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biopet.biopet
Commits
02639191
Commit
02639191
authored
Nov 25, 2015
by
Peter van 't Hof
Browse files
Style fixes
parent
05233c6b
Changes
11
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public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/TargetRegions.scala
View file @
02639191
...
...
@@ -5,8 +5,8 @@ import java.io.File
import
nl.lumc.sasc.biopet.utils.config.Configurable
/**
* Created by pjvan_thof on 11/20/15.
*/
* Created by pjvan_thof on 11/20/15.
*/
trait
TargetRegions
extends
Configurable
{
/** Bed files for region of interests */
var
roiBedFiles
:
List
[
File
]
=
config
(
"regions_of_interest"
,
Nil
)
...
...
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
View file @
02639191
...
...
@@ -135,7 +135,7 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
that
.
biopetScript
()
this
match
{
case
s
:
SummaryQScript
=>
s
.
addSummaryQScript
(
that
)
case
_
=>
case
_
=>
}
case
that
:
BiopetQScript
=>
that
.
init
()
...
...
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/vt/Vt.scala
View file @
02639191
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package
nl.lumc.sasc.biopet.extensions.vt
import
nl.lumc.sasc.biopet.core.
{
Version
,
BiopetCommandLineFunction
}
/**
* General bwa extension
*
* Created by pjvan_thof on 1/16/15.
*/
* General bwa extension
*
* Created by pjvan_thof on 1/16/15.
*/
abstract
class
Vt
extends
BiopetCommandLineFunction
{
override
def
subPath
=
"vt"
::
super
.
subPath
executable
=
config
(
"exe"
,
default
=
"vt"
)
...
...
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/vt/VtDecompose.scala
View file @
02639191
...
...
@@ -2,13 +2,13 @@ package nl.lumc.sasc.biopet.extensions.vt
import
java.io.File
import
nl.lumc.sasc.biopet.core.
{
Reference
,
Version
}
import
nl.lumc.sasc.biopet.core.
{
Reference
,
Version
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
/**
* Created by pjvanthof on 20/11/15.
*/
* Created by pjvanthof on 20/11/15.
*/
class
VtDecompose
(
val
root
:
Configurable
)
extends
Vt
with
Version
with
Reference
{
def
versionRegex
=
"""decompose (.*)"""
.
r
override
def
versionExitcode
=
List
(
0
,
1
)
...
...
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/vt/VtNormalize.scala
View file @
02639191
...
...
@@ -2,13 +2,13 @@ package nl.lumc.sasc.biopet.extensions.vt
import
java.io.File
import
nl.lumc.sasc.biopet.core.
{
Reference
,
Version
}
import
nl.lumc.sasc.biopet.core.
{
Reference
,
Version
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Output
,
Input
}
import
org.broadinstitute.gatk.utils.commandline.
{
Output
,
Input
}
/**
* Created by pjvanthof on 20/11/15.
*/
* Created by pjvanthof on 20/11/15.
*/
class
VtNormalize
(
val
root
:
Configurable
)
extends
Vt
with
Version
with
Reference
{
def
versionRegex
=
"""normalize (.*)"""
.
r
override
def
versionExitcode
=
List
(
0
,
1
)
...
...
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
View file @
02639191
...
...
@@ -116,7 +116,8 @@ object ShivaReport extends MultisampleReportBuilder {
)).
toList
.
sortBy
(
_
.
_1
),
List
(),
Map
())
)
else
None
)
else
None
}
/** Files page, can be used general or at sample level */
...
...
@@ -192,7 +193,7 @@ object ShivaReport extends MultisampleReportBuilder {
def
getLine
(
summary
:
Summary
,
sample
:
String
,
lib
:
Option
[
String
]
=
None
)
:
String
=
{
val
path
=
target
match
{
case
Some
(
t
)
=>
List
(
"shivavariantcalling"
,
"stats"
,
s
"multisample-vcfstats-$caller-$t"
,
"genotype"
)
case
_
=>
List
(
"shivavariantcalling"
,
"stats"
,
s
"multisample-vcfstats-$caller"
,
"genotype"
)
case
_
=>
List
(
"shivavariantcalling"
,
"stats"
,
s
"multisample-vcfstats-$caller"
,
"genotype"
)
}
val
homVar
=
new
SummaryValue
(
path
:+
"HomVar"
,
summary
,
Some
(
sample
),
lib
).
value
.
getOrElse
(
0
).
toString
.
toLong
val
homRef
=
new
SummaryValue
(
path
:+
"HomRef"
,
summary
,
Some
(
sample
),
lib
).
value
.
getOrElse
(
0
).
toString
.
toLong
...
