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biopet.biopet
Commits
dcff73d6
Commit
dcff73d6
authored
Feb 09, 2017
by
Peter van 't Hof
Browse files
Rename root to parent
parent
463f8002
Changes
290
Hide whitespace changes
Inline
Side-by-side
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala
View file @
dcff73d6
...
...
@@ -20,7 +20,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Input
,
Output
}
/** Extension for bedtools intersect */
class
BedtoolsIntersect
(
val
roo
t
:
Configurable
)
extends
Bedtools
{
class
BedtoolsIntersect
(
val
paren
t
:
Configurable
)
extends
Bedtools
{
@Input
(
doc
=
"Input file (bed/gff/vcf/bam)"
)
var
input
:
File
=
null
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsMerge.scala
View file @
dcff73d6
...
...
@@ -22,7 +22,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument, Output, Input }
/**
* Created by ahbbollen on 5-1-16.
*/
class
BedtoolsMerge
(
val
roo
t
:
Configurable
)
extends
Bedtools
{
class
BedtoolsMerge
(
val
paren
t
:
Configurable
)
extends
Bedtools
{
@Input
(
doc
=
"Input bed file"
)
var
input
:
File
=
_
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsSort.scala
View file @
dcff73d6
...
...
@@ -23,7 +23,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
/**
* Created by Sander Bollen on 26-5-16.
*/
class
BedtoolsSort
(
val
roo
t
:
Configurable
)
extends
Bedtools
with
Reference
{
class
BedtoolsSort
(
val
paren
t
:
Configurable
)
extends
Bedtools
with
Reference
{
@Input
var
input
:
File
=
null
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie.scala
View file @
dcff73d6
...
...
@@ -26,7 +26,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
*
* Based on version 1.1.1
*/
class
Bowtie
(
val
roo
t
:
Configurable
)
extends
BiopetCommandLineFunction
with
Reference
with
Version
{
class
Bowtie
(
val
paren
t
:
Configurable
)
extends
BiopetCommandLineFunction
with
Reference
with
Version
{
@Input
(
doc
=
"Fastq file R1"
,
shortName
=
"R1"
)
var
R1
:
File
=
null
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2.scala
View file @
dcff73d6
...
...
@@ -26,7 +26,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
*
* Based on version 2.2.6
*/
class
Bowtie2
(
val
roo
t
:
Configurable
)
extends
BiopetCommandLineFunction
with
Reference
with
Version
{
class
Bowtie2
(
val
paren
t
:
Configurable
)
extends
BiopetCommandLineFunction
with
Reference
with
Version
{
@Input
(
doc
=
"Fastq file R1"
,
shortName
=
"R1"
)
var
R1
:
File
=
null
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2Build.scala
View file @
dcff73d6
...
...
@@ -23,7 +23,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
/**
* Created by pjvan_thof on 8/15/15.
*/
class
Bowtie2Build
(
val
roo
t
:
Configurable
)
extends
BiopetCommandLineFunction
with
Version
{
class
Bowtie2Build
(
val
paren
t
:
Configurable
)
extends
BiopetCommandLineFunction
with
Version
{
@Input
(
required
=
true
)
var
reference
:
File
=
_
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/BowtieBuild.scala
View file @
dcff73d6
...
...
@@ -23,7 +23,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
/**
* Created by pjvan_thof on 8/15/15.
*/
class
BowtieBuild
(
val
roo
t
:
Configurable
)
extends
BiopetCommandLineFunction
with
Version
{
class
BowtieBuild
(
val
paren
t
:
Configurable
)
extends
BiopetCommandLineFunction
with
Version
{
@Input
(
required
=
true
)
var
reference
:
File
=
_
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerCaller.scala
View file @
dcff73d6
...
...
@@ -20,7 +20,7 @@ import nl.lumc.sasc.biopet.core.{ Version, BiopetCommandLineFunction }
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
class
BreakdancerCaller
(
val
roo
t
:
Configurable
)
extends
BiopetCommandLineFunction
with
Version
{
class
BreakdancerCaller
(
val
paren
t
:
Configurable
)
extends
BiopetCommandLineFunction
with
Version
{
executable
=
config
(
"exe"
,
default
=
"breakdancer-max"
,
freeVar
=
false
)
override
def
defaultThreads
=
1
// breakdancer can only work on 1 single thread
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerConfig.scala
View file @
dcff73d6
...
...
@@ -20,7 +20,7 @@ import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
class
BreakdancerConfig
(
val
roo
t
:
Configurable
)
extends
BiopetCommandLineFunction
{
class
BreakdancerConfig
(
val
paren
t
:
Configurable
)
extends
BiopetCommandLineFunction
{
executable
=
config
(
"exe"
,
default
=
"bam2cfg.pl"
,
freeVar
=
false
)
@Input
(
doc
=
"Bam File"
)
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala
View file @
dcff73d6
...
...
@@ -20,7 +20,7 @@ import nl.lumc.sasc.biopet.core.extensions.PythonCommandLineFunction
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline._
class
BreakdancerVCF
(
val
roo
t
:
Configurable
)
extends
PythonCommandLineFunction
{
class
BreakdancerVCF
(
val
paren
t
:
Configurable
)
extends
PythonCommandLineFunction
{
setPythonScript
(
"breakdancer2vcf.py"
)
@Input
(
doc
=
"Breakdancer TSV"
)
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
View file @
dcff73d6
...
