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biopet.biopet
Commits
7892b57c
Commit
7892b57c
authored
Aug 18, 2014
by
Peter van 't Hof
Browse files
Changed run to library
parent
eac4ec9e
Changes
3
Hide whitespace changes
Inline
Side-by-side
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
View file @
7892b57c
...
...
@@ -26,20 +26,20 @@ trait MultiSampleQScript extends BiopetQScript {
return
runSingleSampleJobs
(
Configurable
.
any2map
(
samples
(
sample
)))
}
final
def
run
Runs
Jobs
(
sampleConfig
:
Map
[
String
,
Any
])
:
Map
[
String
,
Map
[
String
,
File
]]
=
{
final
def
run
Library
Jobs
(
sampleConfig
:
Map
[
String
,
Any
])
:
Map
[
String
,
Map
[
String
,
File
]]
=
{
var
output
:
Map
[
String
,
Map
[
String
,
File
]]
=
Map
()
val
sampleID
=
sampleConfig
(
"ID"
)
if
(
sampleConfig
.
contains
(
"
run
s"
))
{
val
runs
=
Configurable
.
any2map
(
sampleConfig
(
"
run
s"
))
if
(
sampleConfig
.
contains
(
"
library
s"
))
{
val
runs
=
Configurable
.
any2map
(
sampleConfig
(
"
library
s"
))
for
((
key
,
value
)
<-
runs
)
{
var
run
=
Configurable
.
any2map
(
value
)
if
(!
run
.
contains
(
"ID"
))
run
+=
(
"ID"
->
key
)
if
(
run
(
"ID"
)
==
key
)
{
output
+=
key
->
runSingle
RunJobs
(
run
,
sampleConfig
)
var
library
=
Configurable
.
any2map
(
value
)
if
(!
library
.
contains
(
"ID"
))
library
+=
(
"ID"
->
key
)
if
(
library
(
"ID"
)
==
key
)
{
output
+=
key
->
runSingle
LibraryJobs
(
library
,
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
runSingle
Run
Jobs
(
runConfig
:
Map
[
String
,
Any
],
sampleConfig
:
Map
[
String
,
Any
])
:
Map
[
String
,
File
]
def
runSingle
Library
Jobs
(
runConfig
:
Map
[
String
,
Any
],
sampleConfig
:
Map
[
String
,
Any
])
:
Map
[
String
,
File
]
}
gatk/gatk-pipeline/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
View file @
7892b57c
...
...
@@ -70,17 +70,17 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
// Called for each sample
def
runSingleSampleJobs
(
sampleConfig
:
Map
[
String
,
Any
])
:
Map
[
String
,
List
[
File
]]
=
{
var
outputFiles
:
Map
[
String
,
List
[
File
]]
=
Map
()
var
run
Bamfiles
:
List
[
File
]
=
List
()
var
library
Bamfiles
:
List
[
File
]
=
List
()
var
sampleID
:
String
=
sampleConfig
(
"ID"
).
toString
for
((
run
,
run
Files
)
<-
run
Runs
Jobs
(
sampleConfig
))
{
run
Bamfiles
+:=
run
Files
(
"FinalBam"
)
for
((
library
,
library
Files
)
<-
run
Library
Jobs
(
sampleConfig
))
{
library
Bamfiles
+:=
library
Files
(
"FinalBam"
)
}
outputFiles
+=
(
"FinalBams"
->
run
Bamfiles
)
outputFiles
+=
(
"FinalBams"
->
library
Bamfiles
)
if
(
run
Bamfiles
.
size
>
0
)
{
finalBamFiles
++=
run
Bamfiles
if
(
library
Bamfiles
.
size
>
0
)
{
finalBamFiles
++=
library
Bamfiles
val
gatkVariantcalling
=
new
GatkVariantcalling
(
this
)
gatkVariantcalling
.
inputBams
=
run
Bamfiles
gatkVariantcalling
.
inputBams
=
library
Bamfiles
gatkVariantcalling
.
outputDir
=
outputDir
+
sampleID
+
"/variantcalling/"
gatkVariantcalling
.
init
gatkVariantcalling
.
biopetScript
...
...
@@ -91,7 +91,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
}
// Called for each run from a sample
def
runSingle
Run
Jobs
(
runConfig
:
Map
[
String
,
Any
],
sampleConfig
:
Map
[
String
,
Any
])
:
Map
[
String
,
File
]
=
{
def
runSingle
Library
Jobs
(
runConfig
:
Map
[
String
,
Any
],
sampleConfig
:
Map
[
String
,
Any
])
:
Map
[
String
,
File
]
=
{
var
outputFiles
:
Map
[
String
,
File
]
=
Map
()
val
runID
:
String
=
runConfig
(
"ID"
).
toString
val
sampleID
:
String
=
sampleConfig
(
"ID"
).
toString
...
...
@@ -100,7 +100,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
if
(
runConfig
.
contains
(
"inputtype"
))
inputType
=
runConfig
(
"inputtype"
).
toString
else
inputType
=
config
(
"inputtype"
,
default
=
"dna"
).
toString
if
(
runConfig
.
contains
(
"R1"
))
{
val
mapping
=
Mapping
.
loadFrom
Run
Config
(
this
,
runConfig
,
sampleConfig
,
runDir
)
val
mapping
=
Mapping
.
loadFrom
Library
Config
(
this
,
runConfig
,
sampleConfig
,
runDir
)
addAll
(
mapping
.
functions
)
// Add functions of mapping to curent function pool
outputFiles
+=
(
"FinalBam"
->
mapping
.
outputFiles
(
"finalBamFile"
))
...
...
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
7892b57c
...
...
@@ -288,7 +288,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
object
Mapping
extends
PipelineCommand
{
override
val
pipeline
=
"/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.class"
def
loadFrom
Run
Config
(
root
:
Configurable
,
runConfig
:
Map
[
String
,
Any
],
sampleConfig
:
Map
[
String
,
Any
],
runDir
:
String
)
:
Mapping
=
{
def
loadFrom
Library
Config
(
root
:
Configurable
,
runConfig
:
Map
[
String
,
Any
],
sampleConfig
:
Map
[
String
,
Any
],
runDir
:
String
)
:
Mapping
=
{
val
mapping
=
new
Mapping
(
root
)
logger
.
debug
(
"Mapping runconfig: "
+
runConfig
)
...
...
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