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biopet.biopet
Commits
bcadec7e
Commit
bcadec7e
authored
9 years ago
by
Peter van 't Hof
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Added version command for star
parent
3925dac1
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public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
+5
-2
5 additions, 2 deletions
.../src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
with
5 additions
and
2 deletions
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
+
5
−
2
View file @
bcadec7e
...
...
@@ -18,13 +18,13 @@ package nl.lumc.sasc.biopet.extensions
import
java.io.File
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.core.
{
BiopetCommandLineFunction
,
Reference
}
import
nl.lumc.sasc.biopet.core.
{
Version
,
BiopetCommandLineFunction
,
Reference
}
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Input
,
Output
}
/**
* Extension for STAR
*/
class
Star
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
with
Reference
{
class
Star
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
with
Reference
with
Version
{
@Input
(
doc
=
"The reference file for the bam files."
,
required
=
false
)
var
reference
:
File
=
null
...
...
@@ -54,6 +54,9 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction with Refere
executable
=
config
(
"exe"
,
"STAR"
)
def
versionCommand
=
executable
+
" --version"
def
versionRegex
=
"""(.*)"""
.
r
@Argument
(
doc
=
"Output Directory"
)
var
outputDir
:
File
=
_
...
...
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