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biopet.biopet
Commits
571223aa
Commit
571223aa
authored
Jul 27, 2015
by
Peter van 't Hof
Browse files
Remove unused source
parent
a5ecd049
Changes
1
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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/Clever.scala
deleted
100644 → 0
View file @
a5ecd049
/**
* 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.clever
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.core.
{
BiopetQScript
,
PipelineCommand
}
import
org.broadinstitute.gatk.queue.QScript
class
Clever
(
val
root
:
Configurable
)
extends
QScript
with
BiopetQScript
{
def
this
()
=
this
(
null
)
@Input
(
doc
=
"Input file (bam)"
)
var
input
:
File
=
_
@Input
(
doc
=
"Reference"
)
var
reference
:
File
=
_
@Argument
(
doc
=
"Work directory"
)
var
workdir
:
String
=
_
@Argument
(
doc
=
"Current working directory"
)
var
cwd
:
String
=
_
override
def
init
()
{
}
def
biopetScript
()
{
// write the pipeline here
logger
.
info
(
"Starting Clever Pipeline"
)
/// start clever and then copy the vcf into the root directory "<sample>.clever/"
val
clever
=
CleverCaller
(
this
,
input
,
reference
,
cwd
,
workdir
)
outputFiles
+=
(
"clever_vcf"
->
clever
.
outputvcf
)
add
(
clever
)
}
}
object
Clever
extends
PipelineCommand
{
override
val
pipeline
=
"/nl/lumc/sasc/biopet/extensions/svcallers/Clever/Clever.class"
def
apply
(
root
:
Configurable
,
input
:
File
,
runDir
:
String
)
:
Clever
=
{
val
cleverpipeline
=
new
Clever
(
root
)
cleverpipeline
.
input
=
input
cleverpipeline
.
workdir
=
runDir
cleverpipeline
.
init
()
cleverpipeline
.
biopetScript
()
cleverpipeline
}
}
\ No newline at end of file
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