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
46c811a1
Commit
46c811a1
authored
Feb 04, 2015
by
bow
Browse files
Merge branch 'develop' into patch-flexiprep-parse-adapters
parents
4a9e765c
74077f92
Changes
28
Hide whitespace changes
Inline
Side-by-side
protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
View file @
46c811a1
...
...
@@ -41,7 +41,7 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
var
outputSnps
:
FastaOutput
=
_
protected
def
addJobs
()
:
Unit
=
{
addLib
s
Jobs
()
add
Per
LibJobs
()
output
=
addGenerateFasta
(
sampleId
,
sampleDir
)
outputSnps
=
addGenerateFasta
(
sampleId
,
sampleDir
,
snpsOnly
=
true
)
}
...
...
@@ -56,11 +56,13 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
gatkPipeline
.
biopetScript
addAll
(
gatkPipeline
.
functions
)
addSamplesJobs
()
}
def
addMultiSampleJobs
()
:
Unit
=
{
val
refVariants
=
addGenerateFasta
(
null
,
outputDir
+
"reference/"
,
outputName
=
"reference"
)
val
refVariantSnps
=
addGenerateFasta
(
null
,
outputDir
+
"reference/"
,
outputName
=
"reference"
,
snpsOnly
=
true
)
addSamplesJobs
()
val
catVariants
=
Cat
(
this
,
refVariants
.
variants
::
samples
.
map
(
_
.
_2
.
output
.
variants
).
toList
,
outputDir
+
"fastas/variant.fasta"
)
add
(
catVariants
)
val
catVariantsSnps
=
Cat
(
this
,
refVariantSnps
.
variants
::
samples
.
map
(
_
.
_2
.
outputSnps
.
variants
).
toList
,
outputDir
+
"fastas/variant.snps_only.fasta"
)
...
...
@@ -122,13 +124,14 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
val
gubbins
=
new
RunGubbins
(
this
)
gubbins
.
fastafile
=
concensusVariants
gubbins
.
startingTree
=
raxmlBi
.
getBipartitionsFile
gubbins
.
startingTree
=
Some
(
raxmlBi
.
getBipartitionsFile
)
gubbins
.
outputDirectory
=
outputDir
+
dirSufixGubbins
add
(
gubbins
)
}
addTreeJobs
(
catVariantsSnps
.
output
,
catConsensusVariantsSnps
.
output
,
outputDir
+
"trees"
+
File
.
separator
+
"snps_only"
,
"snps_only"
)
addTreeJobs
(
catVariants
.
output
,
catConsensusVariants
.
output
,
outputDir
+
"trees"
+
File
.
separator
+
"snps_indels"
,
"snps_indels"
)
}
def
addGenerateFasta
(
sampleName
:
String
,
outputDir
:
String
,
outputName
:
String
=
null
,
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/BaseRecalibrator.scala
View file @
46c811a1
...
...
@@ -12,7 +12,7 @@ class BaseRecalibrator(val root: Configurable) extends org.broadinstitute.gatk.q
memoryLimit
=
Option
(
4
)
override
val
defaultVmem
=
"8G"
if
(
config
.
contains
(
"scattercount"
))
scatterCount
=
config
(
"scattercount"
)
if
(
config
.
contains
(
"scattercount"
))
scatterCount
=
config
(
"scattercount"
,
default
=
1
)
if
(
config
.
contains
(
"dbsnp"
))
knownSites
:+=
new
File
(
config
(
"dbsnp"
).
asString
)
if
(
config
.
contains
(
"known_sites"
))
knownSites
:+=
new
File
(
config
(
"known_sites"
).
asString
)
}
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GatkGeneral.scala
View file @
46c811a1
...
...
@@ -19,7 +19,7 @@ trait GatkGeneral extends CommandLineGATK with BiopetJavaCommandLineFunction {
if
(
config
.
contains
(
"intervals"
))
intervals
=
config
(
"intervals"
).
asFileList
if
(
config
.
contains
(
"exclude_intervals"
))
excludeIntervals
=
config
(
"exclude_intervals"
).
asFileList
reference_sequence
=
config
(
"reference"
)
gatk_key
=
config
(
"gatk_key"
)
reference_sequence
=
config
(
"reference"
,
required
=
true
)
if
(
config
.
contains
(
"gatk_key"
))
gatk_key
=
config
(
"gatk_key"
)
if
(
config
.
contains
(
"pedigree"
))
pedigree
=
config
(
"pedigree"
).
asFileList
}
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
View file @
46c811a1
...
