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Mirrors
biopet.biopet
Commits
a161a802
Commit
a161a802
authored
Jan 06, 2016
by
Sander Bollen
Browse files
fix merge request issues
parent
19bbb31c
Changes
20
Hide whitespace changes
Inline
Side-by-side
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala
View file @
a161a802
...
...
@@ -8,7 +8,7 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import
java.io.File
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Gather
,
Output
}
import
org.broadinstitute.gatk.utils.commandline.
{
Gather
,
Output
}
class
GenotypeGVCFs
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
GenotypeGVCFs
with
GatkGeneral
{
...
...
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsView.scala
View file @
a161a802
...
...
@@ -17,10 +17,10 @@ class BcftoolsView(val root: Configurable) extends Bcftools {
var
output
:
File
=
_
@Argument
(
doc
=
"drop individual genotypes"
,
required
=
false
)
var
dropGenotype
:
Boolean
=
false
var
dropGenotype
:
Boolean
=
config
(
"drop_genotype"
,
default
=
false
)
@Argument
(
doc
=
"header only"
,
required
=
false
)
var
headerOnly
:
Boolean
=
false
var
headerOnly
:
Boolean
=
config
(
"header_only"
,
false
)
@Argument
(
doc
=
"Compression level"
,
required
=
false
)
var
compressionLevel
:
Int
=
9
...
...
@@ -29,88 +29,88 @@ class BcftoolsView(val root: Configurable) extends Bcftools {
var
outputType
:
String
=
"z"
@Argument
(
doc
=
"regions"
,
required
=
false
)
var
regions
:
String
=
_
var
regions
:
Option
[
String
]
=
config
(
"r"
)
@Argument
(
doc
=
"region file"
,
required
=
false
)
var
regionFile
:
File
=
_
var
regionFile
:
Option
[
File
]
=
config
(
"R"
)
@Argument
(
doc
=
"targets"
,
required
=
false
)
var
targets
:
String
=
_
var
targets
:
Option
[
String
]
=
config
(
"t"
)
@Argument
(
doc
=
"targets file"
,
required
=
false
)
var
targetFile
:
File
=
_
var
targetFile
:
Option
[
File
]
=
config
(
"T"
)
@Argument
(
doc
=
"trim alt alleles"
,
required
=
false
)
var
trimAltAlleles
:
Boolean
=
false
var
trimAltAlleles
:
Boolean
=
config
(
"trim_alt_allele"
,
default
=
false
)
@Argument
(
doc
=
"no update"
,
required
=
false
)
var
noUpdate
:
Boolean
=
false
var
noUpdate
:
Boolean
=
config
(
"no_update"
,
default
=
false
)
@Argument
(
doc
=
"samples"
,
required
=
false
)
var
samples
:
List
[
String
]
=
Nil
var
samples
:
List
[
String
]
=
config
(
"s"
,
default
=
Nil
)
@Argument
(
doc
=
"samples file"
,
required
=
false
)
var
sampleFile
:
File
=
_
var
sampleFile
:
Option
[
File
]
=
config
(
"S"
)
@Argument
(
doc
=
"minimum allele count"
,
required
=
false
)
var
minAC
:
Option
[
Int
]
=
_
var
minAC
:
Option
[
Int
]
=
config
(
"c"
)
@Argument
(
doc
=
"max allele count"
,
required
=
false
)
var
maxAC
:
Option
[
Int
]
=
_
var
maxAC
:
Option
[
Int
]
=
config
(
"C"
)
@Argument
(
doc
=
"exclude (expression)"
,
required
=
false
)
var
exclude
:
String
=
_
var
exclude
:
Option
[
String
]
=
config
(
"e"
)
@Argument
(
doc
=
"apply filters"
,
required
=
false
)
var
applyFilters
:
List
[
String
]
=
Nil
var
applyFilters
:
List
[
String
]
=
config
(
"F"
,
default
=
Nil
)
@Argument
(
doc
=
"genotype"
,
required
=
false
)
var
genotype
:
String
