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biopet.biopet
Commits
a8a0e1b0
Commit
a8a0e1b0
authored
Oct 03, 2016
by
Peter van 't Hof
Browse files
Fix type
parent
091a2657
Changes
3
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala
View file @
a8a0e1b0
...
...
@@ -35,11 +35,11 @@ class Cuffquant(val root: Configurable) extends BiopetCommandLineFunction with V
means we have 2 samples, each with 2 replicates
so our input is a list of lists of Files
*/
var
input
:
List
[
List
[
File
]]
=
List
.
empty
[
List
[
File
]]
var
input
:
List
[
List
[
File
]]
=
Nil
/** input GTF file */
@Input
(
doc
=
"Input GTF file"
,
required
=
true
)
var
transcriptsGtf
:
File
=
null
var
transcriptsGtf
:
File
=
_
/** output file, computed automatically from output directory */
@Output
(
doc
=
"Output CXB file"
)
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/centrifuge/Centrifuge.scala
View file @
a8a0e1b0
...
...
@@ -38,9 +38,9 @@ class Centrifuge(val root: Configurable) extends BiopetCommandLineFunction with
override
def
beforeGraph
()
:
Unit
=
{
super
.
beforeGraph
()
deps
:+=
index
+
".1.cf"
deps
:+=
index
+
".2.cf"
deps
:+=
index
+
".3.cf"
deps
:+=
new
File
(
index
+
".1.cf"
)
deps
:+=
new
File
(
index
+
".2.cf"
)
deps
:+=
new
File
(
index
+
".3.cf"
)
}
/**
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/centrifuge/CentrifugeKreport.scala
View file @
a8a0e1b0
...
...
@@ -31,9 +31,9 @@ class CentrifugeKreport(val root: Configurable) extends BiopetCommandLineFunctio
override
def
beforeGraph
()
:
Unit
=
{
super
.
beforeGraph
()
deps
:+=
index
+
".1.cf"
deps
:+=
index
+
".2.cf"
deps
:+=
index
+
".3.cf"
deps
:+=
new
File
(
index
+
".1.cf"
)
deps
:+=
new
File
(
index
+
".2.cf"
)
deps
:+=
new
File
(
index
+
".3.cf"
)
}
def
cmdLine
=
executable
+
...
...
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