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
e2b5ad1d
Commit
e2b5ad1d
authored
May 11, 2016
by
Peter van 't Hof
Browse files
Added cnv to summary settings
parent
ef10b38d
Changes
2
Hide whitespace changes
Inline
Side-by-side
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala
View file @
e2b5ad1d
...
...
@@ -209,6 +209,7 @@ class Shiva(val root: Configurable) extends QScript with MultisampleMappingTrait
"annotation"
->
annotation
.
isDefined
,
"multisample_variantcalling"
->
multisampleVariantCalling
.
isDefined
,
"sv_calling"
->
svCalling
.
isDefined
,
"cnv_calling"
->
cnvCalling
.
isDefined
,
"regions_of_interest"
->
roiBedFiles
.
map
(
_
.
getName
.
stripSuffix
(
".bed"
)),
"amplicon_bed"
->
ampliconBedFile
.
map
(
_
.
getName
.
stripSuffix
(
".bed"
))
)
...
...
shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
View file @
e2b5ad1d
...
...
@@ -104,6 +104,7 @@ trait ShivaTestTrait extends TestNGSuite with Matchers {
pipeline
.
summarySettings
.
get
(
"annotation"
)
shouldBe
Some
(
annotation
)
pipeline
.
summarySettings
.
get
(
"sv_calling"
)
shouldBe
Some
(
svCalling
)
pipeline
.
summarySettings
.
get
(
"cnv_calling"
)
shouldBe
Some
(
cnvCalling
)
pipeline
.
samples
foreach
{
case
(
sampleId
,
sample
)
=>
...
...
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