=
_
var
genotype
:
Option
[
String
]
=
config
(
"g"
)
@Argument
(
doc
=
"include (expression)"
,
required
=
false
)
var
include
:
String
=
_
var
include
:
Option
[
String
]
=
config
(
"i"
)
@Argument
(
doc
=
"Known (ID field is not .) only"
,
required
=
false
)
var
known
:
Boolean
=
false
var
known
:
Boolean
=
config
(
"k"
,
default
=
false
)
@Argument
(
doc
=
"min alleles"
,
required
=
false
)
var
minAlleles
:
Option
[
Int
]
=
_
var
minAlleles
:
Option
[
Int
]
=
config
(
"m"
)
@Argument
(
doc
=
"max alleles"
,
required
=
false
)
var
maxAlleles
:
Option
[
Int
]
=
_
var
maxAlleles
:
Option
[
Int
]
=
config
(
"M"
)
@Argument
(
doc
=
"novel (ID field is .) only"
,
required
=
false
)
var
novel
:
Boolean
=
false
var
novel
:
Boolean
=
config
(
"n"
,
false
)
@Argument
(
doc
=
"phased only"
,
required
=
false
)
var
phased
:
Boolean
=
false
var
phased
:
Boolean
=
config
(
"p"
,
false
)
@Argument
(
doc
=
"exclude phased (only)"
,
required
=
false
)
var
excludePhased
:
Boolean
=
false
var
excludePhased
:
Boolean
=
config
(
"P"
,
false
)
@Argument
(
doc
=
"min allele frequency"
,
required
=
false
)
var
minAF
:
Option
[
Int
]
=
_
var
minAF
:
Option
[
Int
]
=
config
(
"q"
)
@Argument
(
doc
=
"max allele frequency"
,
required
=
false
)
var
maxAF
:
Option
[
Int
]
=
_
var
maxAF
:
Option
[
Int
]
=
config
(
"Q"
)
@Argument
(
doc
=
"uncalled only"
,
required
=
false
)
var
uncalled
:
Boolean
=
false
var
uncalled
:
Boolean
=
config
(
"u"
,
default
=
false
)
@Argument
(
doc
=
"exclude uncalled (only)"
,
required
=
false
)
var
excludeUncalled
:
Boolean
=
false
var
excludeUncalled
:
Boolean
=
config
(
"U"
,
default
=
false
)
@Argument
(
doc
=
"types"
,
required
=
false
)
var
types
:
String
=
_
var
types
:
Option
[
String
]
=
config
(
"v"
)
@Argument
(
doc
=
"exclude types"
,
required
=
false
)
var
excludeTypes
:
String
=
_
var
excludeTypes
:
Option
[
String
]
=
config
(
"V"
)
@Argument
(
doc
=
"private (requires samples)"
,
required
=
false
)
var
onlyPrivate
:
Boolean
=
false
var
onlyPrivate
:
Boolean
=
config
(
"x"
,
default
=
false
)
@Argument
(
doc
=
"Exclude privates"
,
required
=
false
)
var
excludePrivate
:
Boolean
=
false
var
excludePrivate
:
Boolean
=
config
(
"X"
,
default
=
false
)
override
def
beforeGraph
()
=
{
super
.
beforeGraph
()
...
...
@@ -123,21 +123,39 @@ class BcftoolsView(val root: Configurable) extends Bcftools {
}
def
baseCmd
=
{
executable
+
" view "
+
conditional
(
dropGenotype
,
"-G"
)
+
conditional
(
headerOnly
,
"-h"
)
+
required
(
"-l"
,
compressionLevel
)
+
required
(
"-O"
,
outputType
)
+
optional
(
"-r"
,
regions
)
+
optional
(
"-R"
,
regionFile
)
+
optional
(
"-t"
,
targets
)
+
optional
(
"-T"
,
targetFile
)
+
conditional
(
trimAltAlleles
,
"-a"
)
+
conditional
(
noUpdate
,
"-I"
)
+
repeat
(
"-s"
,
samples
)
+
optional
(
"-S"
,
sampleFile
)
+
optional
(
"-c"
,
minAC
)
+
optional
(
"-C"
,
maxAC
)
+
optional
(
"-e"
,
exclude
)
+
optional
(
"-f"
,
applyFilters
)
+
optional
(
"-g"
,
genotype
)
+
optional
(
"-i"
,
include
)
+
conditional
(
known
,
"-k"
)
+
optional
(
"-m"
,
minAlleles
)
+
optional
(
"-M"
,
maxAlleles
)
+
conditional
(
novel
,
"-n"
)
+
conditional
(
phased
,
"-p"
)
+
conditional
(
