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biopet.biopet
Commits
c46b3983
Commit
c46b3983
authored
Jul 25, 2017
by
Peter van 't Hof
Browse files
Removing sample and library variantcalling
parent
dd937c3a
Changes
1
Hide whitespace changes
Inline
Side-by-side
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala
View file @
c46b3983
...
...
@@ -101,17 +101,13 @@ class Shiva(val parent: Configurable)
/** Sample specific settings */
override
def
summarySettings
:
Map
[
String
,
Any
]
=
super
.
summarySettings
++
Map
(
"single_sample_variantcalling"
->
variantcalling
.
isDefined
,
"use_indel_realigner"
->
useIndelRealigner
)
Map
(
"use_indel_realigner"
->
useIndelRealigner
)
/** Class to generate jobs for a library */
class
Library
(
libId
:
String
)
extends
super
.
Library
(
libId
)
{
override
def
summaryFiles
:
Map
[
String
,
File
]
=
super
.
summaryFiles
++
variantcalling
.
map
(
"final"
->
_
.
finalFile
)
++
bqsrFile
.
map
(
"baserecal"
->
_
)
++
bqsrAfterFile
.
map
(
"baserecal_after"
->
_
)
...
...
@@ -140,20 +136,10 @@ class Shiva(val parent: Configurable)
/** Library specific settings */
override
def
summarySettings
:
Map
[
String
,
Any
]
=
super
.
summarySettings
++
Map
(
"library_variantcalling"
->
variantcalling
.
isDefined
,
"use_base_recalibration"
->
useBaseRecalibration
,
"useAnalyze_covariates"
->
useAnalyzeCovariates
)
lazy
val
variantcalling
:
Option
[
ShivaVariantcalling
with
QScript
]
=
if
(
config
(
"library_variantcalling"
,
default
=
false
).
asBoolean
&&
(
bamFile
.
isDefined
||
preProcessBam
.
isDefined
))
{
Some
(
makeVariantcalling
(
multisample
=
false
,
sample
=
Some
(
sampleId
),
library
=
Some
(
libId
)))
}
else
None
/** This will add jobs for this library */
override
def
addJobs
()
:
Unit
=
{
super
.
addJobs
()
...
...
@@ -164,15 +150,6 @@ class Shiva(val parent: Configurable)
useIndelRealigner
||
libraries
.
size
>
1
,
usePrintReads
)
}
variantcalling
.
foreach
(
vc
=>
{
vc
.
sampleId
=
Some
(
sampleId
)
vc
.
libId
=
Some
(
libId
)
vc
.
outputDir
=
new
File
(
libDir
,
"variantcalling"
)
if
(
preProcessBam
.
isDefined
)
vc
.
inputBams
=
Map
(
sampleId
->
preProcessBam
.
get
)
else
vc
.
inputBams
=
Map
(
sampleId
->
bamFile
.
get
)
add
(
vc
)
})
}
/** Adds base recalibration jobs */
...
...
@@ -220,11 +197,6 @@ class Shiva(val parent: Configurable)
}
}
lazy
val
variantcalling
:
Option
[
ShivaVariantcalling
with
QScript
]
=
if
(
config
(
"single_sample_variantcalling"
,
default
=
false
).
asBoolean
)
{
Some
(
makeVariantcalling
(
multisample
=
false
,
sample
=
Some
(
sampleId
)))
}
else
None
override
def
keepMergedFiles
:
Boolean
=
config
(
"keep_merged_files"
,
default
=
!
useIndelRealigner
)
...
...
@@ -235,9 +207,6 @@ class Shiva(val parent: Configurable)
bamFile
.
map
(
swapExt
(
sampleDir
,
_
,
".bam"
,
".realign.bam"
))
}
else
bamFile
override
def
summaryFiles
:
Map
[
String
,
File
]
=
super
.
summaryFiles
++
variantcalling
.
map
(
"final"
->
_
.
finalFile
)
/** This will add sample jobs */
override
def
addJobs
()
:
Unit
=
{
super
.
addJobs
()
...
...
@@ -245,15 +214,6 @@ class Shiva(val parent: Configurable)
if
(
useIndelRealigner
)
{
addIndelRealign
(
bamFile
.
get
,
sampleDir
,
isIntermediate
=
false
)
}
preProcessBam
.
foreach
{
bam
=>
variantcalling
.
foreach
(
vc
=>
{
vc
.
sampleId
=
Some
(
sampleId
)
vc
.
outputDir
=
new
File
(
sampleDir
,
"variantcalling"
)
vc
.
inputBams
=
Map
(
sampleId
->
bam
)
add
(
vc
)
})
}
}
}
// End of sample
...
...
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