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biopet.biopet
Commits
6ebf4f39
Commit
6ebf4f39
authored
Jan 11, 2016
by
Peter van 't Hof
Browse files
Change gvcf input
parent
7bedb39b
Changes
1
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Inline
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public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
View file @
6ebf4f39
...
...
@@ -15,17 +15,15 @@
*/
package
nl.lumc.sasc.biopet.pipelines.toucan
import
java.io.
{
File
,
PrintWriter
}
import
nl.lumc.sasc.biopet.core._
import
nl.lumc.sasc.biopet.core.summary.SummaryQScript
import
nl.lumc.sasc.biopet.extensions.bcftools.BcftoolsView
import
nl.lumc.sasc.biopet.extensions.bedtools.
{
BedtoolsMerge
,
BedtoolsIntersect
}
import
nl.lumc.sasc.biopet.extensions.manwe.
{
ManweSamplesImport
,
ManweAnnotateVcf
,
ManweDataSourcesAnnotate
}
import
nl.lumc.sasc.biopet.extensions.bedtools.
{
BedtoolsIntersect
,
BedtoolsMerge
}
import
nl.lumc.sasc.biopet.extensions.manwe.
{
ManweAnnotateVcf
,
ManweSamplesImport
}
import
nl.lumc.sasc.biopet.extensions.tools.
{
GvcfToBed
,
VcfWithVcf
,
VepNormalizer
}
import
nl.lumc.sasc.biopet.extensions.
{
Bgzip
,
Ln
,
VariantEffectPredictor
}
import
nl.lumc.sasc.biopet.utils.VcfUtils
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.core.summary.SummaryQScript
import
nl.lumc.sasc.biopet.core._
import
nl.lumc.sasc.biopet.extensions.
{
Bgzip
,
Ln
,
Gzip
,
VariantEffectPredictor
}
import
nl.lumc.sasc.biopet.extensions.tools.
{
GvcfToBed
,
VcfFilter
,
VcfWithVcf
,
VepNormalizer
}
import
nl.lumc.sasc.biopet.utils.
{
VcfUtils
,
ConfigUtils
}
import
org.broadinstitute.gatk.queue.QScript
/**
...
...
@@ -39,6 +37,9 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
@Input
(
doc
=
"Input VCF file"
,
shortName
=
"Input"
,
required
=
true
)
var
inputVCF
:
File
=
_
@Input
(
doc
=
"Input GVCF file"
,
shortName
=
"Input"
,
required
=
false
)
var
inputGvcf
:
Option
[
File
]
=
None
var
sampleIds
:
List
[
String
]
=
Nil
def
init
()
:
Unit
=
{
inputFiles
:+=
new
InputFile
(
inputVCF
)
...
...
@@ -53,17 +54,14 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
override
def
defaults
=
Map
(
"varianteffectpredictor"
->
Map
(
"everything"
->
true
,
"failed"
->
1
,
"allow_non_variant"
->
true
)
)
//defaults ++= Map("varianteffectpredictor" -> Map("everything" -> true))
def
biopetScript
()
:
Unit
=
{
val
doVarda
:
Boolean
=
config
(
"use_varda"
,
default
=
false
)
val
useVcf
:
File
=
if
(
doVarda
)
{
val
gVcfRoot
:
Option
[
File
]
=
config
(
"varda_gvcf"
)
val
gVcf
=
gVcfRoot
match
{
case
Some
(
s
)
=>
s
inputGvcf
match
{
case
Some
(
s
)
=>
varda
(
inputVCF
,
s
)
case
_
=>
throw
new
IllegalArgumentException
(
"You have not specified a GVCF file"
)
}
varda
(
inputVCF
,
gVcf
)
}
else
inputVCF
val
vep
=
new
VariantEffectPredictor
(
this
)
vep
.
input
=
useVcf
...
...
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