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
ba36a06a
Commit
ba36a06a
authored
May 19, 2016
by
Peter van 't Hof
Browse files
Fix tabix step
parent
fa41ea50
Changes
1
Hide whitespace changes
Inline
Side-by-side
generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/GenerateIndexes.scala
View file @
ba36a06a
...
...
@@ -187,13 +187,11 @@ class GenerateIndexes(val root: Configurable) extends QScript with BiopetQScript
downloadCmd
.
isIntermediate
=
true
add
(
downloadCmd
)
if
(
curl
.
output
.
getName
.
endsWith
(
".vcf.gz"
))
{
val
tabix
=
new
Tabix
(
this
)
tabix
.
input
=
output
tabix
.
p
=
Some
(
"vcf"
)
tabix
.
isIntermediate
=
true
add
(
tabix
)
}
val
tabix
=
new
Tabix
(
this
)
tabix
.
input
=
output
tabix
.
p
=
Some
(
"vcf"
)
tabix
.
isIntermediate
=
true
add
(
tabix
)
cv
.
variant
:+=
output
}
...
...
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