...
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala
View file @
02639191
...
...
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.pipelines.shiva
import
nl.lumc.sasc.biopet.core.summary.SummaryQScript
import
nl.lumc.sasc.biopet.core.
{
PipelineCommand
,
Reference
,
SampleLibraryTag
}
import
nl.lumc.sasc.biopet.pipelines.shiva.svcallers.
{
Delly
,
Breakdancer
,
Clever
,
SvCaller
}
import
nl.lumc.sasc.biopet.pipelines.shiva.svcallers.
{
Delly
,
Breakdancer
,
Clever
,
SvCaller
}
import
nl.lumc.sasc.biopet.utils.
{
BamUtils
,
Logging
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.queue.QScript
...
...
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
View file @
02639191
...
...
@@ -19,7 +19,7 @@ import htsjdk.samtools.SamReaderFactory
import
nl.lumc.sasc.biopet.core.
{
MultiSampleQScript
,
Reference
}
import
nl.lumc.sasc.biopet.extensions.Ln
import
nl.lumc.sasc.biopet.extensions.picard.
{
AddOrReplaceReadGroups
,
MarkDuplicates
,
SamToFastq
}
import
nl.lumc.sasc.biopet.pipelines.bammetrics.
{
TargetRegions
,
BamMetrics
}
import
nl.lumc.sasc.biopet.pipelines.bammetrics.
{
TargetRegions
,
BamMetrics
}
import
nl.lumc.sasc.biopet.pipelines.mapping.Mapping
import
nl.lumc.sasc.biopet.pipelines.toucan.Toucan
import
nl.lumc.sasc.biopet.utils.Logging
...
...
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
View file @
02639191
...
...
@@ -19,7 +19,7 @@ import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import
nl.lumc.sasc.biopet.core.
{
Reference
,
SampleLibraryTag
}
import
nl.lumc.sasc.biopet.extensions.gatk.
{
CombineVariants
,
GenotypeConcordance
}
import
nl.lumc.sasc.biopet.extensions.tools.VcfStats
import
nl.lumc.sasc.biopet.extensions.vt.
{
VtDecompose
,
VtNormalize
}
import
nl.lumc.sasc.biopet.extensions.vt.
{
VtDecompose
,
VtNormalize
}
import
nl.lumc.sasc.biopet.pipelines.bammetrics.TargetRegions
import
nl.lumc.sasc.biopet.pipelines.shiva.variantcallers._
import
nl.lumc.sasc.biopet.utils.
{
BamUtils
,
Logging
}
...
...
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Breakdancer.scala
View file @
02639191
package
nl.lumc.sasc.biopet.pipelines.shiva.svcallers
import
nl.lumc.sasc.biopet.extensions.breakdancer.
{
BreakdancerVCF
,
BreakdancerCaller
,
BreakdancerConfig
}
import
nl.lumc.sasc.biopet.extensions.breakdancer.
{
BreakdancerVCF
,
BreakdancerCaller
,
BreakdancerConfig
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
/** Script for sv caler Breakdancer */
...
...
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/SvCaller.scala
View file @
02639191
package
nl.lumc.sasc.biopet.pipelines.shiva.svcallers
import
nl.lumc.sasc.biopet.core.
{
Reference
,
BiopetQScript
}
import
nl.lumc.sasc.biopet.core.
{
Reference
,
BiopetQScript
}
import
org.broadinstitute.gatk.queue.QScript
/**
* Created by pjvanthof on 23/11/15.
*/
* Created by pjvanthof on 23/11/15.
*/
trait
SvCaller
extends
QScript
with
BiopetQScript
with
Reference
{
/** Name of mode, this should also be used in the config */
...
...
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