Some
(
libId
))
}
/** Adds the library jobs */
final
def
addAndTrackJobs
()
:
Unit
=
{
currentSample
=
Some
(
sampleId
)
currentLib
=
Some
(
libId
)
addJobs
()
addSummarizable
(
this
,
"pipeline"
,
Some
(
sampleId
),
Some
(
libId
))
qscript
.
addSummarizable
(
this
,
"pipeline"
,
Some
(
sampleId
),
Some
(
libId
))
currentLib
=
None
currentSample
=
None
}
...
...
@@ -87,11 +96,20 @@ trait MultiSampleQScript extends SummaryQScript {
ConfigUtils
.
getMapFromPath
(
globalConfig
.
map
,
List
(
"samples"
,
sampleId
,
"libraries"
)).
getOrElse
(
Map
()).
keySet
}
/**
* Name overules the one from qscript
* @param summarizable
* @param name
*/
def
addSummarizable
(
summarizable
:
Summarizable
,
name
:
String
)
:
Unit
=
{
qscript
.
addSummarizable
(
summarizable
,
name
,
Some
(
sampleId
))
}
/** Adds sample jobs */
final
def
addAndTrackJobs
()
:
Unit
=
{
currentSample
=
Some
(
sampleId
)
addJobs
()
addSummarizable
(
this
,
"pipeline"
,
Some
(
sampleId
))
qscript
.
addSummarizable
(
this
,
"pipeline"
,
Some
(
sampleId
))
currentSample
=
None
}
...
...
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