...
@@ -27,7 +27,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
*
* Created by pjvan_thof on 1/16/15.
*/
class
BwaAln
(
val
roo
t
:
Configurable
)
extends
Bwa
with
Reference
{
class
BwaAln
(
val
paren
t
:
Configurable
)
extends
Bwa
with
Reference
{
@Input
(
doc
=
"Fastq file"
,
required
=
true
)
var
fastq
:
File
=
_
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaIndex.scala
View file @
dcff73d6
...
...
@@ -26,7 +26,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
*
* Created by pjvan_thof on 1/16/15.
*/
class
BwaIndex
(
val
roo
t
:
Configurable
)
extends
Bwa
{
class
BwaIndex
(
val
paren
t
:
Configurable
)
extends
Bwa
{
@Input
(
doc
=
"Fastq file"
,
required
=
true
)
var
reference
:
File
=
_
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
View file @
dcff73d6
...
...
@@ -25,7 +25,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
*
* Based on version 0.7.12-r1039
*/
class
BwaMem
(
val
roo
t
:
Configurable
)
extends
Bwa
with
Reference
{
class
BwaMem
(
val
paren
t
:
Configurable
)
extends
Bwa
with
Reference
{
@Input
(
doc
=
"Fastq file R1"
,
shortName
=
"R1"
)
var
R1
:
File
=
_
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
View file @
dcff73d6
...
...
@@ -26,7 +26,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
* based on executable version 0.7.10-r789
*
*/
class
BwaSampe
(
val
roo
t
:
Configurable
)
extends
Bwa
with
Reference
{
class
BwaSampe
(
val
paren
t
:
Configurable
)
extends
Bwa
with
Reference
{
@Input
(
doc
=
"Fastq file R1"
,
required
=
true
)
var
fastqR1
:
File
=
_
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala
View file @
dcff73d6
...
...
@@ -26,7 +26,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
* based on executable version 0.7.10-r789
*
*/
class
BwaSamse
(
val
roo
t
:
Configurable
)
extends
Bwa
with
Reference
{
class
BwaSamse
(
val
paren
t
:
Configurable
)
extends
Bwa
with
Reference
{
@Input
(
doc
=
"Fastq file"
,
required
=
true
)
var
fastq
:
File
=
_
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/centrifuge/Centrifuge.scala
View file @
dcff73d6
...
...
@@ -28,7 +28,7 @@ import scala.util.matching.Regex
/**
* Created by pjvanthof on 19/09/16.
*/
class
Centrifuge
(
val
roo
t
:
Configurable
)
extends
BiopetCommandLineFunction
with
Version
with
Summarizable
{
class
Centrifuge
(
val
paren
t
:
Configurable
)
extends
BiopetCommandLineFunction
with
Version
with
Summarizable
{
@Input
(
doc
=
"Input: FastQ or FastA"
,
required
=
true
)
var
inputR1
:
File
=
_
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/centrifuge/CentrifugeKreport.scala
View file @
dcff73d6
...
...
@@ -23,7 +23,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
* Created by pjvanthof on 19/09/16.
*/
class
CentrifugeKreport
(
val
roo
t
:
Configurable
)
extends
BiopetCommandLineFunction
{
class
CentrifugeKreport
(
val
paren
t
:
Configurable
)
extends
BiopetCommandLineFunction
{
@Input
(
doc
=
"Output files centrifuge"
,
required
=
true
)
var
centrifugeOutputFiles
:
List
[
File
]
=
Nil
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala
View file @
dcff73d6
...
...
@@ -20,7 +20,7 @@ import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Reference, Version
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
class
CleverCaller
(
val
roo
t
:
Configurable
)
extends
BiopetCommandLineFunction
with
Reference
with
Version
{
class
CleverCaller
(
val
paren
t
:
Configurable
)
extends
BiopetCommandLineFunction
with
Reference
with
Version
{
executable
=
config
(
"exe"
,
default
=
"clever"
)
private
lazy
val
versionExecutable
:
File
=
config
(
"version_exe"
,
default
=
new
File
(
executable
).
getParent
+
"/ctk-version"
)
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverFixVCF.scala
View file @
dcff73d6
...
...
@@ -27,7 +27,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
import
scala.io.Source
class
CleverFixVCF
(
val
roo
t
:
Configurable
)
extends
BiopetJavaCommandLineFunction
{
class
CleverFixVCF
(
val
paren
t
:
Configurable
)
extends
BiopetJavaCommandLineFunction
{
javaMainClass
=
getClass
.
getName
@Input
(
doc
=
"Input Clever VCF"
)
var
input
:
File
=
_
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/conifer/ConiferAnalyze.scala
View file @
dcff73d6
...
...
@@ -19,7 +19,7 @@ import java.io.File
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Input
,
Output
}
class
ConiferAnalyze
(
val
roo
t
:
Configurable
)
extends
Conifer
{
class
ConiferAnalyze
(
val
paren
t
:
Configurable
)
extends
Conifer
{
@Input
(
doc
=
"Probes / capture kit definition as bed file: chr,start,stop,gene-annot"
,
required
=
true
)
var
probes
:
File
=
_
...
...
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