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biopet.biopet
Commits
fcc7d9bf
Commit
fcc7d9bf
authored
May 04, 2016
by
Sander Bollen
Browse files
get gvcfs from shiva
parent
ff0d656a
Changes
4
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Inline
Side-by-side
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Grep.scala
View file @
fcc7d9bf
...
...
@@ -7,8 +7,8 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
/**
* Created by pjvanthof on 30/03/16.
*/
* Created by pjvanthof on 30/03/16.
*/
class
Grep
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
{
@Input
(
doc
=
"Input file"
,
required
=
true
)
var
input
:
File
=
_
...
...
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcalling.scala
View file @
fcc7d9bf
...
...
@@ -72,7 +72,7 @@ class ShivaVariantcalling(val root: Configurable) extends QScript
/** Variantcallers requested by the config */
protected
val
configCallers
:
Set
[
String
]
=
config
(
"variantcallers"
)
protected
val
callers
:
List
[
Variantcaller
]
=
{
val
callers
:
List
[
Variantcaller
]
=
{
(
for
(
name
<-
configCallers
)
yield
{
if
(!
callersList
.
exists
(
_
.
name
==
name
))
Logging
.
addError
(
s
"variantcaller '$name' does not exist, possible to use: "
+
callersList
.
map
(
_
.
name
).
mkString
(
", "
))
...
...
@@ -80,6 +80,8 @@ class ShivaVariantcalling(val root: Configurable) extends QScript
}).
flatten
.
toList
.
sortBy
(
_
.
prio
)
}
callers
.
filter
(
_
.
isInstanceOf
[
HaplotypeCallerGvcf
])
/** This will add jobs for this pipeline */
def
biopetScript
()
:
Unit
=
{
require
(
inputBams
.
nonEmpty
,
"No input bams found"
)
...
...
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCallerGvcf.scala
View file @
fcc7d9bf
...
...
@@ -13,14 +13,21 @@ class HaplotypeCallerGvcf(val root: Configurable) extends Variantcaller {
val
name
=
"haplotypecaller_gvcf"
protected
def
defaultPrio
=
5
/**
*
*/
protected
var
gVcfFiles
:
Map
[
String
,
File
]
=
Map
()
def
getGvcfs
=
gVcfFiles
def
biopetScript
()
{
val
gv
cfFiles
=
for
((
sample
,
inputBam
)
<-
inputBams
)
yield
{
gV
cfFiles
=
for
((
sample
,
inputBam
)
<-
inputBams
)
yield
{
val
hc
=
broad
.
HaplotypeCaller
.
gvcf
(
this
,
inputBam
,
new
File
(
outputDir
,
sample
+
".gvcf.vcf.gz"
))
add
(
hc
)
hc
.
out
sample
->
hc
.
out
}
val
genotypeGVCFs
=
broad
.
GenotypeGVCFs
(
this
,
g
v
cfFiles
.
toList
,
outputFile
)
val
genotypeGVCFs
=
broad
.
GenotypeGVCFs
(
this
,
g
V
cfFiles
.
values
.
toList
,
outputFile
)
add
(
genotypeGVCFs
)
}
}
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/Variantcaller.scala
View file @
fcc7d9bf
...
...
@@ -28,6 +28,9 @@ trait Variantcaller extends QScript with BiopetQScript with Reference {
var
namePrefix
:
String
=
_
/**
* Map of samplename -> (preprocessed) bam file
*/
var
inputBams
:
Map
[
String
,
File
]
=
_
def
init
()
=
{}
...
...
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