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Mirrors
biopet.biopet
Commits
5a474415
Commit
5a474415
authored
Nov 22, 2014
by
Peter van 't Hof
Browse files
Remove protected source file from public artifacts
parent
def28b47
Changes
24
Hide whitespace changes
Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/AnalyzeCovariates.scala
deleted
100644 → 0
View file @
def28b47
package
nl.lumc.sasc.biopet.extensions.gatk
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
class
AnalyzeCovariates
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
AnalyzeCovariates
with
GatkGeneral
{
}
object
AnalyzeCovariates
{
def
apply
(
root
:
Configurable
,
before
:
File
,
after
:
File
,
plots
:
File
)
:
AnalyzeCovariates
=
{
val
ac
=
new
AnalyzeCovariates
(
root
)
ac
.
before
=
before
ac
.
after
=
after
ac
.
plots
=
plots
return
ac
}
}
\ No newline at end of file
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/ApplyRecalibration.scala
deleted
100644 → 0
View file @
def28b47
package
nl.lumc.sasc.biopet.extensions.gatk
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
class
ApplyRecalibration
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
ApplyRecalibration
with
GatkGeneral
{
override
def
afterGraph
{
super
.
afterGraph
if
(
config
.
contains
(
"scattercount"
))
scatterCount
=
config
(
"scattercount"
)
nt
=
Option
(
getThreads
(
3
))
memoryLimit
=
Option
(
nt
.
getOrElse
(
1
)
*
2
)
ts_filter_level
=
config
(
"ts_filter_level"
)
}
}
object
ApplyRecalibration
{
def
apply
(
root
:
Configurable
,
input
:
File
,
output
:
File
,
recal_file
:
File
,
tranches_file
:
File
,
indel
:
Boolean
=
false
)
:
ApplyRecalibration
=
{
val
ar
=
if
(
indel
)
new
ApplyRecalibration
(
root
)
{
mode
=
org
.
broadinstitute
.
gatk
.
tools
.
walkers
.
variantrecalibration
.
VariantRecalibratorArgumentCollection
.
Mode
.
INDEL
defaults
++=
Map
(
"ts_filter_level"
->
99.0
)
}
else
new
ApplyRecalibration
(
root
)
{
mode
=
org
.
broadinstitute
.
gatk
.
tools
.
walkers
.
variantrecalibration
.
VariantRecalibratorArgumentCollection
.
Mode
.
SNP
defaults
++=
Map
(
"ts_filter_level"
->
99.5
)
}
ar
.
input
:+=
input
ar
.
recal_file
=
recal_file
ar
.
tranches_file
=
tranches_file
ar
.
out
=
output
return
ar
}
}
\ No newline at end of file
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/BaseRecalibrator.scala
deleted
100644 → 0
View file @
def28b47
package
nl.lumc.sasc.biopet.extensions.gatk
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
class
BaseRecalibrator
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
BaseRecalibrator
with
GatkGeneral
{
memoryLimit
=
Option
(
4
)
override
val
defaultVmem
=
"8G"
if
(
config
.
contains
(
"scattercount"
))
scatterCount
=
config
(
"scattercount"
)
if
(
config
.
contains
(
"dbsnp"
))
knownSites
:+=
new
File
(
config
(
"dbsnp"
).
asString
)
if
(
config
.
contains
(
"known_sites"
))
knownSites
:+=
new
File
(
config
(
"known_sites"
).
asString
)
}
object
BaseRecalibrator
{
def
apply
(
root
:
Configurable
,
input
:
File
,
output
:
File
)
:
BaseRecalibrator
=
{
val
br
=
new
BaseRecalibrator
(
root
)
br
.
input_file
:+=
input
br
.
out
=
output
br
.
afterGraph
return
br
}
}
\ No newline at end of file
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineGVCFs.scala
deleted
100644 → 0
View file @
def28b47
package
nl.lumc.sasc.biopet.extensions.gatk
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
class
CombineGVCFs
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
CombineGVCFs
with
GatkGeneral
{
if
(
config
.
contains
(
"scattercount"
))
scatterCount
=
config
(
"scattercount"
)
}
object
CombineGVCFs
{
def
apply
(
root
:
Configurable
,
input
:
List
[
File
],
output
:
File
)
:
CombineGVCFs
=
{
val
cg
=
new
CombineGVCFs
(
root
)
cg
.
variant
=
input
cg
.
o
=
output
return
cg
}
}
\ No newline at end of file
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala
deleted
100644 → 0
View file @
def28b47
package
nl.lumc.sasc.biopet.extensions.gatk
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
class
CombineVariants
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
CombineVariants
with
GatkGeneral
{
if
(
config
.
contains
(
"scattercount"
))
scatterCount
=
config
(
"scattercount"
)
}
object
CombineVariants
{
def
apply
(
root
:
Configurable
,
input
:
List
[
File
],
output
:
File
)
:
CombineVariants
=
{
val
cv
=
new
CombineVariants
(
root
)
cv
.
variant
=
input
cv
.
out
=
output
return
cv
}
}
\ No newline at end of file
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GatkGeneral.scala
deleted
100644 → 0
View file @
def28b47
package
nl.lumc.sasc.biopet.extensions.gatk
import
nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import
org.broadinstitute.gatk.queue.extensions.gatk.CommandLineGATK
trait
GatkGeneral
extends
CommandLineGATK
with
BiopetJavaCommandLineFunction
{
memoryLimit
=
Option
(
3
)
if
(
config
.
contains
(
"gatk_jar"
))
jarFile
=
config
(
"gatk_jar"
)
override
val
defaultVmem
=
"7G"
if
(
config
.
contains
(
"intervals"
,
submodule
=
"gatk"
))
intervals
=
config
(
"intervals"
,
submodule
=
"gatk"
).
asFileList
if
(
config
.
contains
(
"exclude_intervals"
,
submodule
=
"gatk"
))
excludeIntervals
=
config
(
"exclude_intervals"
,
submodule
=
"gatk"
).
asFileList
reference_sequence
=
config
(
"reference"
,
submodule
=
"gatk"
)
gatk_key
=
config
(
"gatk_key"
,
submodule
=
"gatk"
)
if
(
config
.
contains
(
"pedigree"
,
submodule
=
"gatk"
))
pedigree
=
config
(
"pedigree"
,
submodule
=
"gatk"
).
asFileList
}
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GenotypeGVCFs.scala
deleted
100644 → 0
View file @
def28b47
package
nl.lumc.sasc.biopet.extensions.gatk
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
class
GenotypeGVCFs
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
GenotypeGVCFs
with
GatkGeneral
{
annotation
++=
config
(
"annotation"
,
default
=
Seq
(
"FisherStrand"
,
"QualByDepth"
,
"ChromosomeCounts"
)).
asStringList
if
(
config
.
contains
(
"dbsnp"
))
dbsnp
=
config
(
"dbsnp"
)
if
(
config
.
contains
(
"scattercount"
,
"genotypegvcfs"
))
scatterCount
=
config
(
"scattercount"
)
if
(
config
(
"inputtype"
,
default
=
"dna"
).
asString
==
"rna"
)
{
stand_call_conf
=
config
(
"stand_call_conf"
,
default
=
20
)
stand_emit_conf
=
config
(
"stand_emit_conf"
,
default
=
0
)
}
else
{
stand_call_conf
=
config
(
"stand_call_conf"
,
default
=
30
)
stand_emit_conf
=
config
(
"stand_emit_conf"
,
default
=
0
)
}
}
object
GenotypeGVCFs
{
def
apply
(
root
:
Configurable
,
gvcfFiles
:
List
[
File
],
output
:
File
)
:
GenotypeGVCFs
=
{
val
gg
=
new
GenotypeGVCFs
(
root
)
gg
.
variant
=
gvcfFiles
gg
.
out
=
output
return
gg
}
}
\ No newline at end of file
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
deleted
100644 → 0
View file @
def28b47
package
nl.lumc.sasc.biopet.extensions.gatk
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.utils.variant.GATKVCFIndexType
class
HaplotypeCaller
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
HaplotypeCaller
with
GatkGeneral
{
override
def
afterGraph
{
super
.
afterGraph
min_mapping_quality_score
=
config
(
"minMappingQualityScore"
,
default
=
20
)
if
(
config
.
contains
(
"scattercount"
))
scatterCount
=
config
(
"scattercount"
)
if
(
config
.
contains
(
"dbsnp"
))
this
.
dbsnp
=
config
(
"dbsnp"
)
this
.
sample_ploidy
=
config
(
"ploidy"
)
nct
=
config
(
"threads"
,
default
=
1
)
bamOutput
=
config
(
"bamOutput"
)
memoryLimit
=
Option
(
nct
.
getOrElse
(
1
)
*
2
)
if
(
config
.
contains
(
"allSitePLs"
))
this
.
allSitePLs
=
config
(
"allSitePLs"
)
if
(
config
.
contains
(
"output_mode"
))
{
import
org.broadinstitute.gatk.tools.walkers.genotyper.OutputMode._
config
(
"output_mode"
).
asString
match
{
case
"EMIT_ALL_CONFIDENT_SITES"
=>
output_mode
=
EMIT_ALL_CONFIDENT_SITES
case
"EMIT_ALL_SITES"
=>
output_mode
=
EMIT_ALL_SITES
case
"EMIT_VARIANTS_ONLY"
=>
output_mode
=
EMIT_VARIANTS_ONLY
case
e
=>
logger
.
warn
(
"output mode '"
+
e
+
"' does not exist"
)
}
}
if
(
config
(
"inputtype"
,
default
=
"dna"
).
asString
==
"rna"
)
{
dontUseSoftClippedBases
=
config
(
"dontusesoftclippedbases"
,
default
=
true
)
stand_call_conf
=
config
(
"stand_call_conf"
,
default
=
5
)
stand_emit_conf
=
config
(
"stand_emit_conf"
,
default
=
0
)
}
else
{
dontUseSoftClippedBases
=
config
(
"dontusesoftclippedbases"
,
default
=
false
)
stand_call_conf
=
config
(
"stand_call_conf"
,
default
=
5
)
stand_emit_conf
=
config
(
"stand_emit_conf"
,
default
=
0
)
}
if
(
bamOutput
!=
null
&&
nct
.
getOrElse
(
1
)
>
1
)
{
nct
=
Option
(
1
)
logger
.
warn
(
"BamOutput is on, nct/threads is forced to set on 1, this option is only for debug"
)
}
}
def
useGvcf
()
{
emitRefConfidence
=
org
.
broadinstitute
.
gatk
.
tools
.
walkers
.
haplotypecaller
.
ReferenceConfidenceMode
.
GVCF
variant_index_type
=
GATKVCFIndexType
.
LINEAR
variant_index_parameter
=
config
(
"variant_index_parameter"
,
default
=
128000
)
}
}
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/IndelRealigner.scala
deleted
100644 → 0
View file @
def28b47
package
nl.lumc.sasc.biopet.extensions.gatk
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
class
IndelRealigner
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
IndelRealigner
with
GatkGeneral
{
if
(
config
.
contains
(
"scattercount"
))
scatterCount
=
config
(
"scattercount"
)
}
object
IndelRealigner
{
def
apply
(
root
:
Configurable
,
input
:
File
,
targetIntervals
:
File
,
outputDir
:
String
)
:
IndelRealigner
=
{
val
ir
=
new
IndelRealigner
(
root
)
ir
.
input_file
:+=
input
ir
.
targetIntervals
=
targetIntervals
ir
.
out
=
new
File
(
outputDir
,
input
.
getName
.
stripSuffix
(
".bam"
)
+
".realign.bam"
)
return
ir
}
}
\ No newline at end of file
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/PrintReads.scala
deleted
100644 → 0
View file @
def28b47
package
nl.lumc.sasc.biopet.extensions.gatk
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
class
PrintReads
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
PrintReads
with
GatkGeneral
{
memoryLimit
=
Option
(
4
)
override
val
defaultVmem
=
"8G"
if
(
config
.
contains
(
"scattercount"
))
scatterCount
=
config
(
"scattercount"
)
}
object
PrintReads
{
def
apply
(
root
:
Configurable
,
input
:
File
,
output
:
File
)
:
PrintReads
=
{
val
br
=
new
PrintReads
(
root
)
br
.
input_file
:+=
input
br
.
out
=
output
return
br
}
}
\ No newline at end of file
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/RealignerTargetCreator.scala
deleted
100644 → 0
View file @
def28b47
package
nl.lumc.sasc.biopet.extensions.gatk
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
class
RealignerTargetCreator
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
RealignerTargetCreator
with
GatkGeneral
{
override
val
defaultVmem
=
"6G"
memoryLimit
=
Some
(
2.5
)
if
(
config
.
contains
(
"scattercount"
))
scatterCount
=
config
(
"scattercount"
)
if
(
config
.
contains
(
"known"
))
known
++=
config
(
"known"
).
asFileList
}
object
RealignerTargetCreator
{
def
apply
(
root
:
Configurable
,
input
:
File
,
outputDir
:
String
)
:
RealignerTargetCreator
=
{
val
re
=
new
RealignerTargetCreator
(
root
)
re
.
input_file
:+=
input
re
.
out
=
new
File
(
outputDir
,
input
.
getName
.
stripSuffix
(
".bam"
)
+
".realign.intervals"
)
return
re
}
}
\ No newline at end of file
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/SelectVariants.scala
deleted
100644 → 0
View file @
def28b47
package
nl.lumc.sasc.biopet.extensions.gatk
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
class
SelectVariants
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
SelectVariants
with
GatkGeneral
{
if
(
config
.
contains
(
"scattercount"
))
scatterCount
=
config
(
"scattercount"
)
}
object
SelectVariants
{
def
apply
(
root
:
Configurable
,
input
:
File
,
output
:
File
)
:
SelectVariants
=
{
val
sv
=
new
SelectVariants
(
root
)
sv
.
variant
=
input
sv
.
out
=
output
return
sv
}
}
\ No newline at end of file
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala
deleted
100644 → 0
View file @
def28b47
package
nl.lumc.sasc.biopet.extensions.gatk
import
nl.lumc.sasc.biopet.core.config.Configurable
class
UnifiedGenotyper
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
UnifiedGenotyper
with
GatkGeneral
{
override
def
afterGraph
{
super
.
afterGraph
genotype_likelihoods_model
=
org
.
broadinstitute
.
gatk
.
tools
.
walkers
.
genotyper
.
GenotypeLikelihoodsCalculationModel
.
Model
.
BOTH
if
(
config
.
contains
(
"scattercount"
))
scatterCount
=
config
(
"scattercount"
)
if
(
config
.
contains
(
"dbsnp"
))
this
.
dbsnp
=
config
(
"dbsnp"
)
this
.
sample_ploidy
=
config
(
"ploidy"
)
nct
=
config
(
"threads"
,
default
=
1
)
memoryLimit
=
Option
(
nct
.
getOrElse
(
1
)
*
2
)
if
(
config
.
contains
(
"allSitePLs"
))
this
.
allSitePLs
=
config
(
"allSitePLs"
)
if
(
config
.
contains
(
"output_mode"
))
{
import
org.broadinstitute.gatk.tools.walkers.genotyper.OutputMode._
config
(
"output_mode"
).
asString
match
{
case
"EMIT_ALL_CONFIDENT_SITES"
=>
output_mode
=
EMIT_ALL_CONFIDENT_SITES
case
"EMIT_ALL_SITES"
=>
output_mode
=
EMIT_ALL_SITES
case
"EMIT_VARIANTS_ONLY"
=>
output_mode
=
EMIT_VARIANTS_ONLY
case
e
=>
logger
.
warn
(
"output mode '"
+
e
+
"' does not exist"
)
}
}
if
(
config
(
"inputtype"
,
default
=
"dna"
).
asString
==
"rna"
)
{
stand_call_conf
=
config
(
"stand_call_conf"
,
default
=
5
)
stand_emit_conf
=
config
(
"stand_emit_conf"
,
default
=
0
)
}
else
{
stand_call_conf
=
config
(
"stand_call_conf"
,
default
=
5
)
stand_emit_conf
=
config
(
"stand_emit_conf"
,
default
=
0
)
}
}
}
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantAnnotator.scala
deleted
100644 → 0
View file @
def28b47
package
nl.lumc.sasc.biopet.extensions.gatk
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
class
VariantAnnotator
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
VariantAnnotator
with
GatkGeneral
{
if
(
config
.
contains
(
"scattercount"
))
scatterCount
=
config
(
"scattercount"
)
dbsnp
=
config
(
"dbsnp"
)
}
object
VariantAnnotator
{
def
apply
(
root
:
Configurable
,
input
:
File
,
bamFiles
:
List
[
File
],
output
:
File
)
:
VariantAnnotator
=
{
val
va
=
new
VariantAnnotator
(
root
)
va
.
variant
=
input
va
.
input_file
=
bamFiles
va
.
out
=
output
return
va
}
}
\ No newline at end of file
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantEval.scala
deleted
100644 → 0
View file @
def28b47
package
nl.lumc.sasc.biopet.extensions.gatk
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
class
VariantEval
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
VariantEval
with
GatkGeneral
{
override
def
afterGraph
{
super
.
afterGraph
}
}
object
VariantEval
{
def
apply
(
root
:
Configurable
,
sample
:
File
,
compareWith
:
File
,
output
:
File
)
:
VariantEval
=
{
val
vareval
=
new
VariantEval
(
root
)
vareval
.
eval
=
Seq
(
sample
)
vareval
.
comp
=
Seq
(
compareWith
)
vareval
.
out
=
output
vareval
.
afterGraph
return
vareval
}
def
apply
(
root
:
Configurable
,
sample
:
File
,
compareWith
:
File
,
output
:
File
,
ST
:
Seq
[
String
],
EV
:
Seq
[
String
])
:
VariantEval
=
{
val
vareval
=
new
VariantEval
(
root
)
vareval
.
eval
=
Seq
(
sample
)
vareval
.
comp
=
Seq
(
compareWith
)
vareval
.
out
=
output
vareval
.
noST
=
true
vareval
.
ST
=
ST
vareval
.
noEV
=
true
vareval
.
EV
=
EV
vareval
.
afterGraph
return
vareval
}
}
\ No newline at end of file
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantRecalibrator.scala
deleted
100644 → 0
View file @
def28b47
package
nl.lumc.sasc.biopet.extensions.gatk
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
class
VariantRecalibrator
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
VariantRecalibrator
with
GatkGeneral
{
nt
=
Option
(
getThreads
(
4
))
memoryLimit
=
Option
(
nt
.
getOrElse
(
1
)
*
2
)
if
(
config
.
contains
(
"dbsnp"
))
resource
:+=
new
TaggedFile
(
config
(
"dbsnp"
).
asString
,
"known=true,training=false,truth=false,prior=2.0"
)
an
=
config
(
"annotation"
,
default
=
List
(
"QD"
,
"DP"
,
"FS"
,
"ReadPosRankSum"
,
"MQRankSum"
)).
asStringList
minNumBadVariants
=
config
(
"minnumbadvariants"
)
maxGaussians
=
config
(
"maxgaussians"
)
}
object
VariantRecalibrator
{
def
apply
(
root
:
Configurable
,
input
:
File
,
recal_file
:
File
,
tranches_file
:
File
,
indel
:
Boolean
=
false
)
:
VariantRecalibrator
=
{
val
vr
=
new
VariantRecalibrator
(
root
)
{
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
)
if
(
config
.
contains
(
"mills"
))
resource
:+=
new
TaggedFile
(
config
(
"mills"
).
asString
,
"known=false,training=true,truth=true,prior=12.0"
)
}
else
{
mode
=
org
.
broadinstitute
.
gatk
.
tools
.
walkers
.
variantrecalibration
.