excludePhased
,
"-P"
)
+
optional
(
"-q"
,
minAF
)
+
optional
(
"-Q"
,
maxAF
)
+
conditional
(
uncalled
,
"-u"
)
+
conditional
(
excludeUncalled
,
"-U"
)
+
optional
(
"-v"
,
types
)
+
conditional
(
onlyPrivate
,
"-x"
)
+
executable
+
required
(
"view"
)
+
conditional
(
dropGenotype
,
"-G"
)
+
conditional
(
headerOnly
,
"-h"
)
+
required
(
"-l"
,
compressionLevel
)
+
required
(
"-O"
,
outputType
)
+
optional
(
"-r"
,
regions
)
+
optional
(
"-R"
,
regionFile
)
+
optional
(
"-t"
,
targets
)
+
optional
(
"-T"
,
targetFile
)
+
conditional
(
trimAltAlleles
,
"-a"
)
+
conditional
(
noUpdate
,
"-I"
)
+
repeat
(
"-s"
,
samples
)
+
optional
(
"-S"
,
sampleFile
)
+
optional
(
"-c"
,
minAC
)
+
optional
(
"-C"
,
maxAC
)
+
optional
(
"-e"
,
exclude
)
+
optional
(
"-f"
,
applyFilters
)
+
optional
(
"-g"
,
genotype
)
+
optional
(
"-i"
,
include
)
+
conditional
(
known
,
"-k"
)
+
optional
(
"-m"
,
minAlleles
)
+
optional
(
"-M"
,
maxAlleles
)
+
conditional
(
novel
,
"-n"
)
+
conditional
(
phased
,
"-p"
)
+
conditional
(
excludePhased
,
"-P"
)
+
optional
(
"-q"
,
minAF
)
+
optional
(
"-Q"
,
maxAF
)
+
conditional
(
uncalled
,
"-u"
)
+
conditional
(
excludeUncalled
,
"-U"
)
+
optional
(
"-v"
,
types
)
+
optional
(
"-V"
,
excludeTypes
)
+
conditional
(
onlyPrivate
,
"-x"
)
+
conditional
(
excludePrivate
,
"-X"
)
}
...
...
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsMerge.scala
View file @
a161a802
...
...
@@ -14,7 +14,7 @@ class BedtoolsMerge(val root: Configurable) extends Bedtools {
var
input
:
File
=
_
@Argument
(
doc
=
"Distance"
)
var
dist
:
Int
=
1
//default of tool is 1
var
dist
:
Option
[
Int
]
=
config
(
"dist"
)
//default of tool is 1
@Output
(
doc
=
"Output bed file"
)
var
output
:
File
=
_
...
...
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/Manwe.scala
View file @
a161a802
...
...
@@ -13,9 +13,6 @@ import org.broadinstitute.gatk.utils.commandline.{ Output, Argument }
abstract
class
Manwe
extends
BiopetCommandLineFunction
{
executable
=
config
(
"exe"
,
default
=
"manwe"
,
submodule
=
"manwe"
)
override
def
defaultCoreMemory
=
2.0
override
def
defaultThreads
=
1
var
manweConfig
:
File
=
createManweConfig
(
None
)
@Output
(
doc
=
"the output file"
)
...
...
@@ -58,31 +55,28 @@ abstract class Manwe extends BiopetCommandLineFunction {
val
dataBufferSize
:
Option
[
Int
]
=
config
(
"varda_buffer_size"
,
default
=
1024
*
1024
)
val
taskPollWait
:
Option
[
Int
]
=
config
(
"varda_task_poll_wait"
,
default
=
2
)
val
urlString
=
s
"API_ROOT = '${url.toString}'"
val
tokenString
=
s
"TOKEN = '${token.toString}'"
val
sslSettingString
=
sslSettings
match
{
case
Some
(
"true"
)
=>
"VERIFY_CERTIFICATE = True"
case
Some
(
"false"
)
=>
"VERIFY_CERTIFICATE = False"
case
Some
(
x
)
=>
s
"VERIFY_CERTIFICATE = '$x'"
case
_
=>
"VERIFY_CERTIFICATE = True"
}
val
settingsMap
:
Map
[
String
,
Any
]
=
Map
(
"API_ROOT"
->
s
"'$url'"
,
"TOKEN"
->
s
"'$token'"
,
"VERIFY_CERTIFICATE"
->
(
sslSettings
match
{
case
Some
(
"true"
)
=>
"True"
case
Some
(
"false"
)
=>
"False"
case
Some
(
x
)
=>
s
"'$x'"
case
_
=>
"True"
}),
"COLLECTION_CACHE_SIZE"
->
collectionCacheSize
.
getOrElse
(
20
),
"DATA_BUFFER_SIZE"
->
dataBufferSize
.
