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biopet.biopet
Commits
0d14a49a
Commit
0d14a49a
authored
May 17, 2016
by
Peter van 't Hof
Browse files
Adding gtf download
parent
142c815a
Changes
1
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Inline
Side-by-side
generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/GenerateIndexes.scala
View file @
0d14a49a
...
...
@@ -196,6 +196,21 @@ class GenerateIndexes(val root: Configurable) extends QScript with BiopetQScript
outputConfig
+=
"dbsnp"
->
cv
.
out
}
val
gtfFile
:
Option
[
File
]
=
genomeConfig
.
get
(
"gtf_uri"
).
map
{
gtfUri
=>
val
curl
=
new
Curl
(
this
)
curl
.
url
=
gtfUri
.
toString
curl
.
output
=
new
File
(
annotationDir
,
new
File
(
curl
.
url
).
getName
)
add
(
curl
)
outputConfig
+=
"annotation_gtf"
->
curl
.
output
curl
.
output
}
val
refFlatFile
:
Option
[
File
]
=
gtfFile
.
map
{
gtf
=>
val
refFlat
=
new
File
(
gtf
+
".refFlat"
)
//TODO: gtf to refFlat conversion
refFlat
}
// Bwa index
val
bwaIndex
=
new
BwaIndex
(
this
)
bwaIndex
.
reference
=
createLinks
(
new
File
(
genomeDir
,
"bwa"
))
...
...
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