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biopet.biopet
Commits
04434f88
Commit
04434f88
authored
Jul 13, 2017
by
Peter van 't Hof
Browse files
Style fixes
parent
1be6069f
Changes
5
Hide whitespace changes
Inline
Side-by-side
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
View file @
04434f88
...
...
@@ -92,10 +92,12 @@ class Raxml(val parent: Configurable) extends BiopetCommandLineFunction with Ver
}
/** Returns bestTree file */
def
getBestTreeFile
:
Option
[
File
]
=
option
(
f
==
"d"
&&
b
.
isEmpty
,
new
File
(
w
,
"RAxML_bestTree."
+
n
))
def
getBestTreeFile
:
Option
[
File
]
=
option
(
f
==
"d"
&&
b
.
isEmpty
,
new
File
(
w
,
"RAxML_bestTree."
+
n
))
/** Returns bootstrap file */
def
getBootstrapFile
:
Option
[
File
]
=
option
(
f
==
"d"
&&
b
.
isDefined
,
new
File
(
w
,
"RAxML_bootstrap."
+
n
))
def
getBootstrapFile
:
Option
[
File
]
=
option
(
f
==
"d"
&&
b
.
isDefined
,
new
File
(
w
,
"RAxML_bootstrap."
+
n
))
/** Returns bipartitions file */
def
getBipartitionsFile
:
Option
[
File
]
=
option
(
f
==
"b"
,
new
File
(
w
,
"RAxML_bipartitions."
+
n
))
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/centrifuge/Centrifuge.scala
View file @
04434f88
...
...
@@ -163,7 +163,8 @@ class Centrifuge(val parent: Configurable)
.
map
{
file
=>
val
reader
=
Source
.
fromFile
(
file
)
val
header
=
reader
.
getLines
().
next
().
split
(
"\t"
)
val
values
=
reader
.
getLines
().
next
().
split
(
"\t"
).
map
(
tryToParseNumber
(
_
,
fallBack
=
true
).
get
)
val
values
=
reader
.
getLines
().
next
().
split
(
"\t"
).
map
(
tryToParseNumber
(
_
,
fallBack
=
true
).
get
)
reader
.
close
()
Map
(
"metrics"
->
header
.
zip
(
values
).
toMap
)
}
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/freec/FreeC.scala
View file @
04434f88
/**
* 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 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.
*/
* 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 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.freec
import
java.io.
{
File
,
PrintWriter
}
...
...
@@ -22,7 +22,10 @@ import org.broadinstitute.gatk.utils.commandline._
import
scala.util.matching.Regex
class
FreeC
(
val
parent
:
Configurable
)
extends
BiopetCommandLineFunction
with
Reference
with
Version
{
class
FreeC
(
val
parent
:
Configurable
)
extends
BiopetCommandLineFunction
with
Reference
with
Version
{
override
def
defaults
=
Map
(
"max_walltime_limit"
->
7200
)
...
...
@@ -62,7 +65,8 @@ class FreeC(val parent: Configurable) extends BiopetCommandLineFunction with Ref
executable
=
config
(
"exe"
,
default
=
"freec"
,
freeVar
=
false
)
var
bedGraphOutput
:
Boolean
=
config
(
"BedGraphOutput"
,
default
=
false
)
var
bedtools
:
Option
[
File
]
=
config
(
"exe"
,
default
=
"bedtools"
,
namespace
=
"bedtools"
,
freeVar
=
false
)
var
bedtools
:
Option
[
File
]
=
config
(
"exe"
,
default
=
"bedtools"
,
namespace
=
"bedtools"
,
freeVar
=
false
)
var
breakPointThreshold
:
Option
[
Double
]
=
config
(
"breakPointThreshold"
)
var
breakPointType
:
Option
[
Int
]
=
config
(
"breakPointType"
)
...
...
@@ -162,19 +166,31 @@ class FreeC(val parent: Configurable) extends BiopetCommandLineFunction with Ref
optional
(
"breakPointType="
,
breakPointType
,
spaceSeparated
=
false
,
escape
=
false
)
+
"\n"
+
required
(
"chrFiles="
,
chrFiles
,
spaceSeparated
=
false
,
escape
=
false
)
+
"\n"
+
required
(
"chrLenFile="
,
chrLenFile
,
spaceSeparated
=
false
,
escape
=
false
)
+
"\n"
+
optional
(
"coefficientOfVariation="
,
coefficientOfVariation
,
spaceSeparated
=
false
,
escape
=
false
)
+
"\n"
+
optional
(
"coefficientOfVariation="
,
coefficientOfVariation
,
spaceSeparated
=
false
,
escape
=
false
)
+
"\n"
+
optional
(
"contamination="
,
contamination
,
spaceSeparated
=
false
,
escape
=
false
)
+
"\n"
+
conditional
(
contaminationAdjustment
,
"contaminationAdjustment=TRUE"
,
escape
=
false
)
+
"\n"
+
optional
(
"degree="
,
degree
,
spaceSeparated
=
false
,
escape
=
false
)
+
"\n"
+
optional
(
"forceGCcontentNormalization="
,
forceGCcontentNormalization
,
spaceSeparated
=
false
,
escape
=
false
)
+
"\n"
+
optional
(
"forceGCcontentNormalization="
,
forceGCcontentNormalization
,
spaceSeparated
=
false
,
escape
=
false
)
+
"\n"
+
optional
(
"GCcontentProfile="
,
gcContentProfile
