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biopet.biopet
Commits
36e763df
Commit
36e763df
authored
Jan 16, 2015
by
Peter van 't Hof
Browse files
Make new package for bwa
parent
695650c2
Changes
2
Hide whitespace changes
Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/Bwa.scala
0 → 100644
View file @
36e763df
package
nl.lumc.sasc.biopet.extensions.bwa
import
nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
/**
* Created by pjvan_thof on 1/16/15.
*/
abstract
class
Bwa
extends
BiopetCommandLineFunction
{
override
def
subPath
=
"bwa"
::
super
.
subPath
executable
=
config
(
"exe"
,
default
=
"bwa"
)
override
val
versionRegex
=
"""Version: (.*)"""
.
r
override
val
versionExitcode
=
List
(
0
,
1
)
override
def
versionCommand
=
executable
}
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/
aligners
/Bwa.scala
→
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/
bwa
/Bwa
Mem
.scala
View file @
36e763df
...
...
@@ -13,14 +13,15 @@
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package
nl.lumc.sasc.biopet.extensions.aligners
package
nl.lumc.sasc.biopet.extensions.bwa
import
java.io.File
import
nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
java.io.File
class
Bwa
(
val
root
:
Configurable
)
extends
B
iopetCommandLineFunction
{
class
Bwa
Mem
(
val
root
:
Configurable
)
extends
B
wa
{
@Input
(
doc
=
"Fastq file R1"
,
shortName
=
"R1"
)
var
R1
:
File
=
_
...
...
@@ -62,15 +63,9 @@ class Bwa(val root: Configurable) extends BiopetCommandLineFunction {
var
Y
:
Boolean
=
config
(
"Y"
,
default
=
false
)
var
I
:
String
=
config
(
"I"
)
executable
=
config
(
"exe"
,
default
=
"bwa"
,
freeVar
=
false
)
override
val
versionRegex
=
"""Version: (.*)"""
.
r
override
val
versionExitcode
=
List
(
0
,
1
)
override
val
defaultVmem
=
"6G"
override
val
defaultThreads
=
8
override
def
versionCommand
=
executable
def
cmdLine
=
{
required
(
executable
)
+
required
(
"mem"
)
+
...
...
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