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biopet.biopet
Commits
ee4de907
Commit
ee4de907
authored
Jul 25, 2017
by
pjvan_thof
Browse files
Style fixes
parent
26ff1d93
Changes
4
Hide whitespace changes
Inline
Side-by-side
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/stringtie/Stringtie.scala
View file @
ee4de907
...
...
@@ -9,7 +9,7 @@ import org.broadinstitute.gatk.utils.commandline.{Input, Output}
import
scala.util.matching.Regex
class
Stringtie
(
val
parent
:
Configurable
)
extends
BiopetCommandLineFunction
extends
BiopetCommandLineFunction
with
Reference
with
Version
{
...
...
@@ -54,28 +54,29 @@ class Stringtie(val parent: Configurable)
/** Regex to get version from version command output */
def
versionRegex
:
Regex
=
".*"
.
r
def
cmdLine
:
String
=
required
(
executable
)
+
required
(
inputBam
)
+
conditional
(
v
,
"-v"
)
+
required
(
"-p"
,
threads
)
+
conditional
(
rf
,
"--rf"
)
+
conditional
(
fr
,
"--fr"
)
+
optional
(
"-l"
,
l
)
+
optional
(
"-f"
,
f
)
+
optional
(
"-m"
,
m
)
+
optional
(
"-A"
,
geneAbundances
)
+
optional
(
"-C"
,
referenceCoverage
)
+
optional
(
"-a"
,
a
)
+
optional
(
"-j"
,
j
)
+
conditional
(
t
,
"-t"
)
+
optional
(
"-c"
,
c
)
+
optional
(
"-g"
,
g
)
+
conditional
(
B
,
"-B"
)
+
optional
(
"-b"
,
b
)
+
conditional
(
e
,
"-e"
)
+
optional
(
"-M"
,
M
)
+
optional
(
"-G"
,
referenceGtf
)
+
(
if
(
x
.
nonEmpty
)
optional
(
"-x"
,
x
.
mkString
(
","
))
else
""
)
+
(
if
(
outputAsStdout
)
""
else
required
(
"-o"
,
outputGtf
))
def
cmdLine
:
String
=
required
(
executable
)
+
required
(
inputBam
)
+
conditional
(
v
,
"-v"
)
+
required
(
"-p"
,
threads
)
+
conditional
(
rf
,
"--rf"
)
+
conditional
(
fr
,
"--fr"
)
+
optional
(
"-l"
,
l
)
+
optional
(
"-f"
,
f
)
+
optional
(
"-m"
,
m
)
+
optional
(
"-A"
,
geneAbundances
)
+
optional
(
"-C"
,
referenceCoverage
)
+
optional
(
"-a"
,
a
)
+
optional
(
"-j"
,
j
)
+
conditional
(
t
,
"-t"
)
+
optional
(
"-c"
,
c
)
+
optional
(
"-g"
,
g
)
+
conditional
(
B
,
"-B"
)
+
optional
(
"-b"
,
b
)
+
conditional
(
e
,
"-e"
)
+
optional
(
"-M"
,
M
)
+
optional
(
"-G"
,
referenceGtf
)
+
(
if
(
x
.
nonEmpty
)
optional
(
"-x"
,
x
.
mkString
(
","
))
else
""
)
+
(
if
(
outputAsStdout
)
""
else
required
(
"-o"
,
outputGtf
))
}
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/stringtie/StringtieMerge.scala
View file @
ee4de907
...
...
@@ -9,48 +9,49 @@ import org.broadinstitute.gatk.utils.commandline.{Input, Output}
import
scala.util.matching.Regex
class
StringtieMerge
(
val
parent
:
Configurable
)
extends
BiopetCommandLineFunction
with
Reference
with
Version
{
extends
BiopetCommandLineFunction
with
Reference
with
Version
{
executable
=
config
(
"exe"
,
"stringtie"
)
executable
=
config
(
"exe"
,
"stringtie"
)
@Input
(
required
=
true
)
var
inputGtfs
:
List
[
File
]
=
Nil
@Input
(
required
=
true
)
var
inputGtfs
:
List
[
File
]
=
Nil
@Input
(
required
=
false
)
var
referenceGtf
:
Option
[
File
]
=
None
@Input
(
required
=
false
)
var
referenceGtf
:
Option
[
File
]
=
None
@Output
var
outputGtf
:
File
=
_
@Output
var
outputGtf
:
File
=
_
var
v
:
Boolean
=
config
(
"v"
,
default
=
logger
.
