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biopet.biopet
Commits
23a0b18f
Commit
23a0b18f
authored
Jul 25, 2017
by
pjvan_thof
Browse files
No merging with only 1 sample
parent
532f837c
Changes
2
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Inline
Side-by-side
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
View file @
23a0b18f
...
...
@@ -80,7 +80,7 @@ class Star(val parent: Configurable)
var
genomeSAindexNbases
:
Option
[
Long
]
=
config
(
"genomesaindexnbases"
)
var
genomeSAsparseD
:
Option
[
Int
]
=
config
(
"genomesasparsed"
)
val
defaultGtf
:
Option
[
File
]
=
config
(
"annotation_gtf"
)
private
def
defaultGtf
:
Option
[
File
]
=
config
(
"annotation_gtf"
)
@Input
(
required
=
false
)
var
sjdbGTFfile
:
Option
[
File
]
=
defaultGtf
match
{
case
Some
(
file
)
=>
config
(
"sjdbgtfile"
,
default
=
file
)
...
...
gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/Measurement.scala
View file @
23a0b18f
...
...
@@ -54,7 +54,7 @@ trait Measurement extends SummaryQScript with Reference { qscript: QScript =>
require
(
bamFiles
.
nonEmpty
)
}
lazy
val
mergeCountFiles
:
Boolean
=
config
(
"merge_count_files"
,
default
=
true
)
lazy
val
mergeCountFiles
:
Boolean
=
config
(
"merge_count_files"
,
default
=
bamFiles
.
size
>
1
)
private
var
extraSummaryFiles
:
Map
[
String
,
File
]
=
Map
()
...
...
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