...
@@ -36,7 +36,6 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
var
singleSampleCalling
=
config
(
"single_sample_calling"
,
default
=
true
)
var
reference
:
File
=
config
(
"reference"
,
required
=
true
)
var
dbsnp
:
File
=
config
(
"dbsnp"
)
var
useAllelesOption
:
Boolean
=
config
(
"use_alleles_option"
,
default
=
false
)
val
externalGvcfs
=
config
(
"external_gvcfs_files"
,
default
=
Nil
).
asFileList
...
...
@@ -72,7 +71,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
samToFastq
.
isIntermediate
=
true
qscript
.
add
(
samToFastq
)
mapping
.
input_R1
=
samToFastq
.
fastqR1
mapping
.
input_R2
=
samToFastq
.
fastqR2
mapping
.
input_R2
=
Some
(
samToFastq
.
fastqR2
)
mapping
.
init
mapping
.
biopetScript
addAll
(
mapping
.
functions
)
// Add functions of mapping to curent function pool
...
...
@@ -127,7 +126,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
gatkVariantcalling
.
outputDir
=
sampleDir
+
"/variantcalling/"
protected
def
addJobs
()
:
Unit
=
{
addLib
s
Jobs
()
add
Per
LibJobs
()
gatkVariantcalling
.
inputBams
=
libraries
.
map
(
_
.
_2
.
mapping
.
finalBamFile
).
toList
gatkVariantcalling
.
preProcesBams
=
false
if
(!
singleSampleCalling
)
{
...
...
@@ -150,10 +149,11 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
override
def
configPath
:
List
[
String
]
=
super
.
configPath
:::
"multisample"
::
Nil
}
def
biopetScript
()
{
addSamplesJobs
def
biopetScript
()
:
Unit
=
{
addSamplesJobs
()
}
//SampleWide jobs
def
addMultiSampleJobs
()
:
Unit
=
{
val
gvcfFiles
:
List
[
File
]
=
if
(
mergeGvcfs
&&
externalGvcfs
.
size
+
samples
.
size
>
1
)
{
val
newFile
=
outputDir
+
"merged.gvcf.vcf.gz"
add
(
CombineGVCFs
(
this
,
externalGvcfs
++
samples
.
map
(
_
.
_2
.
gatkVariantcalling
.
scriptOutput
.
gvcfFile
),
newFile
))
...
...
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
View file @
46c811a1
...
...
@@ -32,9 +32,6 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
@Argument
(
doc
=
"Reference"
,
shortName
=
"R"
,
required
=
false
)
var
reference
:
File
=
config
(
"reference"
,
required
=
true
)
@Argument
(
doc
=
"Dbsnp"
,
shortName
=
"dbsnp"
,
required
=
false
)
var
dbsnp
:
File
=
config
(
"dbsnp"
)
@Argument
(
doc
=
"OutputName"
,
required
=
false
)
var
outputName
:
String
=
_
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
View file @
46c811a1
...
...
@@ -38,7 +38,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
val
defaultThreads
=
1
@Argument
(
doc
=
"Vmem"
,
required
=
false
)
var
vmem
:
String
=
_
var
vmem
:
Option
[
String
]
=
None
val
defaultVmem
:
String
=
""
@Argument
(
doc
=
"Executable"
,
required
=
false
)
...
...
@@ -58,9 +58,9 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
if
(
threads
==
0
)
threads
=
getThreads
(
defaultThreads
)
if
(
threads
>
1
)
nCoresRequest
=
Option
(
threads
)
if
(
vmem
==
null
)
{
if
(
vmem
.
isEmpty
)
{
vmem
=
config
(
"vmem"
)
if
(
vmem
==
null
&&
!
defaultVmem
.
is
Empty
)
vmem
=
defaultVmem
if
(
vmem
.
isEmpty
&&
defaultVmem
.
non
Empty
)
vmem
=
Some
(
defaultVmem
)
}
if
(
vmem
!=
null
)
jobResourceRequests
:+=
"h_vmem="
+
vmem
jobName
=
configName
+
":"
+
firstOutput
.
getName
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
View file @
46c811a1
...
