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biopet.biopet
Commits
34024cc5
Commit
34024cc5
authored
Oct 16, 2015
by
Sander van der Zeeuw
Browse files
add bcf merge to shiva and create wrapper
parent
f1599432
Changes
3
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public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala
View file @
34024cc5
...
...
@@ -34,13 +34,13 @@ class BcftoolsCall(val root: Configurable) extends Bcftools {
var
m
:
Boolean
=
config
(
"m"
,
default
=
false
)
var
r
:
Option
[
String
]
=
config
(
"r"
)
@Input
(
required
=
false
)
var
R
:
Option
[
String
]
=
config
(
"R"
)
var
R
:
Option
[
File
]
=
config
(
"R"
)
var
s
:
Option
[
String
]
=
config
(
"s"
)
@Input
(
required
=
false
)
var
S
:
Option
[
File
]
=
config
(
"S"
)
var
t
:
Option
[
String
]
=
config
(
"t"
)
@Input
(
required
=
false
)
var
T
:
Option
[
String
]
=
config
(
"T"
)
var
T
:
Option
[
File
]
=
config
(
"T"
)
var
A
:
Boolean
=
config
(
"A"
,
default
=
false
)
var
f
:
List
[
String
]
=
config
(
"f"
,
default
=
Nil
)
var
g
:
Option
[
Int
]
=
config
(
"g"
)
...
...
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsMerge.scala
0 → 100644
View file @
34024cc5
package
nl.lumc.sasc.biopet.extensions.bcftools
import
java.io.File
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Output
,
Input
}
/**
* Created by sajvanderzeeuw on 16-10-15.
*/
class
BcftoolsMerge
(
val
root
:
Configurable
)
extends
Bcftools
{
@Input
(
doc
=
"Input File"
,
required
=
true
)
var
input
:
List
[
File
]
=
Nil
@Output
(
doc
=
"output File"
,
required
=
false
)
var
output
:
File
=
_
@Input
(
required
=
false
)
var
R
:
Option
[
File
]
=
config
(
"R"
)
@Input
(
required
=
false
)
var
useheader
:
Option
[
File
]
=
config
(
"useheader"
)
@Input
(
required
=
false
)
var
l
:
Option
[
File
]
=
config
(
"l"
)
var
forcesamples
:
Boolean
=
config
(
"forcesamples"
,
default
=
false
)
var
printheader
:
Boolean
=
config
(
"printheader"
,
default
=
false
)
var
f
:
List
[
String
]
=
config
(
"f"
,
default
=
Nil
)
var
i
:
List
[
String
]
=
config
(
"i"
,
default
=
Nil
)
var
m
:
Option
[
String
]
=
config
(
"m"
)
var
O
:
Option
[
String
]
=
config
(
"O"
)
var
r
:
List
[
String
]
=
config
(
"r"
,
default
=
Nil
)
def
cmdLine
=
required
(
executable
)
+
required
(
"merge"
)
+
(
if
(
outputAsStsout
)
""
else
required
(
"-o"
,
output
))
+
conditional
(
forcesamples
,
"--force-samples"
)
+
conditional
(
printheader
,
"--print-header"
)
+
optional
(
"--use-header"
,
useheader
)
+
optional
(
"-f"
,
f
)
+
optional
(
"-i"
,
i
)
+
optional
(
"-l"
,
l
)
+
optional
(
"-m"
,
m
)
+
optional
(
"-O"
,
O
)
+
optional
(
"-r"
,
r
)
+
optional
(
"-R"
,
R
)
+
repeat
(
input
)
}
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
View file @
34024cc5
...
...
@@ -19,7 +19,7 @@ import java.io.File
import
nl.lumc.sasc.biopet.core.summary.SummaryQScript
import
nl.lumc.sasc.biopet.core.
{
Reference
,
SampleLibraryTag
}
import
nl.lumc.sasc.biopet.extensions.bcftools.BcftoolsCall
import
nl.lumc.sasc.biopet.extensions.bcftools.
{
BcftoolsMerge
,
BcftoolsCall
}
import
nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
import
nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup
import
nl.lumc.sasc.biopet.extensions.tools.
{
MpileupToVcf
,
VcfFilter
,
VcfStats
}
...
...
@@ -201,11 +201,12 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag with
bt
.
output
}
val
cv
=
new
CombineVariants
(
qscript
)
cv
.
inputFiles
=
sampleVcfs
cv
.
outputFile
=
outputFile
cv
.
setKey
=
"null"
add
(
cv
)
val
bcfmerge
=
new
BcftoolsMerge
(
qscript
)
bcfmerge
.
input
=
sampleVcfs
bcfmerge
.
output
=
outputFile
bcfmerge
.
O
=
Some
(
"z"
)
add
(
bcfmerge
)
add
(
Tabix
(
qscript
,
outputFile
))
}
}
...
...
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