Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Mirrors
biopet.biopet
Commits
693e61b8
Commit
693e61b8
authored
Sep 22, 2014
by
Peter van 't Hof
Browse files
Fixe namespaces
parent
a1f807a5
Changes
4
Hide whitespace changes
Inline
Side-by-side
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
View file @
693e61b8
...
...
@@ -13,7 +13,7 @@ import java.io.FileInputStream
import
java.security.MessageDigest
trait
BiopetCommandLineFunctionTrait
extends
CommandLineFunction
with
Configurable
{
analysisName
=
getClass
.
getSimple
Name
analysisName
=
config
Name
@Input
(
doc
=
"deps"
,
required
=
false
)
var
deps
:
List
[
File
]
=
Nil
...
...
@@ -38,7 +38,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
override
def
freezeFieldValues
()
{
checkExecutable
afterGraph
jobOutputFile
=
new
File
(
firstOutput
.
getParent
+
"/."
+
firstOutput
.
getName
+
"."
+
analysis
Name
+
".out"
)
jobOutputFile
=
new
File
(
firstOutput
.
getParent
+
"/."
+
firstOutput
.
getName
+
"."
+
config
Name
+
".out"
)
if
(
threads
==
0
)
threads
=
getThreads
(
defaultThreads
)
if
(
threads
>
1
)
nCoresRequest
=
Option
(
threads
)
...
...
@@ -48,7 +48,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
if
(
vmem
==
null
&&
!
defaultVmem
.
isEmpty
)
vmem
=
defaultVmem
}
if
(
vmem
!=
null
)
jobResourceRequests
:+=
"h_vmem="
+
vmem
jobName
=
this
.
analysis
Name
+
":"
+
firstOutput
.
getName
jobName
=
config
Name
+
":"
+
firstOutput
.
getName
super
.
freezeFieldValues
()
}
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala
View file @
693e61b8
...
...
@@ -6,9 +6,9 @@ import org.broadinstitute.gatk.queue.util.Logging
trait
Configurable
extends
Logging
{
val
root
:
Configurable
val
globalConfig
:
Config
=
if
(
root
!=
null
)
root
.
globalConfig
else
new
Config
()
val
configPath
:
List
[
String
]
=
if
(
root
!=
null
)
root
.
configFullPath
else
List
()
protected
val
configName
=
getClass
.
getSimpleName
.
toLowerCase
protected
val
configFullPath
=
configName
::
configPath
def
configPath
:
List
[
String
]
=
if
(
root
!=
null
)
root
.
configFullPath
else
List
()
protected
lazy
val
configName
=
getClass
.
getSimpleName
.
toLowerCase
protected
lazy
val
configFullPath
=
configName
::
configPath
var
defaults
:
scala.collection.mutable.Map
[
String
,
Any
]
=
if
(
root
!=
null
)
scala
.
collection
.
mutable
.
Map
(
root
.
defaults
.
toArray
:_
*
)
else
scala
.
collection
.
mutable
.
Map
()
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantRecalibrator.scala
View file @
693e61b8
...
...
@@ -18,8 +18,8 @@ class VariantRecalibrator(val root: Configurable) extends org.broadinstitute.gat
object
VariantRecalibrator
{
def
apply
(
root
:
Configurable
,
input
:
File
,
recal_file
:
File
,
tranches_file
:
File
,
indel
:
Boolean
=
false
)
:
VariantRecalibrator
=
{
val
vr
=
new
VariantRecalibrator
(
root
)
{
override
val
configName
=
"variantrecalibrator"
override
val
config
Full
Path
=
(
if
(
indel
)
"indel"
else
"snp"
)
::
configName
::
configPath
override
lazy
val
configName
=
"variantrecalibrator"
override
def
configPath
:
List
[
String
]
=
(
if
(
indel
)
"indel"
else
"snp"
)
::
super
.
configPath
if
(
indel
)
{
mode
=
org
.
broadinstitute
.
gatk
.
tools
.
walkers
.
variantrecalibration
.
VariantRecalibratorArgumentCollection
.
Mode
.
INDEL
defaults
++=
Map
(
"ts_filter_level"
->
99.0
)
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
View file @
693e61b8
...
...
@@ -92,18 +92,22 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
val
allBamfiles
=
for
((
sampleID
,
sampleOutput
)
<-
samplesOutput
;
file
<-
sampleOutput
.
variantcalling
.
bamFiles
)
yield
file
val
allRawVcfFiles
=
for
((
sampleID
,
sampleOutput
)
<-
samplesOutput
)
yield
sampleOutput
.
variantcalling
.
rawFilterVcfFile
val
hcDiscorvery
=
new
HaplotypeCaller
(
this
)
val
hcDiscorvery
=
new
HaplotypeCaller
(
this
)
{
override
protected
lazy
val
configName
=
"haplotypecaller"
override
def
configPath
:
List
[
String
]
=
"multisample"
::
super
.
configPath
}
hcDiscorvery
.
input_file
=
allBamfiles
.
toSeq
hcDiscorvery
.
scatterCount
=
config
(
"scattercount"
,
submodule
=
"multisample"
)
hcDiscorvery
.
out
=
outputDir
+
"variantcalling/hc.vcf.gz"
add
(
hcDiscorvery
)
val
cvRaw
=
CombineVariants
(
this
,
allRawVcfFiles
.
toList
,
outputDir
+
"variantcalling/raw.vcf.gz"
)
add
(
cvRaw
)
val
hcRaw
=
new
HaplotypeCaller
(
this
)
val
hcRaw
=
new
HaplotypeCaller
(
this
)
{
override
protected
lazy
val
configName
=
"haplotypecaller"
override
def
configPath
:
List
[
String
]
=
"multisample"
::
super
.
configPath
}
hcRaw
.
input_file
=
allBamfiles
.
toSeq
hcRaw
.
scatterCount
=
config
(
"scattercount"
,
submodule
=
"multisample"
)
hcRaw
.
out
=
outputDir
+
"variantcalling/raw_genotype.vcf.gz"
hcRaw
.
alleles
=
cvRaw
.
out
hcRaw
.
genotyping_mode
=
org
.
broadinstitute
.
gatk
.
tools
.
walkers
.
genotyper
.
GenotypingOutputMode
.
GENOTYPE_GIVEN_ALLELES
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment