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
ca53b210
Commit
ca53b210
authored
Aug 15, 2016
by
Peter van 't Hof
Browse files
Reduce threads for varscan
parent
79b42eea
Changes
1
Hide whitespace changes
Inline
Side-by-side
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/VarscanCnsSingleSample.scala
View file @
ca53b210
...
...
@@ -60,7 +60,9 @@ class VarscanCnsSingleSample(val root: Configurable) extends Variantcaller {
val
varscan
=
new
VarscanMpileup2cns
(
this
)
varscan
.
vcfSampleList
=
Some
(
sampleFile
)
add
(
mpileup
|
new
FixMpileup
(
this
)
|
varscan
|
new
Bgzip
(
this
)
>
sampleVcf
)
val
variantcallingJob
=
mpileup
|
new
FixMpileup
(
this
)
|
varscan
|
new
Bgzip
(
this
)
>
sampleVcf
variantcallingJob
.
threadsCorrection
=
-
2
add
(
variantcallingJob
)
add
(
Tabix
(
this
,
sampleVcf
))
sampleVcf
...
...
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