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biopet.biopet
Commits
ba60c6d4
Commit
ba60c6d4
authored
Dec 10, 2016
by
Peter van 't Hof
Browse files
Adding validateVcf to shiva on dbsnp
parent
831f9ae4
Changes
4
Hide whitespace changes
Inline
Side-by-side
biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/ValidateVcf.scala
0 → 100644
View file @
ba60c6d4
/**
* 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 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.tools
import
java.io.File
import
nl.lumc.sasc.biopet.core.
{
Reference
,
ToolCommandFunction
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.Input
class
ValidateVcf
(
val
root
:
Configurable
)
extends
ToolCommandFunction
with
Reference
{
def
toolObject
=
nl
.
lumc
.
sasc
.
biopet
.
tools
.
ValidateVcf
@Input
(
required
=
true
)
var
inputVcf
:
File
=
_
@Input
(
required
=
true
)
var
reference
:
File
=
_
var
disableFail
:
Boolean
=
false
override
def
defaultCoreMemory
=
4.0
override
def
beforeGraph
()
:
Unit
=
{
super
.
beforeGraph
()
if
(
reference
==
null
)
reference
=
referenceFasta
()
}
override
def
cmdLine
=
super
.
cmdLine
+
required
(
"-i"
,
inputVcf
)
+
required
(
"-R"
,
reference
)
+
conditional
(
disableFail
,
"--disableFail"
)
}
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/CheckValidateVcf.scala
0 → 100644
View file @
ba60c6d4
/**
* 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 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.pipelines.shiva
import
java.io.File
import
org.broadinstitute.gatk.queue.function.InProcessFunction
import
org.broadinstitute.gatk.utils.commandline.Input
import
scala.io.Source
/**
* This class checks md5sums and give an exit code 1 when md5sum is not the same
*
* Created by pjvanthof on 16/08/15.
*/
class
CheckValidateVcf
extends
InProcessFunction
{
@Input
(
required
=
true
)
var
inputLogFile
:
File
=
_
/** Exits whenever the input md5sum is not the same as the output md5sum */
def
run
:
Unit
=
{
val
reader
=
Source
.
fromFile
(
inputLogFile
)
reader
.
getLines
().
foreach
{
line
=>
if
(
line
.
startsWith
(
"ERROR"
))
{
logger
.
error
(
"Corrupt vcf file found, aborting pipeline"
)
// 130 Simulates a ctr-C
Runtime
.
getRuntime
.
halt
(
130
)
}
}
reader
.
close
()
}
}
\ No newline at end of file
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala
View file @
ba60c6d4
...
...
@@ -14,15 +14,19 @@
*/
package
nl.lumc.sasc.biopet.pipelines.shiva
import
nl.lumc.sasc.biopet.core.
{
PipelineCommand
,
Reference
}
import
java.io.File
import
nl.lumc.sasc.biopet.core.
{
PipelineCommand
,
Reference
}
import
nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
import
nl.lumc.sasc.biopet.extensions.gatk._
import
nl.lumc.sasc.biopet.extensions.tools.ValidateVcf
import
nl.lumc.sasc.biopet.pipelines.bammetrics.TargetRegions
import
nl.lumc.sasc.biopet.pipelines.kopisu.Kopisu
import
nl.lumc.sasc.biopet.pipelines.mapping.MultisampleMappingTrait
import
nl.lumc.sasc.biopet.pipelines.toucan.Toucan
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.queue.QScript
import
org.broadinstitute.gatk.queue.function.QFunction
/**
* This is a trait for the Shiva pipeline
...
...
@@ -175,6 +179,8 @@ class Shiva(val root: Configurable) extends QScript with MultisampleMappingTrait
override
def
addMultiSampleJobs
()
=
{
super
.
addMultiSampleJobs
()
addAll
(
dbsnpVcfFile
.
map
(
Shiva
.
makeValidateVcfJobs
(
this
,
_
,
referenceFasta
())).
getOrElse
(
Nil
))
multisampleVariantCalling
.
foreach
(
vc
=>
{
vc
.
outputDir
=
new
File
(
outputDir
,
"variantcalling"
)
vc
.
inputBams
=
samples
.
flatMap
{
case
(
sampleId
,
sample
)
=>
sample
.
preProcessBam
.
map
(
sampleId
->
_
)
}
...
...
@@ -251,4 +257,23 @@ class Shiva(val root: Configurable) extends QScript with MultisampleMappingTrait
}
/** This object give a default main method to the pipelines */
object
Shiva
extends
PipelineCommand
\ No newline at end of file
object
Shiva
extends
PipelineCommand
{
// This is used to only execute 1 validation per vcf file
private
var
validateVcfSeen
:
Set
[(
File
,
File
)]
=
Set
()
def
makeValidateVcfJobs
(
root
:
Configurable
,
vcfFile
:
File
,
referenceFile
:
File
)
:
List
[
QFunction
]
=
{
if
(
validateVcfSeen
.
contains
((
vcfFile
,
referenceFile
)))
Nil
else
{
validateVcfSeen
++=
Set
((
vcfFile
,
referenceFile
))
val
validateVcf
=
new
ValidateVcf
(
root
)
validateVcf
.
inputVcf
=
vcfFile
validateVcf
.
reference
=
referenceFile
val
checkValidateVcf
=
new
CheckValidateVcf
checkValidateVcf
.
inputLogFile
=
validateVcf
.
jobOutputFile
List
(
validateVcf
,
checkValidateVcf
)
}
}
}
\ No newline at end of file
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcalling.scala
View file @
ba60c6d4
...
...
@@ -85,6 +85,8 @@ class ShivaVariantcalling(val root: Configurable) extends QScript
require
(
inputBams
.
nonEmpty
,
"No input bams found"
)
require
(
callers
.
nonEmpty
,
"must select at least 1 variantcaller, choices are: "
+
callersList
.
map
(
_
.
name
).
mkString
(
", "
))
addAll
(
dbsnpVcfFile
.
map
(
Shiva
.
makeValidateVcfJobs
(
this
,
_
,
referenceFasta
())).
getOrElse
(
Nil
))
val
cv
=
new
CombineVariants
(
qscript
)
cv
.
out
=
finalFile
cv
.
setKey
=
Some
(
"VariantCaller"
)
...
...
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