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biopet.biopet
Commits
3828a150
Commit
3828a150
authored
Apr 22, 2016
by
Peter van 't Hof
Browse files
Change arg to multiarg
parent
a8748725
Changes
1
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public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
View file @
3828a150
...
...
@@ -40,8 +40,8 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction with Refere
@Output
(
doc
=
"Output tab file"
,
required
=
false
)
var
outputTab
:
File
=
_
@Input
(
doc
=
"sjdbFileChrStartEnd file"
,
required
=
false
)
/**Can be a list of file Paths TO BE CHECKED **/
var
sjdbFileChrStartEnd
:
File
=
_
@Input
(
doc
=
"sjdbFileChrStartEnd file"
,
required
=
false
)
var
sjdbFileChrStartEnd
:
List
[
File
]
=
Nil
@Output
(
doc
=
"Output genome file"
,
required
=
false
)
var
outputGenome
:
File
=
_
...
...
@@ -237,7 +237,7 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction with Refere
cmd
+=
required
(
"--readFilesIn"
,
R1
)
+
optional
(
R2
)
}
cmd
+=
required
(
"--genomeDir"
,
genomeDir
)
+
optional
(
"--sjdbFileChrStartEnd"
,
sjdbFileChrStartEnd
)
+
multiArg
(
"--sjdbFileChrStartEnd"
,
sjdbFileChrStartEnd
)
+
optional
(
"--runThreadN"
,
threads
)
+
optional
(
"--outFileNamePrefix"
,
outFileNamePrefix
)
+
optional
(
"--sjdbOverhang"
,
sjdbOverhang
)
+
...
...
@@ -420,7 +420,7 @@ object Star {
starCommandPass1
.
beforeGraph
()
val
starCommandReindex
=
new
Star
(
configurable
)
starCommandReindex
.
sjdbFileChrStartEnd
=
starCommandPass1
.
outputTab
starCommandReindex
.
sjdbFileChrStartEnd
:+
=
starCommandPass1
.
outputTab
starCommandReindex
.
outputDir
=
new
File
(
outputDir
,
"re-index"
)
starCommandReindex
.
runmode
=
"genomeGenerate"
starCommandReindex
.
isIntermediate
=
isIntermediate
...
...
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