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biopet.biopet
Commits
3584a778
Commit
3584a778
authored
Aug 01, 2015
by
Peter van 't Hof
Browse files
Saver execution order
parent
f95a231c
Changes
1
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public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
View file @
3584a778
...
...
@@ -280,9 +280,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
}
else
None
lazy
val
svCalling
=
if
(
config
(
"sv_calling"
,
default
=
false
).
asBoolean
)
{
val
svCalling
=
new
ShivaSvCalling
(
this
)
samples
.
foreach
(
x
=>
x
.
_2
.
preProcessBam
.
foreach
(
bam
=>
svCalling
.
addBamFile
(
bam
,
Some
(
x
.
_1
))))
Some
(
svCalling
)
Some
(
new
ShivaSvCalling
(
this
))
}
else
None
/** This will add the mutisample variantcalling */
...
...
@@ -298,6 +296,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
svCalling
.
foreach
(
sv
=>
{
sv
.
outputDir
=
new
File
(
outputDir
,
"sv_calling"
)
samples
.
foreach
(
x
=>
x
.
_2
.
preProcessBam
.
foreach
(
bam
=>
sv
.
addBamFile
(
bam
,
Some
(
x
.
_1
))))
sv
.
init
()
sv
.
biopetScript
()
addAll
(
sv
.
functions
)
...
...
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