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biopet.biopet
Commits
b7952c01
Commit
b7952c01
authored
Nov 07, 2014
by
Peter van 't Hof
Browse files
Change to config
parent
0bbd5588
Changes
6
Hide whitespace changes
Inline
Side-by-side
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
View file @
b7952c01
...
...
@@ -18,10 +18,10 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
var
input_R2
:
File
=
_
@Argument
(
doc
=
"Skip Trim fastq files"
,
shortName
=
"skiptrim"
,
required
=
false
)
var
skipTrim
:
Boolean
=
false
var
skipTrim
:
Boolean
=
config
(
"skiptrim"
,
default
=
false
)
@Argument
(
doc
=
"Skip Clip fastq files"
,
shortName
=
"skipclip"
,
required
=
false
)
var
skipClip
:
Boolean
=
false
var
skipClip
:
Boolean
=
config
(
"skipclip"
,
default
=
false
)
@Argument
(
doc
=
"Sample name"
,
shortName
=
"sample"
,
required
=
true
)
var
sampleName
:
String
=
_
...
...
@@ -43,8 +43,6 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
val
summary
=
new
FlexiprepSummary
(
this
)
def
init
()
{
if
(!
skipTrim
)
skipTrim
=
config
(
"skiptrim"
,
default
=
false
)
if
(!
skipClip
)
skipClip
=
config
(
"skipclip"
,
default
=
false
)
if
(
input_R1
==
null
)
throw
new
IllegalStateException
(
"Missing R1 on flexiprep module"
)
if
(
outputDir
==
null
)
throw
new
IllegalStateException
(
"Missing Output directory on flexiprep module"
)
if
(
sampleName
==
null
)
throw
new
IllegalStateException
(
"Missing Sample name on flexiprep module"
)
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.scala
View file @
b7952c01
...
...
@@ -18,18 +18,15 @@ class GatkBenchmarkGenotyping(val root: Configurable) extends QScript with Biope
@Input
(
doc
=
"Gvcf files"
,
shortName
=
"I"
,
required
=
false
)
var
gvcfFiles
:
List
[
File
]
=
Nil
@Argument
(
doc
=
"Reference"
,
shortName
=
"R"
,
required
=
false
)
var
reference
:
File
=
_
var
reference
:
File
=
config
(
"reference"
)
@Argument
(
doc
=
"Dbsnp"
,
shortName
=
"dbsnp"
,
required
=
false
)
var
dbsnp
:
File
=
_
var
dbsnp
:
File
=
config
(
"dbsnp"
)
def
init
()
{
if
(
config
.
contains
(
"gvcffiles"
))
for
(
file
<-
config
(
"gvcffiles"
).
getList
)
{
gvcfFiles
::=
file
.
toString
}
if
(
reference
==
null
)
reference
=
config
(
"reference"
)
if
(
dbsnp
==
null
)
dbsnp
=
config
(
"dbsnp"
)
if
(
outputDir
==
null
)
throw
new
IllegalStateException
(
"Missing Output directory on gatk module"
)
else
if
(!
outputDir
.
endsWith
(
"/"
))
outputDir
+=
"/"
}
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala
View file @
b7952c01
...
...
@@ -13,10 +13,10 @@ class GatkGenotyping(val root: Configurable) extends QScript with BiopetQScript
var
inputGvcfs
:
List
[
File
]
=
Nil
@Argument
(
doc
=
"Reference"
,
shortName
=
"R"
,
required
=
false
)
var
reference
:
File
=
_
var
reference
:
File
=
config
(
"reference"
)
@Argument
(
doc
=
"Dbsnp"
,
shortName
=
"dbsnp"
,
required
=
false
)
var
dbsnp
:
File
=
_
var
dbsnp
:
File
=
config
(
"dbsnp"
)
@Argument
(
doc
=
"OutputName"
,
required
=
false
)
var
outputName
:
String
=
"genotype"
...
...
@@ -28,8 +28,6 @@ class GatkGenotyping(val root: Configurable) extends QScript with BiopetQScript
var
samples
:
List
[
String
]
=
Nil
def
init
()
{
if
(
reference
==
null
)
reference
=
config
(
"reference"
)
if
(
dbsnp
==
null
)
dbsnp
=
config
(
"dbsnp"
)
if
(
outputFile
==
null
)
outputFile
=
outputDir
+
outputName
+
".vcf.gz"
if
(
outputDir
==
null
)
throw
new
IllegalStateException
(
"Missing Output directory on gatk module"
)
else
if
(!
outputDir
.
endsWith
(
"/"
))
outputDir
+=
"/"
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
View file @
b7952c01
...
...
@@ -27,17 +27,17 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
var
mergeGvcfs
:
Boolean
=
false
@Argument
(
doc
=
"Joint variantcalling"
,
shortName
=
"jointVariantCalling"
,
required
=
false
)
var
jointVariantcalling
=
false
var
jointVariantcalling
=
config
(
"joint_variantcalling"
,
default
=
false
)
@Argument
(
doc
=
"Joint genotyping"
,
shortName
=
"jointGenotyping"
,
required
=
false
)
var
jointGenotyping
=
false
var
jointGenotyping
=
config
(
"joint_genotyping"
,
default
=
false
)
var
singleSampleCalling
=
true
var
reference
:
File
=
_
var
dbsnp
:
File
=
_
var
singleSampleCalling
=
config
(
"single_sample_calling"
,
default
=
true
)
var
reference
:
File
=
config
(
"reference"
,
required
=
true
)
var
dbsnp
:
File
=
config
(
"dbsnp"
)
var
gvcfFiles
:
List
[
File
]
=
Nil
var
finalBamFiles
:
List
[
File
]
=
Nil
var
useAllelesOption
:
Boolean
=
_
var
useAllelesOption
:
Boolean
=
config
(
"use_alleles_option"
,
default
=
false
)
class
LibraryOutput
extends
AbstractLibraryOutput
{
var
mappedBamFile
:
File
=
_
...