VariantRecalibratorArgumentCollection
.
Mode
.
SNP
defaults
++=
Map
(
"ts_filter_level"
->
99.5
)
if
(
config
.
contains
(
"hapmap"
))
resource
+:=
new
TaggedFile
(
config
(
"hapmap"
).
asString
,
"known=false,training=true,truth=true,prior=15.0"
)
if
(
config
.
contains
(
"omni"
))
resource
+:=
new
TaggedFile
(
config
(
"omni"
).
asString
,
"known=false,training=true,truth=true,prior=12.0"
)
if
(
config
.
contains
(
"1000G"
))
resource
+:=
new
TaggedFile
(
config
(
"1000G"
).
asString
,
"known=false,training=true,truth=false,prior=10.0"
)
}
}
vr
.
input
:+=
input
vr
.
recal_file
=
recal_file
vr
.
tranches_file
=
tranches_file
return
vr
}
}
\ No newline at end of file
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
deleted
100644 → 0
View file @
def28b47
package
nl.lumc.sasc.biopet.pipelines.basty
import
java.io.File
import
nl.lumc.sasc.biopet.core.MultiSampleQScript
import
nl.lumc.sasc.biopet.core.PipelineCommand
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.extensions.Cat
import
nl.lumc.sasc.biopet.extensions.Raxml
import
nl.lumc.sasc.biopet.pipelines.gatk.GatkPipeline
import
nl.lumc.sasc.biopet.tools.BastyGenerateFasta
import
org.broadinstitute.gatk.queue.QScript
class
Basty
(
val
root
:
Configurable
)
extends
QScript
with
MultiSampleQScript
{
def
this
()
=
this
(
null
)
class
LibraryOutput
extends
AbstractLibraryOutput
{
}
case
class
FastaOutput
(
variants
:
File
,
consensus
:
File
,
consensusVariants
:
File
)
class
SampleOutput
extends
AbstractSampleOutput
{
var
output
:
FastaOutput
=
_
var
outputSnps
:
FastaOutput
=
_
}
defaults
++=
Map
(
"ploidy"
->
1
,
"use_haplotypecaller"
->
false
,
"use_unifiedgenotyper"
->
true
,
"joint_variantcalling"
->
true
)
var
gatkPipeline
:
GatkPipeline
=
new
GatkPipeline
(
this
)
gatkPipeline
.
jointVariantcalling
=
true
def
init
()
{
gatkPipeline
.
outputDir
=
outputDir
gatkPipeline
.
init
}
def
biopetScript
()
{
gatkPipeline
.
biopetScript
addAll
(
gatkPipeline
.
functions
)
val
refVariants
=
addGenerateFasta
(
null
,
outputDir
+
"reference/"
,
outputName
=
"reference"
)
val
refVariantSnps
=
addGenerateFasta
(
null
,
outputDir
+
"reference/"
,
outputName
=
"reference"
,
snpsOnly
=
true
)
runSamplesJobs
()
val
catVariants
=
Cat
(
this
,
refVariants
.
variants
::
samplesOutput
.
map
(
_
.
_2
.
output
.
variants
).
toList
,
outputDir
+
"fastas/variant.fasta"
)
add
(
catVariants
)
val
catVariantsSnps
=
Cat
(
this
,
refVariantSnps
.
variants
::
samplesOutput
.
map
(
_
.
