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biopet.biopet
Commits
993d6b05
Commit
993d6b05
authored
Feb 07, 2017
by
Peter van 't Hof
Browse files
Fixing BIOPET-562
parent
cefa43a5
Changes
2
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Inline
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shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcalling.scala
View file @
993d6b05
...
...
@@ -112,21 +112,22 @@ class ShivaVariantcalling(val root: Configurable) extends QScript
vtDecompose
.
inputVcf
=
vtNormalize
.
outputVcf
vtDecompose
.
outputVcf
=
swapExt
(
caller
.
outputDir
,
vtNormalize
.
outputVcf
,
".vcf.gz"
,
".decompose.vcf.gz"
)
add
(
vtDecompose
,
Tabix
(
this
,
vtDecompose
.
outputVcf
))
cv
.
variant
:+=
TaggedFile
(
vtDecompose
.
outputVcf
,
caller
.
name
)
if
(
caller
.
mergeVcfResults
)
cv
.
variant
:+=
TaggedFile
(
vtDecompose
.
outputVcf
,
caller
.
name
)
}
else
if
(
normalize
&&
!
decompose
)
{
vtNormalize
.
outputVcf
=
swapExt
(
caller
.
outputDir
,
caller
.
outputFile
,
".vcf.gz"
,
".normalized.vcf.gz"
)
add
(
vtNormalize
,
Tabix
(
this
,
vtNormalize
.
outputVcf
))
cv
.
variant
:+=
TaggedFile
(
vtNormalize
.
outputVcf
,
caller
.
name
)
if
(
caller
.
mergeVcfResults
)
cv
.
variant
:+=
TaggedFile
(
vtNormalize
.
outputVcf
,
caller
.
name
)
}
else
if
(!
normalize
&&
decompose
)
{
vtDecompose
.
inputVcf
=
caller
.
outputFile
vtDecompose
.
outputVcf
=
swapExt
(
caller
.
outputDir
,
caller
.
outputFile
,
".vcf.gz"
,
".decompose.vcf.gz"
)
add
(
vtDecompose
,
Tabix
(
this
,
vtDecompose
.
outputVcf
))
cv
.
variant
:+=
TaggedFile
(
vtDecompose
.
outputVcf
,
caller
.
name
)
}
else
cv
.
variant
:+=
TaggedFile
(
caller
.
outputFile
,
caller
.
name
)
if
(
caller
.
mergeVcfResults
)
cv
.
variant
:+=
TaggedFile
(
vtDecompose
.
outputVcf
,
caller
.
name
)
}
else
if
(
caller
.
mergeVcfResults
)
cv
.
variant
:+=
TaggedFile
(
caller
.
outputFile
,
caller
.
name
)
}
if
(
cv
.
variant
.
nonEmpty
)
{
add
(
cv
)
addStats
(
finalFile
,
"final"
)
}
add
(
cv
)
addStats
(
finalFile
,
"final"
)
addSummaryJobs
()
}
...
...
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/Variantcaller.scala
View file @
993d6b05
...
...
@@ -27,6 +27,8 @@ trait Variantcaller extends QScript with BiopetQScript with Reference {
var
namePrefix
:
String
=
_
val
mergeVcfResults
:
Boolean
=
config
(
"merge_vcf_results"
,
default
=
true
)
/**
* Map of samplename -> (preprocessed) bam file
*/
...
...
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