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biopet.biopet
Commits
bedfafee
Commit
bedfafee
authored
Feb 26, 2015
by
Peter van 't Hof
Browse files
Added name prefixes
parent
9fe575e8
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
View file @
bedfafee
...
...
@@ -26,7 +26,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
addSummaryJobs
}
def
makeVariantcalling
(
multisample
:
Boolean
=
false
)
=
{
def
makeVariantcalling
(
multisample
:
Boolean
=
false
)
=
{
if
(
multisample
)
new
ShivaVariantcalling
(
qscript
)
{
override
def
configName
=
"shivavariantcalling"
override
def
configPath
:
List
[
String
]
=
super
.
configPath
:::
"multisample"
::
Nil
...
...
@@ -132,6 +132,7 @@ 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
.
outputDir
=
new
File
(
libDir
,
"variantcalling"
)
if
(
preProcessBam
.
isDefined
)
vc
.
inputBams
=
preProcessBam
.
get
::
Nil
else
vc
.
inputBams
=
bamFile
.
get
::
Nil
...
...
@@ -171,14 +172,16 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
(
lib
.
_2
.
bamFile
,
lib
.
_2
.
preProcessBam
)
match
{
case
(
_
,
Some
(
file
))
=>
Some
(
file
)
case
(
Some
(
file
),
_
)
=>
Some
(
file
)
case
_
=>
None
}}).
flatten
.
toList
)
case
_
=>
None
}
}).
flatten
.
toList
)
def
addJobs
()
:
Unit
=
{
addPerLibJobs
()
if
(
config
(
"single_sample_variantcalling"
,
default
=
false
).
asBoolean
&&
preProcessBam
.
isDefined
)
{
val
vc
=
makeVariantcalling
(
multisample
=
false
)
vc
.
namePrefix
=
sampleId
vc
.
outputDir
=
new
File
(
sampleDir
,
"variantcalling"
)
vc
.
inputBams
=
preProcessBam
.
get
::
Nil
vc
.
init
...
...
@@ -191,6 +194,7 @@ 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
...
...
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