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biopet.biopet
Commits
05273365
Commit
05273365
authored
Feb 26, 2015
by
Peter van 't Hof
Browse files
Add variantcalling to summary
parent
5d9d3661
Changes
2
Hide whitespace changes
Inline
Side-by-side
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
View file @
05273365
...
...
@@ -28,6 +28,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
def
makeVariantcalling
(
multisample
:
Boolean
=
false
)
=
{
if
(
multisample
)
new
ShivaVariantcalling
(
qscript
)
{
override
def
namePrefix
=
"multisample."
override
def
configName
=
"shivavariantcalling"
override
def
configPath
:
List
[
String
]
=
super
.
configPath
:::
"multisample"
::
Nil
}
...
...
@@ -132,13 +133,15 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
if
(
config
(
"library_variantcalling"
,
default
=
false
).
asBoolean
&&
(
bamFile
.
isDefined
||
preProcessBam
.
isDefined
))
{
val
vc
=
makeVariantcalling
(
multisample
=
false
)
vc
.
namePrefix
=
sampleId
+
"-"
+
libId
vc
.
sampleId
=
Some
(
libId
)
vc
.
libId
=
Some
(
sampleId
)
vc
.
outputDir
=
new
File
(
libDir
,
"variantcalling"
)
if
(
preProcessBam
.
isDefined
)
vc
.
inputBams
=
preProcessBam
.
get
::
Nil
else
vc
.
inputBams
=
bamFile
.
get
::
Nil
vc
.
init
vc
.
biopetScript
addAll
(
vc
.
functions
)
addSummaryQScript
(
vc
)
}
}
}
...
...
@@ -181,12 +184,13 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
if
(
config
(
"single_sample_variantcalling"
,
default
=
false
).
asBoolean
&&
preProcessBam
.
isDefined
)
{
val
vc
=
makeVariantcalling
(
multisample
=
false
)
vc
.
n
am
ePrefix
=
sampleId
vc
.
s
am
pleId
=
Some
(
sampleId
)
vc
.
outputDir
=
new
File
(
sampleDir
,
"variantcalling"
)
vc
.
inputBams
=
preProcessBam
.
get
::
Nil
vc
.
init
vc
.
biopetScript
addAll
(
vc
.
functions
)
addSummaryQScript
(
vc
)
}
}
}
...
...
@@ -194,12 +198,12 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
def
addMultiSampleJobs
()
:
Unit
=
{
if
(
config
(
"multisample_sample_variantcalling"
,
default
=
true
).
asBoolean
)
{
val
vc
=
makeVariantcalling
(
multisample
=
true
)
vc
.
namePrefix
=
"multisample"
vc
.
outputDir
=
new
File
(
outputDir
,
"variantcalling"
)
vc
.
inputBams
=
samples
.
map
(
_
.
_2
.
preProcessBam
).
flatten
.
toList
vc
.
init
vc
.
biopetScript
addAll
(
vc
.
functions
)
addSummaryQScript
(
vc
)
}
}
...
...
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
View file @
05273365
...
...
@@ -20,7 +20,13 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag {
@Input
(
doc
=
"Bam files (should be deduped bams)"
,
shortName
=
"BAM"
,
required
=
true
)
var
inputBams
:
List
[
File
]
=
Nil
var
namePrefix
:
String
=
""
def
namePrefix
:
String
=
{
(
sampleId
,
libId
)
match
{
case
(
Some
(
sampleId
),
Some
(
libId
))
=>
sampleId
+
"-"
+
libId
+
"."
case
(
Some
(
sampleId
),
_
)
=>
sampleId
+
"."
case
_
=>
""
}
}
def
init
:
Unit
=
{
if
(!
namePrefix
.
isEmpty
&&
!
namePrefix
.
endsWith
(
"."
))
namePrefix
+=
"."
...
...
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