isDebugEnabled
)
var
l
:
Option
[
String
]
=
None
var
f
:
Option
[
Double
]
=
config
(
"f"
)
var
m
:
Option
[
Int
]
=
config
(
"m"
)
var
c
:
Option
[
Float
]
=
config
(
"c"
)
var
F
:
Option
[
Double
]
=
config
(
"F"
)
var
T
:
Option
[
Double
]
=
config
(
"T"
)
var
i
:
Boolean
=
config
(
"i"
,
default
=
false
)
var
v
:
Boolean
=
config
(
"v"
,
default
=
logger
.
isDebugEnabled
)
var
l
:
Option
[
String
]
=
None
var
f
:
Option
[
Double
]
=
config
(
"f"
)
var
m
:
Option
[
Int
]
=
config
(
"m"
)
var
c
:
Option
[
Float
]
=
config
(
"c"
)
var
F
:
Option
[
Double
]
=
config
(
"F"
)
var
T
:
Option
[
Double
]
=
config
(
"T"
)
var
i
:
Boolean
=
config
(
"i"
,
default
=
false
)
/** Command to get version of executable */
def
versionCommand
:
String
=
executable
+
" --version"
/** Command to get version of executable */
def
versionCommand
:
String
=
executable
+
" --version"
/** Regex to get version from version command output */
def
versionRegex
:
Regex
=
".*"
.
r
/** Regex to get version from version command output */
def
versionRegex
:
Regex
=
".*"
.
r
def
cmdLine
:
String
=
required
(
executable
)
+
def
cmdLine
:
String
=
required
(
executable
)
+
required
(
"--merge"
)
conditional
(
v
,
"-v"
)
+
required
(
"-p"
,
threads
)
+
optional
(
"-l"
,
l
)
+
optional
(
"-f"
,
f
)
+
optional
(
"-m"
,
m
)
+
optional
(
"-c"
,
c
)
+
optional
(
"-F"
,
F
)
+
conditional
(
i
,
"-i"
)
+
optional
(
"-G"
,
referenceGtf
)
+
(
if
(
outputAsStdout
)
""
else
required
(
"-o"
,
outputGtf
))
+
repeat
(
inputGtfs
)
}
conditional
(
v
,
"-v"
)
+
required
(
"-p"
,
threads
)
+
optional
(
"-l"
,
l
)
+
optional
(
"-f"
,
f
)
+
optional
(
"-m"
,
m
)
+
optional
(
"-c"
,
c
)
+
optional
(
"-F"
,
F
)
+
conditional
(
i
,
"-i"
)
+
optional
(
"-G"
,
referenceGtf
)
+
(
if
(
outputAsStdout
)
""
else
required
(
"-o"
,
outputGtf
))
+
repeat
(
inputGtfs
)
}
gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
View file @
ee4de907
...
...
@@ -305,7 +305,8 @@ object Gentrap extends PipelineCommand {
/** Enumeration of available expression measures */
object
ExpMeasures
extends
Enumeration
{
val
FragmentsPerGene
,
BaseCounts
,
CufflinksStrict
,
CufflinksGuided
,
CufflinksBlind
,
Stringtie
=
Value
val
FragmentsPerGene
,
BaseCounts
,
CufflinksStrict
,
CufflinksGuided
,
CufflinksBlind
,
Stringtie
=
Value
}
/** Enumeration of available strandedness */
...
...
gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/Stringtie.scala
View file @
ee4de907
...
...
@@ -22,10 +22,7 @@ import org.broadinstitute.gatk.queue.QScript
/**
* Created by pjvan_thof on 1/12/16.
*/
class
Stringtie
(
val
parent
:
Configurable
)
extends
QScript
with
Measurement
with
AnnotationGtf
{
class
Stringtie
(
val
parent
:
Configurable
)
extends
QScript
with
Measurement
with
AnnotationGtf
{
def
mergeArgs
=
MergeArgs
(
idCols
=
List
(
1
),
valCol
=
2
,
fallback
=
"0"
)
/** Pipeline itself */
...
...
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