...
@@ -26,7 +26,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument }
*/
trait
MultiSampleQScript
extends
BiopetQScript
{
@Argument
(
doc
=
"Only Sample"
,
shortName
=
"sample"
,
required
=
false
)
val
onlySample
:
List
[
String
]
=
Nil
private
val
onlySample
s
:
List
[
String
]
=
Nil
require
(
Config
.
global
.
map
.
contains
(
"samples"
),
"No Samples found in config"
)
...
...
@@ -94,7 +94,7 @@ trait MultiSampleQScript extends BiopetQScript {
protected
def
addJobs
()
/** function add all libraries in one call */
protected
final
def
addLib
s
Jobs
()
:
Unit
=
{
protected
final
def
add
Per
LibJobs
()
:
Unit
=
{
for
((
libraryId
,
library
)
<-
libraries
)
{
library
.
addAndTrackJobs
()
}
...
...
@@ -125,17 +125,24 @@ trait MultiSampleQScript extends BiopetQScript {
val
samples
:
Map
[
String
,
Sample
]
=
sampleIds
.
map
(
id
=>
id
->
makeSample
(
id
)).
toMap
/** Returns a list of all sampleIDs */
protected
def
sampleIds
:
Set
[
String
]
=
if
(
onlySample
!=
Nil
)
onlySample
.
toSet
else
{
ConfigUtils
.
any2map
(
Config
.
global
.
map
(
"samples"
)).
keySet
}
protected
def
sampleIds
:
Set
[
String
]
=
ConfigUtils
.
any2map
(
Config
.
global
.
map
(
"samples"
)).
keySet
/** Runs addAndTrackJobs method for each sample */
final
def
addSamplesJobs
()
{
for
((
sampleId
,
sample
)
<-
samples
)
{
sample
.
addAndTrackJobs
()
}
if
(
onlySamples
.
isEmpty
)
{
samples
.
foreach
{
case
(
sampleId
,
sample
)
=>
sample
.
addAndTrackJobs
()
}
addMultiSampleJobs
()
}
else
onlySamples
.
foreach
(
sampleId
=>
samples
.
get
(
sampleId
)
match
{
case
Some
(
sample
)
=>
sample
.
addAndTrackJobs
()
case
None
=>
logger
.
warn
(
"sampleId '"
+
sampleId
+
"' not found"
)
})
}
/**
* Method where the multisample jobs should be added, this will be executed only when running the -sample argument is not given
*/
def
addMultiSampleJobs
()
/** Stores sample state */
private
var
currentSample
:
Option
[
String
]
=
None
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
View file @
46c811a1
...
...
@@ -43,7 +43,7 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction {
override
val
defaultThreads
=
8
var
sam
:
Boolean
=
config
(
"sam"
,
default
=
true
)
var
sam_RG
:
String
=
config
(
"sam-RG"
)
var
sam_RG
:
Option
[
String
]
=
config
(
"sam-RG"
)
var
seedlen
:
Option
[
Int
]
=
config
(
"seedlen"
)
var
seedmms
:
Option
[
Int
]
=
config
(
"seedmms"
)
var
k
:
Option
[
Int
]
=
config
(
"k"
)
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
View file @
46c811a1
...
...
@@ -43,8 +43,8 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction {
if
(
config
.
contains
(
"front"
))
for
(
adapter
<-
config
(
"front"
).
asList
)
opt_front
+=
adapter
.
toString
var
opt_discard
:
Boolean
=
config
(
"discard"
,
default
=
false
)
var
opt_minimum_length
:
String
=
config
(
"minimum_length"
,
1
)
var
opt_maximum_length
:
String
=
config
(
"maximum_length"
)
var
opt_minimum_length
:
Option
[
Int
]
=
config
(
"minimum_length"
,
1
)
var
opt_maximum_length
:
Option
[
Int
]
=
config
(
"maximum_length"
)
def
cmdLine
=
required
(
executable
)
+
// options
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
View file @
46c811a1
...
