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biopet.biopet
Commits
26f84c6a
Commit
26f84c6a
authored
Jan 08, 2016
by
Peter van 't Hof
Browse files
Code improvement
parent
96efe61e
Changes
1
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Inline
Side-by-side
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
View file @
26f84c6a
...
...
@@ -36,10 +36,10 @@ trait ShivaTrait extends MultisampleMappingTrait with Reference with TargetRegio
}
/** Method to make the variantcalling submodule of shiva */
def
makeVariantcalling
(
multisample
:
Boolean
=
false
)
:
ShivaVariantcallingTrait
=
{
def
makeVariantcalling
(
multisample
:
Boolean
=
false
)
=
{
if
(
multisample
)
new
ShivaVariantcalling
(
qscript
)
{
override
def
namePrefix
=
"multisample"
override
def
configName
=
"shivavariantcalling"
override
def
configName
:
String
=
"shivavariantcalling"
override
def
configPath
:
List
[
String
]
=
super
.
configPath
:::
"multisample"
::
Nil
}
else
new
ShivaVariantcalling
(
qscript
)
{
...
...
@@ -69,7 +69,7 @@ trait ShivaTrait extends MultisampleMappingTrait with Reference with TargetRegio
}
else
None
/** This will add jobs for this library */
override
def
addJobs
=
{
override
def
addJobs
()
=
{
super
.
addJobs
()
variantcalling
.
foreach
(
vc
=>
{
...
...
@@ -78,10 +78,7 @@ trait ShivaTrait extends MultisampleMappingTrait with Reference with TargetRegio
vc
.
outputDir
=
new
File
(
libDir
,
"variantcalling"
)
if
(
preProcessBam
.
isDefined
)
vc
.
inputBams
=
Map
(
sampleId
->
preProcessBam
.
get
)
else
vc
.
inputBams
=
Map
(
sampleId
->
bamFile
.
get
)
vc
.
init
()
vc
.
biopetScript
()
addAll
(
vc
.
functions
)
addSummaryQScript
(
vc
)
add
(
vc
)
})
}
}
...
...
@@ -99,10 +96,7 @@ trait ShivaTrait extends MultisampleMappingTrait with Reference with TargetRegio
vc
.
sampleId
=
Some
(
sampleId
)
vc
.
outputDir
=
new
File
(
sampleDir
,
"variantcalling"
)
vc
.
inputBams
=
Map
(
sampleId
->
bam
)
vc
.
init
()
vc
.
biopetScript
()
addAll
(
vc
.
functions
)
addSummaryQScript
(
vc
)
add
(
vc
)
})
}
}
...
...
@@ -122,34 +116,25 @@ trait ShivaTrait extends MultisampleMappingTrait with Reference with TargetRegio
}
else
None
/** This will add the mutisample variantcalling */
override
def
addMultiSampleJobs
=
{
override
def
addMultiSampleJobs
()
=
{
super
.
addMultiSampleJobs
()
multisampleVariantCalling
.
foreach
(
vc
=>
{
vc
.
outputDir
=
new
File
(
outputDir
,
"variantcalling"
)
vc
.
inputBams
=
samples
.
flatMap
{
case
(
sampleId
,
sample
)
=>
sample
.
preProcessBam
.
map
(
sampleId
->
_
)
}
vc
.
init
()
vc
.
biopetScript
()
addAll
(
vc
.
functions
)
addSummaryQScript
(
vc
)
add
(
vc
)
annotation
.
foreach
{
toucan
=>
toucan
.
outputDir
=
new
File
(
outputDir
,
"annotation"
)
toucan
.
inputVCF
=
vc
.
finalFile
toucan
.
init
()
toucan
.
biopetScript
()
addAll
(
toucan
.
functions
)
addSummaryQScript
(
toucan
)
add
(
toucan
)
}
})
svCalling
.
foreach
(
sv
=>
{
sv
.
outputDir
=
new
File
(
outputDir
,
"sv_calling"
)
sv
.
inputBams
=
samples
.
flatMap
{
case
(
sampleId
,
sample
)
=>
sample
.
preProcessBam
.
map
(
sampleId
->
_
)
}
sv
.
init
()
sv
.
biopetScript
()
addAll
(
sv
.
functions
)
addSummaryQScript
(
sv
)
add
(
sv
)
})
}
...
...
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