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
81fd15f8
Commit
81fd15f8
authored
Aug 26, 2014
by
Peter van 't Hof
Browse files
Added defaultAligner var
parent
7b626832
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
81fd15f8
...
...
@@ -77,16 +77,12 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
var
RGPI
:
Int
=
_
var
paired
:
Boolean
=
false
var
defaultAligner
=
"bwa"
val
flexiprep
=
new
Flexiprep
(
this
)
def
init
()
{
for
(
file
<-
configfiles
)
globalConfig
.
loadConfigFile
(
file
)
var
inputtype
:
String
=
config
(
"inputtype"
,
"dna"
)
if
(
aligner
==
null
)
{
if
(
inputtype
==
"rna"
)
aligner
=
config
(
"aligner"
,
"star-2pass"
)
else
aligner
=
config
(
"aligner"
,
"bwa"
)
}
if
(
aligner
==
null
)
aligner
=
config
(
"aligner"
,
default
=
defaultAligner
)
if
(
reference
==
null
)
reference
=
config
(
"reference"
)
if
(
outputDir
==
null
)
throw
new
IllegalStateException
(
"Missing Output directory on mapping module"
)
else
if
(!
outputDir
.
endsWith
(
"/"
))
outputDir
+=
"/"
...
...
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