...
@@ -60,11 +60,11 @@ class Raxml(val root: Configurable) extends BiopetCommandLineFunction {
private
var
out
:
List
[
File
]
=
Nil
var
executableNonThreads
:
String
=
config
(
"exe"
,
default
=
"raxmlHPC"
)
var
executableThreads
:
String
=
config
(
"exe_pthreads"
)
var
executableThreads
:
Option
[
String
]
=
config
(
"exe_pthreads"
)
override
def
afterGraph
{
if
(
threads
==
0
)
threads
=
getThreads
(
defaultThreads
)
executable
=
if
(
threads
>
1
&&
executableThreads
!=
null
)
executableThreads
else
executableNonThreads
executable
=
if
(
threads
>
1
&&
executableThreads
.
isDefined
)
executableThreads
.
get
else
executableNonThreads
super
.
afterGraph
out
+:=
getInfoFile
f
match
{
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
View file @
46c811a1
...
...
@@ -24,7 +24,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
class
RunGubbins
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
{
@Input
(
doc
=
"Contaminants"
,
required
=
false
)
var
startingTree
:
File
=
config
(
"starting_tree"
)
var
startingTree
:
Option
[
File
]
=
config
(
"starting_tree"
)
@Input
(
doc
=
"Fasta file"
,
shortName
=
"FQ"
)
var
fastafile
:
File
=
_
...
...
@@ -36,21 +36,21 @@ class RunGubbins(val root: Configurable) extends BiopetCommandLineFunction {
var
outputDirectory
:
String
=
_
executable
=
config
(
"exe"
,
default
=
"run_gubbins.py"
)
var
outgroup
:
String
=
config
(
"outgroup"
)
var
filterPercentage
:
String
=
config
(
"filter_percentage"
)
var
treeBuilder
:
String
=
config
(
"tree_builder"
)
var
outgroup
:
Option
[
String
]
=
config
(
"outgroup"
)
var
filterPercentage
:
Option
[
String
]
=
config
(
"filter_percentage"
)
var
treeBuilder
:
Option
[
String
]
=
config
(
"tree_builder"
)
var
iterations
:
Option
[
Int
]
=
config
(
"iterations"
)
var
minSnps
:
Option
[
Int
]
=
config
(
"min_snps"
)
var
convergeMethod
:
String
=
config
(
"converge_method"
)
var
convergeMethod
:
Option
[
String
]
=
config
(
"converge_method"
)
var
useTimeStamp
:
Boolean
=
config
(
"use_time_stamp"
,
default
=
false
)
var
prefix
:
String
=
config
(
"prefix"
)
var
prefix
:
Option
[
String
]
=
config
(
"prefix"
)
var
verbose
:
Boolean
=
config
(
"verbose"
,
default
=
false
)
var
noCleanup
:
Boolean
=
config
(
"no_cleanup"
,
default
=
false
)
override
def
afterGraph
:
Unit
=
{
super
.
afterGraph
jobLocalDir
=
new
File
(
outputDirectory
)
if
(
prefix
==
null
)
prefix
=
fastafile
.
getName
if
(
prefix
.
isEmpty
)
prefix
=
Some
(
fastafile
.
getName
)
val
out
:
List
[
String
]
=
List
(
".recombination_predictions.embl"
,
".recombination_predictions.gff"
,
".branch_base_reconstruction.embl"
,
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala
View file @
46c811a1
...
...
@@ -43,7 +43,7 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction {
var
fastqc
:
Fastqc
=
_
executable
=
config
(
"exe"
,
default
=
"sickle"
,
freeVar
=
false
)
var
qualityType
:
String
=
config
(
"qualitytype"
)
var
qualityType
:
Option
[
String
]
=
config
(
"qualitytype"
)
var
qualityThreshold
:
Option
[
Int
]
=
config
(
"qualityThreshold"
)
var
lengthThreshold
:
Option
[
Int
]
=
config
(
"lengthThreshold"
)
var
noFiveprime
:
Boolean
=
config
(
"noFiveprime"
,
default
=
false
)
...
