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
241a7d23
Commit
241a7d23
authored
Nov 20, 2015
by
Peter van 't Hof
Browse files
Added vt normalizer extension
parent
1568a600
Changes
2
Hide whitespace changes
Inline
Side-by-side
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/vt/Vt.scala
0 → 100644
View file @
241a7d23
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* 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.vt
import
nl.lumc.sasc.biopet.core.
{
Version
,
BiopetCommandLineFunction
}
/**
* General bwa extension
*
* Created by pjvan_thof on 1/16/15.
*/
abstract
class
Vt
extends
BiopetCommandLineFunction
{
override
def
subPath
=
"vt"
::
super
.
subPath
executable
=
config
(
"exe"
,
default
=
"vt"
)
}
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/vt/VtNormalize.scala
0 → 100644
View file @
241a7d23
package
nl.lumc.sasc.biopet.extensions.vt
import
java.io.File
import
nl.lumc.sasc.biopet.core.
{
Reference
,
Version
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Output
,
Input
}
/**
* Created by pjvanthof on 20/11/15.
*/
class
VtNormalize
(
val
root
:
Configurable
)
extends
Vt
with
Version
with
Reference
{
def
versionRegex
=
"""normalize (.*)"""
.
r
override
def
versionExitcode
=
List
(
0
,
1
)
def
versionCommand
=
executable
+
" normalize"
@Input
(
required
=
true
)
var
inputVcf
:
File
=
_
@Output
(
required
=
true
)
var
outputVcf
:
File
=
_
var
windowSize
:
Option
[
Int
]
=
config
(
"windows_size"
)
var
intervalsFile
:
Option
[
File
]
=
config
(
"intervals_file"
)
var
reference
:
File
=
_
override
def
beforeGraph
()
:
Unit
=
{
super
.
beforeGraph
()
reference
=
referenceFasta
()
}
def
cmdLine
=
required
(
executable
)
+
required
(
"normalize"
)
+
required
(
"-o"
,
outputVcf
)
+
optional
(
"-w"
,
windowSize
)
+
optional
(
"-I"
,
intervalsFile
)
+
required
(
"-r"
,
reference
)
required
(
inputVcf
)
}
\ No newline at end of file
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