,
spaceSeparated
=
false
,
escape
=
false
)
+
"\n"
+
optional
(
"gemMappabilityFile="
,
gemMappabilityFile
,
spaceSeparated
=
false
,
escape
=
false
)
+
"\n"
+
optional
(
"intercept="
,
intercept
,
spaceSeparated
=
false
,
escape
=
false
)
+
"\n"
+
optional
(
"minCNAlength="
,
minCNAlength
,
spaceSeparated
=
false
,
escape
=
false
)
+
"\n"
+
optional
(
"minMappabilityPerWindow="
,
minMappabilityPerWindow
,
spaceSeparated
=
false
,
escape
=
false
)
+
"\n"
+
optional
(
"minMappabilityPerWindow="
,
minMappabilityPerWindow
,
spaceSeparated
=
false
,
escape
=
false
)
+
"\n"
+
optional
(
"minExpectedGC="
,
minExpectedGC
,
spaceSeparated
=
false
,
escape
=
false
)
+
"\n"
+
optional
(
"maxExpectedGC="
,
maxExpectedGC
,
spaceSeparated
=
false
,
escape
=
false
)
+
"\n"
+
optional
(
"minimalSubclonePresence="
,
minimalSubclonePresence
,
spaceSeparated
=
false
,
escape
=
false
)
+
"\n"
+
optional
(
"minimalSubclonePresence="
,
minimalSubclonePresence
,
spaceSeparated
=
false
,
escape
=
false
)
+
"\n"
+
optional
(
"maxThreads="
,
getThreads
,
spaceSeparated
=
false
,
escape
=
false
)
+
"\n"
+
conditional
(
noisyData
,
"noisyData=TRUE"
,
escape
=
false
)
+
"\n"
+
required
(
"outputDir="
,
outputPath
,
spaceSeparated
=
false
,
escape
=
false
)
+
"\n"
+
...
...
@@ -196,10 +212,16 @@ class FreeC(val parent: Configurable) extends BiopetCommandLineFunction with Ref
required
(
"mateOrientation="
,
mateOrientation
,
spaceSeparated
=
false
,
escape
=
false
)
+
"\n"
+
"[BAF]"
+
"\n"
+
optional
(
"SNPfile="
,
snpFile
,
spaceSeparated
=
false
,
escape
=
false
)
+
"\n"
+
optional
(
"minimalCoveragePerPosition="
,
minimalCoveragePerPosition
,
spaceSeparated
=
false
,
escape
=
false
)
+
"\n"
+
optional
(
"minimalCoveragePerPosition="
,
minimalCoveragePerPosition
,
spaceSeparated
=
false
,
escape
=
false
)
+
"\n"
+
optional
(
"makePileup="
,
makePileup
,
spaceSeparated
=
false
,
escape
=
false
)
+
"\n"
+
optional
(
"fastaFile="
,
fastaFile
,
spaceSeparated
=
false
,
escape
=
false
)
+
"\n"
+
optional
(
"minimalQualityPerPosition="
,
minimalQualityPerPosition
,
spaceSeparated
=
false
,
escape
=
false
)
+
"\n"
+
optional
(
"minimalQualityPerPosition="
,
minimalQualityPerPosition
,
spaceSeparated
=
false
,
escape
=
false
)
+
"\n"
+
optional
(
"shiftInQuality="
,
shiftInQuality
,
spaceSeparated
=
false
,
escape
=
false
)
+
"\n"
+
"[target]"
+
"\n"
+
optional
(
"captureRegions="
,
captureRegions
,
spaceSeparated
=
false
,
escape
=
false
)
+
"\n"
...
...
@@ -208,6 +230,7 @@ class FreeC(val parent: Configurable) extends BiopetCommandLineFunction with Ref
writer
.
close
()
}
def
cmdLine
:
String
=
required
(
executable
)
+
required
(
"--conf"
,
configFile
)
def
cmdLine
:
String
=
required
(
executable
)
+
required
(
"--conf"
,
configFile
)
}
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
View file @
04434f88
...
...
@@ -80,7 +80,8 @@ class CollectGcBiasMetrics(val parent: Configurable)
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
()
/** Returns stats for summary */
def
summaryStats
:
Option
[
Map
[
String
,
List
[
Option
[
Any
]]]]
=
Picard
.
getHistogram
(
output
,
tag
=
"METRICS CLASS"
)
def
summaryStats
:
Option
[
Map
[
String
,
List
[
Option
[
Any
]]]]
=
Picard
.
getHistogram
(
output
,
tag
=
"METRICS CLASS"
)
}
object
CollectGcBiasMetrics
{
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/VarscanMpileup2cns.scala
View file @
04434f88
...
...
@@ -43,8 +43,10 @@ class VarscanMpileup2cns(val parent: Configurable) extends Varscan {
override
def
beforeGraph
()
:
Unit
=
{
val
validValues
:
Set
[
Int
]
=
Set
(
0
,
1
)
// check for boolean vars that are passed as ints
strandFilter
.
foreach
(
v
=>
require
(
validValues
.
contains
(
v
),
"strand_filter value must be either 0 or 1"
))
outputVcf
.
foreach
(
v
=>
require
(
validValues
.
contains
(
v
),
"output_vcf value must be either 0 or 1"
))
strandFilter
.
foreach
(
v
=>
require
(
validValues
.
contains
(
v
),
"strand_filter value must be either 0 or 1"
))
outputVcf
.
foreach
(
v
=>
require
(
validValues
.
contains
(
v
),
"output_vcf value must be either 0 or 1"
))
variants
.
foreach
(
v
=>
require
(
validValues
.
contains
(
v
),
"variants value must be either 0 or 1"
))
}
...
...
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