getOrElse
(
1048576
),
"TASK_POLL_WAIT"
->
taskPollWait
.
getOrElse
(
2
)
)
val
collectionString
=
s
"COLLECTION_CACHE_SIZE = ${collectionCacheSize.getOrElse(20)}"
val
dataString
=
s
"DATA_BUFFER_SIZE = ${dataBufferSize.getOrElse(1048576)}"
val
taskString
=
s
"TASK_POLL_WAIT = ${taskPollWait.getOrElse(2)}"
val
file
=
directory
match
{
case
Some
(
dir
)
=>
File
.
createTempFile
(
"manwe_config"
,
".py"
,
dir
)
case
None
=>
File
.
createTempFile
(
"manwe_config"
,
".py"
)
}
file
.
deleteOnExit
()
val
writer
=
new
PrintWriter
(
file
)
writer
.
println
(
urlString
)
writer
.
println
(
tokenString
)
writer
.
println
(
sslSettingString
)
writer
.
println
(
collectionString
)
writer
.
println
(
dataString
)
writer
.
println
(
taskString
)
settingsMap
.
foreach
{
case
(
key
,
value
)
=>
writer
.
println
(
s
"$key = $value"
)
}
writer
.
close
()
file
}
...
...
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweAnnotateBed.scala
View file @
a161a802
...
...
@@ -25,7 +25,8 @@ class ManweAnnotateBed(val root: Configurable) extends Manwe {
def
subCommand
=
{
required
(
"annotate-bed"
)
+
required
(
bed
)
+
conditional
(
alreadyUploaded
,
"-u"
)
+
repeat
(
"-q"
,
queries
)
+
conditional
(
waitToComplete
,
"--wait"
)
repeat
(
"-q"
,
queries
)
+
conditional
(
waitToComplete
,
"--wait"
)
}
}
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweAnnotateVcf.scala
View file @
a161a802
...
...
@@ -25,7 +25,8 @@ class ManweAnnotateVcf(val root: Configurable) extends Manwe {
def
subCommand
=
{
required
(
"annotate-vcf"
)
+
required
(
vcf
)
+
conditional
(
alreadyUploaded
,
"-u"
)
+
repeat
(
"-q"
,
queries
)
+
conditional
(
waitToComplete
,
"--wait"
)
repeat
(
"-q"
,
queries
)
+
conditional
(
waitToComplete
,
"--wait"
)
}
}
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweDataSourcesAnnotate.scala
View file @
a161a802
...
...
@@ -19,7 +19,8 @@ class ManweDataSourcesAnnotate(val root: Configurable) extends Manwe {
def
subCommand
=
{
required
(
"data-sources"
)
+
required
(
"annotate"
)
+
required
(
uri
)
+
repeat
(
"-q"
,
queries
)
+
required
(
uri
)
+
repeat
(
"-q"
,
queries
)
+
conditional
(
waitToComplete
,
"--wait"
)
}
...
...
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweDataSourcesDownload.scala
View file @
a161a802
...
...
@@ -12,9 +12,8 @@ class ManweDataSourcesDownload(val root: Configurable) extends Manwe {
var
uri
:
String
=
_
def
subCommand
=
{
required
(
"data-sources"
)
+
required
(
"download"
)
+
required
(
uri
)
required
(
"data-sources"
)
+
required
(
"download"
)
+
required
(
uri
)
}
this
.
deps
}
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweDataSourcesList.scala
View file @
a161a802
...
...
@@ -14,7 +14,8 @@ class ManweDataSourcesList(val root: Configurable) extends Manwe {
var
user
:
Option
[
String
]
=
_
def
subCommand
=
{
required
(
"data-sources"
)
+
required
(
"list"
)
+
required
(
"data-sources"
)
+
required
(
"list"
)
+
optional
(
"-u"
,
user
)
}
...
...
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweDataSourcesShow.scala
View file @
a161a802
...
...
@@ -14,7 +14,8 @@ class ManweDataSourcesShow(val root: Configurable) extends Manwe {
var
uri
:
Option
[
String
]
=
_
def
subCommand
=
{
required
(
"data-sources"
)
+
required
(
"show"
)
+
required
(
"data-sources"
)
+
required
(
"show"
)
+
required
(
uri
)
}
...
...
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesActivate.scala
View file @
a161a802
...
...
