Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Mirrors
biopet.biopet
Commits
6cb4dcbe
Commit
6cb4dcbe
authored
Nov 29, 2015
by
Peter van 't Hof
Browse files
Added index to vt jobs
parent
050af98d
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
View file @
6cb4dcbe
...
...
@@ -17,6 +17,7 @@ package nl.lumc.sasc.biopet.pipelines.shiva
import
nl.lumc.sasc.biopet.core.summary.SummaryQScript
import
nl.lumc.sasc.biopet.core.
{
Reference
,
SampleLibraryTag
}
import
nl.lumc.sasc.biopet.extensions.Tabix
import
nl.lumc.sasc.biopet.extensions.gatk.
{
CombineVariants
,
GenotypeConcordance
}
import
nl.lumc.sasc.biopet.extensions.tools.VcfStats
import
nl.lumc.sasc.biopet.extensions.vt.
{
VtDecompose
,
VtNormalize
}
...
...
@@ -101,19 +102,19 @@ trait ShivaVariantcallingTrait extends SummaryQScript
if
(
normalize
&&
decompose
)
{
vtNormalize
.
outputVcf
=
swapExt
(
caller
.
outputDir
,
caller
.
outputFile
,
".vcf.gz"
,
".normaize.vcf.gz"
)
vtNormalize
.
isIntermediate
=
true
add
(
vtNormalize
)
add
(
vtNormalize
,
Tabix
(
this
,
vtNormalize
.
outputVcf
)
)
vtDecompose
.
inputVcf
=
vtNormalize
.
outputVcf
vtDecompose
.
outputVcf
=
swapExt
(
caller
.
outputDir
,
vtNormalize
.
outputVcf
,
".vcf.gz"
,
".decompose.vcf.gz"
)
add
(
vtDecompose
)
add
(
vtDecompose
,
Tabix
(
this
,
vtDecompose
.
outputVcf
)
)
cv
.
addInput
(
vtDecompose
.
outputVcf
,
caller
.
name
)
}
else
if
(
normalize
&&
!
decompose
)
{
vtNormalize
.
outputVcf
=
swapExt
(
caller
.
outputDir
,
caller
.
outputFile
,
".vcf.gz"
,
".normaize.vcf.gz"
)
add
(
vtNormalize
)
add
(
vtNormalize
,
Tabix
(
this
,
vtNormalize
.
outputVcf
)
)
cv
.
addInput
(
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
)
add
(
vtDecompose
,
Tabix
(
this
,
vtDecompose
.
outputVcf
)
)
cv
.
addInput
(
vtDecompose
.
outputVcf
,
caller
.
name
)
}
else
cv
.
addInput
(
caller
.
outputFile
,
caller
.
name
)
}
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment