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biopet.biopet
Commits
d60a291a
Commit
d60a291a
authored
Jun 23, 2014
by
Peter van 't Hof
Browse files
General QScript with default configfiles, outputDir and outputFiles
parent
027a6ff3
Changes
1
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Inline
Side-by-side
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
View file @
d60a291a
...
...
@@ -3,54 +3,23 @@ package nl.lumc.sasc.biopet.core
//import org.broadinstitute.sting.queue.QScript
import
java.io.File
import
nl.lumc.sasc.biopet.core.config._
import
org.broadinstitute.sting.commandline._
abstract
trait
BiopetQScript
extends
Configurable
{
//var config: Config = _
var
outputFiles
:
Map
[
String
,
File
]
=
Map
()
var
samples
:
Map
[
String
,
Any
]
=
Map
()
trait
BiopetQScript
extends
Configurable
{
@Argument
(
doc
=
"Config Json file"
,
shortName
=
"config"
,
required
=
false
)
val
configfiles
:
List
[
File
]
=
Nil
final
def
runSamplesJobs
:
Map
[
String
,
Map
[
String
,
File
]]
=
{
var
output
:
Map
[
String
,
Map
[
String
,
File
]]
=
Map
()
samples
=
config
(
"samples"
)
if
(
globalConfig
.
contains
(
"samples"
))
for
((
key
,
value
)
<-
samples
)
{
var
sample
=
Configurable
.
any2map
(
value
)
if
(!
sample
.
contains
(
"ID"
))
sample
+=
(
"ID"
->
key
)
if
(
sample
(
"ID"
)
==
key
)
{
var
files
:
Map
[
String
,
List
[
File
]]
=
runSingleSampleJobs
(
sample
)
}
else
logger
.
warn
(
"Key is not the same as ID on value for sample"
)
}
else
logger
.
warn
(
"No Samples found in config"
)
return
output
}
@Argument
(
doc
=
"Output directory"
,
shortName
=
"outputDir"
,
required
=
true
)
var
outputDir
:
String
=
_
def
runSingleSampleJobs
(
sample
:
String
)
:
Map
[
String
,
List
[
File
]]
={
return
runSingleSampleJobs
(
Configurable
.
any2map
(
samples
(
sample
)))
}
def
runSingleSampleJobs
(
sampleConfig
:
Map
[
String
,
Any
])
:
Map
[
String
,
List
[
File
]]
=
{
logger
.
debug
(
"Default sample function, function 'runSingleSampleJobs' not defined in pipeline"
)
runRunsJobs
(
sampleConfig
)
return
Map
()
}
var
outputFiles
:
Map
[
String
,
File
]
=
Map
()
final
def
runRunsJobs
(
sampleConfig
:
Map
[
String
,
Any
])
:
Map
[
String
,
Map
[
String
,
File
]]
=
{
var
output
:
Map
[
String
,
Map
[
String
,
File
]]
=
Map
()
val
sampleID
=
sampleConfig
(
"ID"
)
if
(
sampleConfig
.
contains
(
"runs"
))
{
val
runs
=
Configurable
.
any2map
(
sampleConfig
(
"runs"
))
for
((
key
,
value
)
<-
runs
)
{
var
run
=
Configurable
.
any2map
(
value
)
if
(!
run
.
contains
(
"ID"
))
run
+=
(
"ID"
->
key
)
if
(
run
(
"ID"
)
==
key
)
{
output
+=
key
->
runSingleRunJobs
(
run
,
sampleConfig
)
}
else
logger
.
warn
(
"Key is not the same as ID on value for run of sample: "
+
sampleID
)
}
}
else
logger
.
warn
(
"No runs found in config for sample: "
+
sampleID
)
return
output
}
def
runSingleRunJobs
(
runConfig
:
Map
[
String
,
Any
],
sampleConfig
:
Map
[
String
,
Any
])
:
Map
[
String
,
File
]
=
{
logger
.
debug
(
"Default run function, function 'runSingleRunJobs' not defined in pipeline"
)
return
Map
()
def
init
def
biopetScript
final
def
script
()
{
init
biopetScript
// TODO: Config report
}
}
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