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biopet.biopet
Commits
4ff7fc14
Commit
4ff7fc14
authored
Mar 22, 2017
by
Peter van 't Hof
Browse files
Fixing library tags for variantcalling
(cherry picked from commit d7b8714)
parent
73d6d6d7
Changes
1
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Inline
Side-by-side
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala
View file @
4ff7fc14
...
...
@@ -51,7 +51,7 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra
)
/** Method to make the variantcalling namespace of shiva */
def
makeVariantcalling
(
multisample
:
Boolean
=
fals
e
)
:
ShivaVariantcalling
with
QScript
=
{
def
makeVariantcalling
(
multisample
:
Boolean
,
sample
:
Option
[
String
]
=
None
,
library
:
Option
[
String
]
=
Non
e
)
:
ShivaVariantcalling
with
QScript
=
{
if
(
multisample
)
new
ShivaVariantcalling
(
qscript
)
{
override
def
namePrefix
=
"multisample"
override
def
configNamespace
:
String
=
"shivavariantcalling"
...
...
@@ -59,6 +59,8 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra
}
else
new
ShivaVariantcalling
(
qscript
)
{
override
def
configNamespace
=
"shivavariantcalling"
sampleId
=
sample
libId
=
library
}
}
...
...
@@ -104,7 +106,7 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra
lazy
val
variantcalling
=
if
(
config
(
"library_variantcalling"
,
default
=
false
).
asBoolean
&&
(
bamFile
.
isDefined
||
preProcessBam
.
isDefined
))
{
Some
(
makeVariantcalling
(
multisample
=
false
))
Some
(
makeVariantcalling
(
multisample
=
false
,
sample
=
Some
(
sampleId
),
library
=
Some
(
libId
)
))
}
else
None
/** This will add jobs for this library */
...
...
@@ -132,7 +134,7 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra
}
lazy
val
variantcalling
=
if
(
config
(
"single_sample_variantcalling"
,
default
=
false
).
asBoolean
)
{
Some
(
makeVariantcalling
(
multisample
=
false
))
Some
(
makeVariantcalling
(
multisample
=
false
,
sample
=
Some
(
sampleId
)
))
}
else
None
override
def
keepMergedFiles
:
Boolean
=
config
(
"keep_merged_files"
,
default
=
!
useIndelRealigner
)
...
...
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