...
@@ -49,15 +49,9 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
}
def
init
()
{
useAllelesOption
=
config
(
"use_alleles_option"
,
default
=
false
)
reference
=
config
(
"reference"
,
required
=
true
)
dbsnp
=
config
(
"dbsnp"
)
if
(
config
.
contains
(
"target_bed"
))
{
defaults
++=
Map
(
"gatk"
->
Map
((
"intervals"
->
config
(
"target_bed"
).
getStringList
)))
}
jointVariantcalling
=
config
(
"joint_variantcalling"
,
default
=
false
)
jointGenotyping
=
config
(
"joint_genotyping"
,
default
=
false
)
singleSampleCalling
=
config
(
"single_sample_calling"
,
default
=
true
)
if
(
config
.
contains
(
"gvcfFiles"
))
for
(
file
<-
config
(
"gvcfFiles"
).
getList
)
gvcfFiles
:+=
file
.
toString
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
View file @
b7952c01
...
...
@@ -24,10 +24,10 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
var
rawVcfInput
:
File
=
_
@Argument
(
doc
=
"Reference"
,
shortName
=
"R"
,
required
=
false
)
var
reference
:
File
=
_
var
reference
:
File
=
config
(
"reference"
,
required
=
true
)
@Argument
(
doc
=
"Dbsnp"
,
shortName
=
"dbsnp"
,
required
=
false
)
var
dbsnp
:
File
=
_
var
dbsnp
:
File
=
config
(
"dbsnp"
)
@Argument
(
doc
=
"OutputName"
,
required
=
false
)
var
outputName
:
String
=
_
...
...
@@ -35,21 +35,14 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
@Argument
(
doc
=
"Sample name"
,
required
=
false
)
var
sampleID
:
String
=
_
var
preProcesBams
:
Option
[
Boolean
]
=
N
on
e
var
preProcesBams
:
Option
[
Boolean
]
=
c
on
fig
(
"pre_proces_bams"
,
default
=
true
)
var
variantcalling
:
Boolean
=
true
var
doublePreProces
:
Option
[
Boolean
]
=
N
on
e
var
useHaplotypecaller
:
Option
[
Boolean
]
=
N
on
e
var
useUnifiedGenotyper
:
Option
[
Boolean
]
=
N
on
e
var
useAllelesOption
:
Option
[
Boolean
]
=
None
var
doublePreProces
:
Option
[
Boolean
]
=
c
on
fig
(
"double_pre_proces"
,
default
=
true
)
var
useHaplotypecaller
:
Option
[
Boolean
]
=
c
on
fig
(
"use_haplotypecaller"
,
default
=
true
)
var
useUnifiedGenotyper
:
Option
[
Boolean
]
=
c
on
fig
(
"use_unifiedgenotyper"
,
default
=
false
)
var
useAllelesOption
:
Option
[
Boolean
]
=
config
(
"use_alleles_option"
,
default
=
false
)
def
init
()
{
if
(
useAllelesOption
==
None
)
useAllelesOption
=
config
(
"use_alleles_option"
,
default
=
false
)
if
(
preProcesBams
==
None
)
preProcesBams
=
config
(
"pre_proces_bams"
,
default
=
true
)
if
(
doublePreProces
==
None
)
doublePreProces
=
config
(
"double_pre_proces"
,
default
=
true
)
if
(
useHaplotypecaller
==
None
)
useHaplotypecaller
=
config
(
"use_haplotypecaller"
,
default
=
true
)
if
(
useUnifiedGenotyper
==
None
)
useUnifiedGenotyper
=
config
(
"use_unifiedgenotyper"
,
default
=
false
)
if
(
reference
==
null
)
reference
=
config
(
"reference"
,
required
=
true
)
if
(
dbsnp
==
null
)
dbsnp
=
config
(
"dbsnp"
)
if
(
outputName
==
null
&&
sampleID
!=
null
)
outputName
=
sampleID
else
if
(
outputName
==
null
)
outputName
=
"noname"
if
(
outputDir
==
null
)
throw
new
IllegalStateException
(
"Missing Output directory on gatk module"
)
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVcfSampleCompare.scala
View file @
b7952c01
...
...
@@ -16,7 +16,7 @@ class GatkVcfSampleCompare(val root: Configurable) extends QScript with BiopetQS
var
vcfFiles
:
List
[
File
]
=
_
@Argument
(
doc
=
"Reference"
,
shortName
=
"R"
,
required
=
false
)
var
reference
:
File
=
_
var
reference
:
File
=
config
(
"reference"
)
@Argument
(
doc
=
"Target bed"
,
shortName
=
"targetBed"
,
required
=
false
)
var
targetBed
:
List
[
File
]
=
Nil
...
...
@@ -29,7 +29,6 @@ class GatkVcfSampleCompare(val root: Configurable) extends QScript with BiopetQS
def
generalSampleDir
=
outputDir
+
"samples/"
def
init
()
{
if
(
reference
==
null
)
reference
=
config
(
"reference"
)
if
(
config
.
contains
(
"target_bed"
))
for
(
bed
<-
config
(
"target_bed"
).
getList
)
targetBed
:+=
bed
.
toString
...
...
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