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biopet.biopet
Commits
e8ea73f7
Commit
e8ea73f7
authored
Dec 22, 2016
by
Peter van 't Hof
Browse files
Fix style
parent
78a3291b
Changes
7
Hide whitespace changes
Inline
Side-by-side
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala
View file @
e8ea73f7
...
...
@@ -17,9 +17,9 @@ package nl.lumc.sasc.biopet.core
import
java.io.File
import
htsjdk.samtools.reference.IndexedFastaSequenceFile
import
nl.lumc.sasc.biopet.core.summary.
{
Summarizable
,
SummaryQScript
}
import
nl.lumc.sasc.biopet.core.summary.
{
Summarizable
,
SummaryQScript
}
import
nl.lumc.sasc.biopet.utils._
import
nl.lumc.sasc.biopet.utils.config.
{
Config
,
Configurable
}
import
nl.lumc.sasc.biopet.utils.config.
{
Config
,
Configurable
}
import
scala.collection.JavaConversions._
...
...
@@ -185,7 +185,8 @@ object Reference {
s
"""Species found in general config:
|- ${globalSpecies.keys.toList.sorted.mkString("\n- ")}
|$warn
|"""
.
stripMargin
else
s
"No references found in global config. $warn"
))
|"""
.
stripMargin
else
s
"No references found in global config. $warn"
))
val
globalReferences
=
globalSpecies
.
getOrElse
(
species
,
Map
()).
asInstanceOf
[
Map
[
String
,
Any
]]
val
referenceName
=
Question
.
string
(
"reference_name"
,
...
...
@@ -193,7 +194,8 @@ object Reference {
s
"""Reference for $species found in general config:
|- ${globalReferences.keys.toList.sorted.mkString("\n- ")}
|$warn
|"""
.
stripMargin
else
s
"No references found in global config. $warn"
))
|"""
.
stripMargin
else
s
"No references found in global config. $warn"
))
val
reference
=
globalReferences
.
getOrElse
(
referenceName
,
Map
()).
asInstanceOf
[
Map
[
String
,
Any
]]
val
referenceFasta
:
Option
[
String
]
=
if
(
reference
.
contains
(
"reference_fasta"
))
None
else
{
...
...
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/TemplateTool.scala
View file @
e8ea73f7
...
...
@@ -4,11 +4,11 @@ import java.io.File
import
nl.lumc.sasc.biopet.utils.config.Config
import
nl.lumc.sasc.biopet.utils.summary.Summary
import
nl.lumc.sasc.biopet.utils.
{
ConfigUtils
,
Question
,
ToolCommand
}
import
nl.lumc.sasc.biopet.utils.
{
ConfigUtils
,
Question
,
ToolCommand
}
/**
* Created by pjvanthof on 17/12/2016.
*/
* Created by pjvanthof on 17/12/2016.
*/
trait
TemplateTool
extends
ToolCommand
{
import
TemplateTool._
case
class
Args
(
expert
:
Boolean
=
false
)
extends
AbstractArgs
...
...
@@ -20,10 +20,10 @@ trait TemplateTool extends ToolCommand {
}
/**
* Program will split fastq file in multiple fastq files
*
* @param args the command line arguments
*/
* Program will split fastq file in multiple fastq files
*
* @param args the command line arguments
*/
def
main
(
args
:
Array
[
String
])
:
Unit
=
{
val
argsParser
=
new
OptParser
val
cmdArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
(
throw
new
IllegalArgumentException
)
...
...
@@ -84,7 +84,7 @@ object TemplateTool {
val
sizes
=
configs
.
map
(
new
Summary
(
_
)).
map
(
x
=>
(
x
.
samples
.
size
,
x
.
libraries
.
map
(
_
.
_2
.
size
).
sum
))
val
samples
=
sizes
.
map
(
_
.
_1
).
sum
val
libs
=
sizes
.
map
(
_
.
_2
).
sum
val
mergedConfig
=
new
Summary
(
configs
.
foldLeft
(
Map
[
String
,
Any
]())((
a
,
b
)
=>
ConfigUtils
.
mergeMaps
(
a
,
b
)))
val
mergedConfig
=
new
Summary
(
configs
.
foldLeft
(
Map
[
String
,
Any
]())((
a
,
b
)
=>
ConfigUtils
.
mergeMaps
(
a
,
b
)))
val
mergesSamples
=
mergedConfig
.
samples
.
size
val
mergesLibraries
=
mergedConfig
.
libraries
.
map
(
_
.
_2
.
size
).
sum
if
(
mergesSamples
!=
samples
)
println
(
"WARNING: Overlapping samples detected"
)
...
...
biopet-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutableMain.scala
View file @
e8ea73f7
...
...
@@ -15,7 +15,7 @@
package
nl.lumc.sasc.biopet
import
nl.lumc.sasc.biopet.core.PipelineStatus
import
nl.lumc.sasc.biopet.utils.