_2
.
outputSnps
.
variants
).
toList
,
outputDir
+
"fastas/variant.snps_only.fasta"
)
add
(
catVariantsSnps
)
val
catConsensus
=
Cat
(
this
,
refVariants
.
consensus
::
samplesOutput
.
map
(
_
.
_2
.
output
.
consensus
).
toList
,
outputDir
+
"fastas/consensus.fasta"
)
add
(
catConsensus
)
val
catConsensusSnps
=
Cat
(
this
,
refVariantSnps
.
consensus
::
samplesOutput
.
map
(
_
.
_2
.
outputSnps
.
consensus
).
toList
,
outputDir
+
"fastas/consensus.snps_only.fasta"
)
add
(
catConsensusSnps
)
val
catConsensusVariants
=
Cat
(
this
,
refVariants
.
consensusVariants
::
samplesOutput
.
map
(
_
.
_2
.
output
.
consensusVariants
).
toList
,
outputDir
+
"fastas/consensus.variant.fasta"
)
add
(
catConsensusVariants
)
val
catConsensusVariantsSnps
=
Cat
(
this
,
refVariantSnps
.
consensusVariants
::
samplesOutput
.
map
(
_
.
_2
.
outputSnps
.
consensusVariants
).
toList
,
outputDir
+
"fastas/consensus.variant.snps_only.fasta"
)
add
(
catConsensusVariantsSnps
)
val
seed
:
Int
=
config
(
"seed"
,
default
=
12345
)
def
addRaxml
(
input
:
File
,
outputDir
:
String
,
outputName
:
String
)
{
val
raxmlMl
=
new
Raxml
(
this
)
raxmlMl
.
input
=
input
raxmlMl
.
m
=
config
(
"raxml_ml_model"
,
default
=
"GTRGAMMAX"
)
raxmlMl
.
p
=
seed
raxmlMl
.
n
=
outputName
+
"_ml"
raxmlMl
.
w
=
outputDir
raxmlMl
.
N
=
config
(
"ml_runs"
,
default
=
20
,
submodule
=
"raxml"
)
add
(
raxmlMl
)
val
r
=
new
scala
.
util
.
Random
(
seed
)
val
numBoot
=
config
(
"boot_runs"
,
default
=
100
,
submodule
=
"raxml"
).
asInt
val
bootList
=
for
(
t
<-
0
until
numBoot
)
yield
{
val
raxmlBoot
=
new
Raxml
(
this
)
raxmlBoot
.
threads
=
1
raxmlBoot
.
input
=
input
raxmlBoot
.
m
=
config
(
"raxml_ml_model"
,
default
=
"GTRGAMMAX"
)
raxmlBoot
.
p
=
seed
raxmlBoot
.
b
=
math
.
abs
(
r
.
nextInt
)
raxmlBoot
.
w
=
outputDir
raxmlBoot
.
N
=
1
raxmlBoot
.
n
=
outputName
+
"_boot_"
+
t
add
(
raxmlBoot
)
raxmlBoot
.
getBootstrapFile
}
val
cat
=
Cat
(
this
,
bootList
.
toList
,
outputDir
+
"/boot_list"
)
add
(
cat
)
val
raxmlBi
=
new
Raxml
(
this
)
raxmlBi
.
input
=
input
raxmlBi
.
t
=
raxmlMl
.
getBestTreeFile
raxmlBi
.
z
=
cat
.
output
raxmlBi
.
m
=
config
(
"raxml_ml_model"
,
default
=
"GTRGAMMAX"
)
raxmlBi
.
p
=
seed
raxmlBi
.
f
=
"b"
raxmlBi
.
n
=
outputName
+
"_bi"
raxmlBi
.
w
=
outputDir
add
(
raxmlBi
)
}
addRaxml
(
catVariantsSnps
.
output
,
outputDir
+
"raxml"
,
"snps"
)
}
// Called for each sample
def
runSingleSampleJobs
(
sampleConfig
:
Map
[
String
,
Any
])
:
SampleOutput
=
{
val
sampleOutput
=
new
SampleOutput