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biopet.biopet
Commits
31ea0eee
Commit
31ea0eee
authored
May 21, 2014
by
Peter van 't Hof
Browse files
- Fixed scattercounts
parent
630092d5
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Star.scala
View file @
31ea0eee
...
...
@@ -18,7 +18,7 @@ class Star(private var globalConfig: Config) extends CommandLineFunction {
@Input
(
doc
=
"Fastq file R2"
,
shortName
=
"R2"
,
required
=
false
)
var
R2
:
File
=
_
@Argument
(
doc
=
"Output Directory"
,
shortName
=
"outputDir"
)
var
outputDir
:
String
=
_
@Argument
(
doc
=
"GenomeDir"
,
required
=
false
)
var
genomeDir
:
String
=
_
if
(
genomeDir
==
null
)
genomeDir
=
config
.
getAsString
(
"genomeDir"
,
referenceFile
.
getParent
+
"/star
/ref
"
)
if
(
genomeDir
==
null
)
genomeDir
=
config
.
getAsString
(
"genomeDir"
,
referenceFile
.
getParent
+
"/star"
)
@Argument
(
doc
=
"STAR runmode"
,
shortName
=
"runmode"
,
required
=
false
)
var
runmode
:
String
=
_
...
...
@@ -30,7 +30,7 @@ class Star(private var globalConfig: Config) extends CommandLineFunction {
if
(
threads
>
maxThreads
)
threads
=
maxThreads
nCoresRequest
=
Option
(
threads
)
@Output
var
outputSam
:
File
=
new
File
(
outputDir
+
"/
Aligned.o
ut.sam"
)
@Output
var
outputSam
:
File
=
new
File
(
outputDir
+
"/
star_outp
ut.sam"
)
def
commandLine
:
String
=
{
//init()
...
...
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