@@ -14,7 +14,8 @@ class ManweSamplesActivate(val root: Configurable) extends Manwe {
var
uri
:
String
=
_
def
subCommand
=
{
required
(
"samples"
)
+
required
(
"activate"
)
+
required
(
"samples"
)
+
required
(
"activate"
)
+
required
(
uri
)
}
...
...
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesAdd.scala
View file @
a161a802
...
...
@@ -20,8 +20,11 @@ class ManweSamplesAdd(val root: Configurable) extends Manwe {
var
poolSize
:
Option
[
Int
]
=
_
def
subCommand
=
{
required
(
"samples"
)
+
required
(
"add"
)
+
required
(
name
)
+
optional
(
"-s"
,
poolSize
)
+
repeat
(
"-g"
,
group
)
required
(
"samples"
)
+
required
(
"add"
)
+
required
(
name
)
+
optional
(
"-s"
,
poolSize
)
+
repeat
(
"-g"
,
group
)
}
}
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesAnnotateVariations.scala
View file @
a161a802
...
...
@@ -17,8 +17,10 @@ class ManweSamplesAnnotateVariations(val root: Configurable) extends Manwe {
var
queries
:
List
[
String
]
=
Nil
def
subCommand
=
{
required
(
"samples"
)
+
required
(
"annotate-variations"
)
+
required
(
uri
)
+
repeat
(
"-q"
,
queries
)
required
(
"samples"
)
+
required
(
"annotate-variations"
)
+
required
(
uri
)
+
repeat
(
"-q"
,
queries
)
}
}
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesImport.scala
View file @
a161a802
...
...
@@ -45,10 +45,16 @@ class ManweSamplesImport(val root: Configurable) extends Manwe {
var
waitToComplete
:
Boolean
=
false
def
subCommand
=
{
required
(
"samples"
)
+
required
(
"import"
)
+
required
(
name
)
+
repeat
(
"-g"
,
group
)
+
repeat
(
"--vcf"
,
vcfs
)
+
repeat
(
"--bed"
,
beds
)
+
optional
(
"-s"
,
poolSize
)
+
conditional
(
alreadyUploaded
,
"-u"
)
+
conditional
(
public
,
"-p"
)
+
conditional
(
preferLikelihood
,
"-l"
)
+
required
(
"samples"
)
+
required
(
"import"
)
+
required
(
name
)
+
repeat
(
"-g"
,
group
)
+
repeat
(
"--vcf"
,
vcfs
)
+
repeat
(
"--bed"
,
beds
)
+
optional
(
"-s"
,
poolSize
)
+
conditional
(
alreadyUploaded
,
"-u"
)
+
conditional
(
public
,
"-p"
)
+
conditional
(
preferLikelihood
,
"-l"
)
+
conditional
(
noCoverage
,
"--no-coverage-profile"
)
+
conditional
(
waitToComplete
,
"--wait"
)
}
...
...
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesImportBed.scala
View file @
a161a802
...
...
@@ -27,9 +27,12 @@ class ManweSamplesImportBed(val root: Configurable) extends Manwe {
var
waitToComplete
:
Boolean
=
false
def
subCommand
=
{
required
(
"samples"
)
+
required
(
"import-bed"
)
+
required
(
uri
)
+
required
(
bed
)
+
conditional
(
alreadyUploaded
,
"-u"
)
+
conditional
(
waitToComplete
,
"--wait"
)
required
(
"samples"
)
+
required
(
"import-bed"
)
+
required
(
uri
)
+
required
(
bed
)
+
conditional
(
alreadyUploaded
,
"-u"
)
+
conditional
(
waitToComplete
,
"--wait"
)
}
}
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesImportVcf.scala
View file @
a161a802
...
...
@@ -30,9 +30,11 @@ class ManweSamplesImportVcf(val root: Configurable) extends Manwe {
var
waitToComplete
:
Boolean
=
false
def
subCommand
=
{
required
(
"samples"
)
+
required
(
"import-vcf"
)
+
required
(
"samples"
)
+
required
(
"import-vcf"
)
+
required
(
uri
)
+
required
(
vcf
)
+
conditional
(
alreadyUploaded
,
"-u"
)
+
conditional
(
preferLikelihoods
,
"-l"
)
+
conditional
(
alreadyUploaded
,
"-u"
)
+
conditional
(
preferLikelihoods
,
"-l"
)
+
conditional
(
waitToComplete
,
"--wait"
)
}
...
...
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesList.scala
View file @
a161a802
...
...