...
@@ -54,7 +54,7 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction {
override
def
versionCommand
=
executable
+
" --version"
override
def
afterGraph
{
if
(
qualityType
==
null
&&
defaultQualityType
!=
null
)
qualityType
=
defaultQualityType
if
(
qualityType
.
isEmpty
)
qualityType
=
Some
(
defaultQualityType
)
}
def
cmdLine
=
{
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
View file @
46c811a1
...
...
@@ -34,7 +34,7 @@ class BwaMem(val root: Configurable) extends Bwa {
@Output
(
doc
=
"Output file SAM"
,
shortName
=
"output"
)
var
output
:
File
=
_
var
R
:
String
=
config
(
"R"
)
var
R
:
Option
[
String
]
=
config
(
"R"
)
var
k
:
Option
[
Int
]
=
config
(
"k"
)
var
r
:
Option
[
Float
]
=
config
(
"r"
)
var
S
:
Boolean
=
config
(
"S"
,
default
=
false
)
...
...
@@ -49,11 +49,11 @@ class BwaMem(val root: Configurable) extends Bwa {
var
e
:
Boolean
=
config
(
"e"
,
default
=
false
)
var
A
:
Option
[
Int
]
=
config
(
"A"
)
var
B
:
Option
[
Int
]
=
config
(
"B"
)
var
O
:
String
=
config
(
"O"
)
var
E
:
String
=
config
(
"E"
)
var
L
:
String
=
config
(
"L"
)
var
O
:
Option
[
String
]
=
config
(
"O"
)
var
E
:
Option
[
String
]
=
config
(
"E"
)
var
L
:
Option
[
String
]
=
config
(
"L"
)
var
U
:
Option
[
Int
]
=
config
(
"U"
)
var
x
:
String
=
config
(
"x"
)
var
x
:
Option
[
String
]
=
config
(
"x"
)
var
p
:
Boolean
=
config
(
"p"
,
default
=
false
)
var
v
:
Option
[
Int
]
=
config
(
"v"
)
var
T
:
Option
[
Int
]
=
config
(
"T"
)
...
...
@@ -61,7 +61,7 @@ class BwaMem(val root: Configurable) extends Bwa {
var
a
:
Boolean
=
config
(
"a"
,
default
=
false
)
var
C
:
Boolean
=
config
(
"C"
,
default
=
false
)
var
Y
:
Boolean
=
config
(
"Y"
,
default
=
false
)
var
I
:
String
=
config
(
"I"
)
var
I
:
Option
[
String
]
=
config
(
"I"
)
override
val
defaultVmem
=
"6G"
override
val
defaultThreads
=
8
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala
View file @
46c811a1
...
...
@@ -30,12 +30,12 @@ class Macs2CallPeak(val root: Configurable) extends Macs2 {
@Output
(
doc
=
"Output file gappedPeak"
)
private
var
output_gapped
:
File
=
_
var
fileformat
:
String
=
config
(
"fileformat"
)
var
fileformat
:
Option
[
String
]
=
config
(
"fileformat"
)
var
gsize
:
Option
[
Float
]
=
config
(
"gsize"
)
var
keepdup
:
Boolean
=
config
(
"keep-dup"
,
default
=
false
)
var
buffersize
:
Option
[
Int
]
=
config
(
"buffer-size"
)
var
outputdir
:
String
=
config
(
"outputDir"
)
var
name
:
String
=
config
(
"name"
)
var
outputdir
:
String
=
_
var
name
:
Option
[
String
]
=
config
(
"name"
)
var
bdg
:
Boolean
=
config
(
"bdg"
,
default
=
false
)
var
verbose
:
Boolean
=
config
(
"verbose"
,
default
=
false
)
var
tsize
:
Option
[
Int
]
=
config
(
"tsize"
)
...
...