{
BiopetExecutable
,
MainCommand
}
import
nl.lumc.sasc.biopet.utils.
{
BiopetExecutable
,
MainCommand
}
object
BiopetExecutableMain
extends
BiopetExecutable
{
def
pipelines
:
List
[
MainCommand
]
=
List
(
...
...
biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/Question.scala
View file @
e8ea73f7
package
nl.lumc.sasc.biopet.utils
/**
* Created by pjvanthof on 16/12/2016.
*/
* Created by pjvanthof on 16/12/2016.
*/
object
Question
{
def
string
(
name
:
String
,
...
...
@@ -31,8 +31,8 @@ object Question {
}
def
boolean
(
name
:
String
,
default
:
Option
[
Boolean
]
=
None
,
description
:
Option
[
String
]
=
None
)
:
Boolean
=
{
default
:
Option
[
Boolean
]
=
None
,
description
:
Option
[
String
]
=
None
)
:
Boolean
=
{
description
.
foreach
(
println
)
default
.
foreach
(
x
=>
println
(
s
"Default value: $x"
))
print
(
s
"$name (y/n) > "
)
...
...
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/template/MultiSampleMapping.scala
View file @
e8ea73f7
...
...
@@ -2,12 +2,12 @@ package nl.lumc.sasc.biopet.pipelines.mapping.template
import
java.io.File
import
nl.lumc.sasc.biopet.core.
{
Reference
,
TemplateTool
}
import
nl.lumc.sasc.biopet.core.
{
Reference
,
TemplateTool
}
import
nl.lumc.sasc.biopet.utils.Question
/**
* Created by pjvanthof on 17/12/2016.
*/
* Created by pjvanthof on 17/12/2016.
*/
object
MultiSampleMapping
extends
TemplateTool
{
override
lazy
val
sampleConfigs
:
List
[
File
]
=
TemplateTool
.
askSampleConfigs
()
...
...
@@ -19,10 +19,10 @@ object MultiSampleMapping extends TemplateTool {
val
referenceConfig
=
map
++
Reference
.
askReference
val
aligner
=
if
(
map
.
contains
(
"aligner"
))
map
(
"aligner"
).
toString
else
Question
.
string
(
"Aligner"
,
posibleValues
=
possibleAligners
,
default
=
Some
(
"bwa-mem"
))
else
Question
.
string
(
"Aligner"
,
posibleValues
=
possibleAligners
,
default
=
Some
(
"bwa-mem"
))
referenceConfig
++
Map
(
"aligner"
->
aligner
)
)
}
}
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcalling.scala
View file @
e8ea73f7
...
...
@@ -178,14 +178,14 @@ class ShivaVariantcalling(val root: Configurable) extends QScript
object
ShivaVariantcalling
extends
PipelineCommand
{
/** Will generate all available variantcallers */
protected
[
shiva
]
def
callersList
(
root
:
Configurable
)
:
List
[
Variantcaller
]
=
new
HaplotypeCallerGvcf
(
root
)
::
new
HaplotypeCallerAllele
(
root
)
::
new
UnifiedGenotyperAllele
(
root
)
::
new
UnifiedGenotyper
(
root
)
::
new
HaplotypeCaller
(
root
)
::
new
Freebayes
(
root
)
::
new
RawVcf
(
root
)
::
new
Bcftools
(
root
)
::
new
BcftoolsSingleSample
(
root
)
::
new
VarscanCnsSingleSample
(
root
)
::
Nil
new
HaplotypeCallerGvcf
(
root
)
::
new
HaplotypeCallerAllele
(
root
)
::
new
UnifiedGenotyperAllele
(
root
)
::
new
UnifiedGenotyper
(
root
)
::
new
HaplotypeCaller
(
root
)
::
new
Freebayes
(
root
)
::
new
RawVcf
(
root
)
::
new
Bcftools
(
root
)
::
new
BcftoolsSingleSample
(
root
)
::
new
VarscanCnsSingleSample
(
root
)
::
Nil
}
\ No newline at end of file
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/template/Shiva.scala
View file @
e8ea73f7
...
...
@@ -8,8 +8,8 @@ import nl.lumc.sasc.biopet.pipelines.shiva.ShivaVariantcalling
import
nl.lumc.sasc.biopet.utils.Question
/**
* Created by pjvanthof on 17/12/2016.
*/
* Created by pjvanthof on 17/12/2016.
*/
object
Shiva
extends
TemplateTool
{
override
lazy
val
sampleConfigs
:
List
[
File
]
=
TemplateTool
.
askSampleConfigs
()
...
...
@@ -30,6 +30,6 @@ object Shiva extends TemplateTool {
"variantcallers"
->
variantCallers
,
"use_indel_realigner"
->
useIndelRealigner
,
"use_base_recalibration"
->
useBaseRecalibration
)
)
}
}
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