@@ -19,8 +19,11 @@ class ManweSamplesList(val root: Configurable) extends Manwe {
var
onlyPublic
:
Boolean
=
false
def
subCommand
=
{
required
(
"samples"
)
+
required
(
"list"
)
+
optional
(
"-u"
,
user
)
+
repeat
(
"-g"
,
group
)
+
conditional
(
onlyPublic
,
"-p"
)
required
(
"samples"
)
+
required
(
"list"
)
+
optional
(
"-u"
,
user
)
+
repeat
(
"-g"
,
group
)
+
conditional
(
onlyPublic
,
"-p"
)
}
}
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/ManweSamplesShow.scala
View file @
a161a802
...
...
@@ -14,7 +14,9 @@ class ManweSamplesShow(val root: Configurable) extends Manwe {
var
uri
:
Option
[
String
]
=
_
def
subCommand
=
{
required
(
"samples"
)
+
required
(
"show"
)
+
required
(
uri
)
required
(
"samples"
)
+
required
(
"show"
)
+
required
(
uri
)
}
}
public/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/ManweTest.scala
View file @
a161a802
...
...
@@ -334,14 +334,17 @@ class ManweTest extends TestNGSuite with Matchers {
}
val
file
:
File
=
manwe
.
createManweConfig
(
None
)
val
contents
=
Source
.
fromFile
(
file
).
getLines
().
mkString
(
"\n"
)
val
contents
=
Source
.
fromFile
(
file
).
getLines
().
toList
contents
should
equal
(
"""API_ROOT = 'http://127.0.0.1:5000'
|TOKEN = 'QWERTYUIOPASDFGHJKLZXCVBNM'
|VERIFY_CERTIFICATE = True
|COLLECTION_CACHE_SIZE = 25
|DATA_BUFFER_SIZE = 200
|TASK_POLL_WAIT = 5"""
.
stripMargin
)
val
supposedContent
=
List
(
"API_ROOT = 'http://127.0.0.1:5000'"
,
"TOKEN = 'QWERTYUIOPASDFGHJKLZXCVBNM'"
,
"VERIFY_CERTIFICATE = True"
,
"COLLECTION_CACHE_SIZE = 25"
,
"DATA_BUFFER_SIZE = 200"
,
"TASK_POLL_WAIT = 5"
)
supposedContent
.
sorted
should
equal
(
contents
.
sorted
)
val
manwe2
=
new
ManweAnnotateBed
(
null
)
{
override
def
globalConfig
=
new
Config
(
Map
(
...
...
@@ -354,15 +357,16 @@ class ManweTest extends TestNGSuite with Matchers {
}
val
file2
:
File
=
manwe2
.
createManweConfig
(
None
)
val
contents2
=
Source
.
fromFile
(
file2
).
getLines
().
mkString
(
"\n"
)
contents2
should
equal
(
"""API_ROOT = 'http://127.0.0.1:5000'
|TOKEN = 'QWERTYUIOPASDFGHJKLZXCVBNM'
|VERIFY_CERTIFICATE = '/a/b/c/d.crt'
|COLLECTION_CACHE_SIZE = 25
|DATA_BUFFER_SIZE = 200
|TASK_POLL_WAIT = 5"""
.
stripMargin
)
val
contents2
=
Source
.
fromFile
(
file2
).
getLines
().
toList
val
supposedContent2
=
List
(
"API_ROOT = 'http://127.0.0.1:5000'"
,
"TOKEN = 'QWERTYUIOPASDFGHJKLZXCVBNM'"
,
"VERIFY_CERTIFICATE = '/a/b/c/d.crt'"
,
"COLLECTION_CACHE_SIZE = 25"
,
"DATA_BUFFER_SIZE = 200"
,
"TASK_POLL_WAIT = 5"
)
supposedContent2
.
sorted
should
equal
(
contents2
.
sorted
)
}
}
public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
View file @
a161a802
...
...
@@ -186,7 +186,7 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
*/
def
varda
(
vcf
:
File
,
gVcf
:
File
)
:
File
=
{
val
annotationQueries
:
List
[
String
]
=
config
(
"annotation_queries"
,
default
=
Nil
,
submodule
=
"manwe"
)
val
annotationQueries
:
List
[
String
]
=
config
(
"annotation_queries"
,
default
=
List
(
"GLOBAL *"
)
,
submodule
=
"manwe"
)
//TODO: add groups!!! Need sample-specific group tags for this
val
annotate
=
new
ManweAnnotateVcf
(
this
)
...
...
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