@@ -56,12 +56,14 @@ class Macs2CallPeak(val root: Configurable) extends Macs2 {
var
callsummits
:
Boolean
=
config
(
"callsummits"
,
default
=
false
)
override
def
afterGraph
:
Unit
=
{
output_narrow
=
new
File
(
outputdir
+
name
+
".narrowPeak"
)
output_broad
=
new
File
(
outputdir
+
name
+
".broadPeak"
)
output_xls
=
new
File
(
outputdir
+
name
+
".xls"
)
output_bdg
=
new
File
(
outputdir
+
name
+
".bdg"
)
output_r
=
new
File
(
outputdir
+
name
+
".r"
)
output_gapped
=
new
File
(
outputdir
+
name
+
".gappedPeak"
)
if
(
name
.
isEmpty
)
throw
new
IllegalArgumentException
(
"Name is not defined"
)
if
(
outputdir
==
null
)
throw
new
IllegalArgumentException
(
"Outputdir is not defined"
)
output_narrow
=
new
File
(
outputdir
+
name
.
get
+
".narrowPeak"
)
output_broad
=
new
File
(
outputdir
+
name
.
get
+
".broadPeak"
)
output_xls
=
new
File
(
outputdir
+
name
.
get
+
".xls"
)
output_bdg
=
new
File
(
outputdir
+
name
.
get
+
".bdg"
)
output_r
=
new
File
(
outputdir
+
name
.
get
+
".r"
)
output_gapped
=
new
File
(
outputdir
+
name
.
get
+
".gappedPeak"
)
}
def
cmdLine
=
{
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
View file @
46c811a1
...
...
@@ -32,19 +32,19 @@ class MarkDuplicates(val root: Configurable) extends Picard {
var
outputMetrics
:
File
=
_
@Argument
(
doc
=
"PROGRAM_RECORD_ID"
,
required
=
false
)
var
programRecordId
:
String
=
config
(
"programrecordid"
)
var
programRecordId
:
Option
[
String
]
=
config
(
"programrecordid"
)
@Argument
(
doc
=
"PROGRAM_GROUP_VERSION"
,
required
=
false
)
var
programGroupVersion
:
String
=
config
(
"programgroupversion"
)
var
programGroupVersion
:
Option
[
String
]
=
config
(
"programgroupversion"
)
@Argument
(
doc
=
"PROGRAM_GROUP_COMMAND_LINE"
,
required
=
false
)
var
programGroupCommandLine
:
String
=
config
(
"programgroupcommandline"
)
var
programGroupCommandLine
:
Option
[
String
]
=
config
(
"programgroupcommandline"
)
@Argument
(
doc
=
"PROGRAM_GROUP_NAME"
,
required
=
false
)
var
programGroupName
:
String
=
config
(
"programgroupname"
)
var
programGroupName
:
Option
[
String
]
=
config
(
"programgroupname"
)
@Argument
(
doc
=
"COMMENT"
,
required
=
false
)
var
comment
:
String
=
config
(
"comment"
)
var
comment
:
Option
[
String
]
=
config
(
"comment"
)
@Argument
(
doc
=
"REMOVE_DUPLICATES"
,
required
=
false
)
var
removeDuplicates
:
Boolean
=
config
(
"removeduplicates"
,
default
=
false
)
...
...
@@ -62,7 +62,7 @@ class MarkDuplicates(val root: Configurable) extends Picard {
var
sortingCollectionSizeRatio
:
Option
[
Double
]
=
config
(
"sortingCollectionSizeRatio"
)
@Argument
(
doc
=
"READ_NAME_REGEX"
,
required
=
false
)
var
readNameRegex
:
String
=
config
(
"readNameRegex"
)
var
readNameRegex
:
Option
[
String
]
=
config
(
"readNameRegex"
)
@Argument
(
doc
=
"OPTICAL_DUPLICATE_PIXEL_DISTANCE"
,
required
=
false
)
var
opticalDuplicatePixelDistance
:
Option
[
Int
]
=
config
(
"opticalDuplicatePixelDistance"
)
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala
View file @
46c811a1
...
...
