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biopet.biopet
Commits
7c8fe6be
Commit
7c8fe6be
authored
May 03, 2016
by
Peter van 't Hof
Browse files
Fixed unit tests
parent
c3ec3cb9
Changes
2
Hide whitespace changes
Inline
Side-by-side
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Flash.scala
View file @
7c8fe6be
...
...
@@ -66,31 +66,31 @@ class Flash(val root: Configurable) extends BiopetCommandLineFunction with Versi
@Output
private
var
_combinedFastq
:
File
=
_
def
combinedFastq
=
_combinedFastq
def
combinedFastq
=
new
File
(
outputDirectory
,
s
"$outputPrefix.extendedFrags.$suffix"
)
@Output
private
var
_notCombinedR1
:
File
=
_
def
notCombinedR1
=
_notCombinedR1
def
notCombinedR1
=
new
File
(
outputDirectory
,
s
"$outputPrefix.notCombined_1.$suffix"
)
@Output
private
var
_notCombinedR2
:
File
=
_
def
notCombinedR2
=
_notCombinedR2
def
notCombinedR2
=
new
File
(
outputDirectory
,
s
"$outputPrefix.notCombined_2.$suffix"
)
@Output
private
var
_outputHistogramTable
:
File
=
_
def
outputHistogramTable
=
_outputHistogramTable
def
outputHistogramTable
=
new
File
(
outputDirectory
,
s
"$outputPrefix.hist"
)
@Output
private
var
_outputHistogram
:
File
=
_
def
outputHistogram
=
_outputH
istogram
def
outputHistogram
=
new
File
(
outputDirectory
,
s
"$outputPrefix.h
istogram
"
)
override
def
beforeGraph
()
:
Unit
=
{
super
.
beforeGraph
()
_combinedFastq
=
new
File
(
outputDirectory
,
s
"$outputPrefix.extendedFrags.$suffix"
)
_notCombinedR1
=
n
ew
File
(
outputDirectory
,
s
"$outputPrefix.notCombined_1.$suffix"
)
_notCombinedR2
=
n
ew
File
(
outputDirectory
,
s
"$outputPrefix.notCombined_2.$suffix"
)
_outputHistogramTable
=
new
File
(
outputDirectory
,
s
"$outputPrefix.hist"
)
_outputHistogram
=
new
File
(
outputDirectory
,
s
"$outputPrefix.h
istogram
"
)
_combinedFastq
=
combinedFastq
_notCombinedR1
=
n
otCombinedR1
_notCombinedR2
=
n
otCombinedR2
_outputHistogramTable
=
outputHistogramTable
_outputHistogram
=
outputH
istogram
}
def
cmdLine
=
executable
+
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/SplitLibrariesFastq.scala
View file @
7c8fe6be
...
...
@@ -54,10 +54,10 @@ class SplitLibrariesFastq(val root: Configurable) extends BiopetCommandLineFunct
var
maxBarcodeErrors
:
Option
[
Double
]
=
config
(
"max_barcode_errors"
)
var
phredOffset
:
Option
[
String
]
=
config
(
"phred_offset"
)
def
outputSeqs
=
_outputSeqs
def
outputSeqs
=
new
File
(
outputDir
,
"seqs.fna"
)
@Output
var
_outputSeqs
:
File
=
_
private
var
_outputSeqs
:
File
=
_
override
def
defaultCoreMemory
=
4.0
...
...
@@ -65,7 +65,7 @@ class SplitLibrariesFastq(val root: Configurable) extends BiopetCommandLineFunct
super
.
beforeGraph
()
require
(
input
.
nonEmpty
)
require
(
outputDir
!=
null
)
_outputSeqs
=
new
File
(
outputDir
,
"seqs.fna"
)
_outputSeqs
=
outputSeqs
}
def
cmdLine
=
executable
+
...
...
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