@@ -41,7 +41,7 @@ class MergeSamFiles(val root: Configurable) extends Picard {
var
useThreading
:
Boolean
=
config
(
"use_threading"
,
default
=
false
)
@Argument
(
doc
=
"COMMENT"
,
required
=
false
)
var
comment
:
String
=
config
(
"comment"
)
var
comment
:
Option
[
String
]
=
config
(
"comment"
)
override
def
commandLine
=
super
.
commandLine
+
repeat
(
"INPUT="
,
input
,
spaceSeparated
=
false
)
+
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
View file @
46c811a1
...
...
@@ -22,13 +22,13 @@ abstract class Picard extends BiopetJavaCommandLineFunction {
override
def
subPath
=
"picard"
::
super
.
subPath
@Argument
(
doc
=
"VERBOSITY"
,
required
=
false
)
var
verbosity
:
String
=
config
(
"verbosity"
)
var
verbosity
:
Option
[
String
]
=
config
(
"verbosity"
)
@Argument
(
doc
=
"QUIET"
,
required
=
false
)
var
quiet
:
Boolean
=
config
(
"quiet"
,
default
=
false
)
@Argument
(
doc
=
"VALIDATION_STRINGENCY"
,
required
=
false
)
var
stringency
:
String
=
config
(
"validationstringency"
)
var
stringency
:
Option
[
String
]
=
config
(
"validationstringency"
)
@Argument
(
doc
=
"COMPRESSION_LEVEL"
,
required
=
false
)
var
compression
:
Option
[
Int
]
=
config
(
"compressionlevel"
)
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala
View file @
46c811a1
...
...
@@ -38,7 +38,7 @@ class SamToFastq(val root: Configurable) extends Picard {
var
outputPerRg
:
Boolean
=
config
(
"outputPerRg"
,
default
=
false
)
@Argument
(
doc
=
"Output dir"
,
required
=
false
)
var
outputDir
:
String
=
config
(
"outputDir"
)
var
outputDir
:
String
=
_
@Argument
(
doc
=
"re reverse"
,
required
=
false
)
var
reReverse
:
Boolean
=
config
(
"reReverse"
,
default
=
false
)
...
...
@@ -53,7 +53,7 @@ class SamToFastq(val root: Configurable) extends Picard {
var
clippingAtribute
:
String
=
config
(
"clippingAtribute"
)
@Argument
(
doc
=
"clippingAction"
,
required
=
false
)
var
clippingAction
:
String
=
config
(
"clippingAction"
)
var
clippingAction
:
Option
[
String
]
=
config
(
"clippingAction"
)
@Argument
(
doc
=
"read1Trim"
,
required
=
false
)
var
read1Trim
:
Option
[
Int
]
=
config
(
"read1Trim"
)
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala
View file @
46c811a1
...
...
@@ -30,7 +30,7 @@ class SamtoolsMpileup(val root: Configurable) extends Samtools {
var
reference
:
File
=
config
(
"reference"
)
@Input
(
doc
=
"Interval bed"
)
var
intervalBed
:
File
=
config
(
"interval_bed"
)
var
intervalBed
:
Option
[
File
]
=
config
(
"interval_bed"
)
var
disableBaq
:
Boolean
=
config
(
"disable_baq"
)
var
minMapQuality
:
Option
[
Int
]
=
config
(
"min_map_quality"
)
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala
View file @
46c811a1
...
...
@@ -37,7 +37,7 @@ class SeqtkSeq(val root: Configurable) extends Seqtk {
var
q
:
Option
[
Int
]
=
config
(
"q"
)
/** masked bases converted to CHAR; 0 for lowercase [0] */
var
n
:
String
=
config
(
"n"
)
var
n
:
Option
[
String
]
=
config
(
"n"
)
/** number of residues per line; 0 for 2^32-1 [0] */
var
l
:
Option
[
Int
]
=
config
(
"l"
)
...
...
@@ -52,7 +52,7 @@ class SeqtkSeq(val root: Configurable) extends Seqtk {
var
f
:
Option
[
Int
]
=
config
(
"f"
)
/** mask regions in BED or name list FILE [null] */
var
M
:
File
=
config
(
"M"
)
var
M
:
Option
[
File
]
=
config
(
"M"
)
/** drop sequences with length shorter than INT [0] */
var
L
:
Option
[
Int
]
=
config
(
"L"
)
...
...
Prev
1
2
Next
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