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biopet.biopet
Commits
b0ef88db
Commit
b0ef88db
authored
Jul 11, 2017
by
pjvan_thof
Browse files
Adding missing argument
parent
76e1a93b
Changes
2
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Inline
Side-by-side
biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/RefflatStats.scala
View file @
b0ef88db
...
...
@@ -49,7 +49,7 @@ class RefflatStats(val parent: Configurable) extends ToolCommandFunction with Re
if
(
reference
==
null
)
reference
=
referenceFasta
()
}
override
def
cmdLine
=
override
def
cmdLine
:
String
=
super
.
cmdLine
+
required
(
"-a"
,
refflatFile
)
+
required
(
"-R"
,
reference
)
+
...
...
gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
View file @
b0ef88db
...
...
@@ -237,6 +237,8 @@ class Gentrap(val parent: Configurable)
new
File
(
outputDir
,
"expression_measures"
+
File
.
separator
+
"transcript.stats"
)
refflatStats
.
exonOutput
=
new
File
(
outputDir
,
"expression_measures"
+
File
.
separator
+
"exon.stats"
)
refflatStats
.
intronOutput
=
new
File
(
outputDir
,
"expression_measures"
+
File
.
separator
+
"intron.stats"
)
refflatStats
.
jobOutputFile
=
new
File
(
outputDir
,
".reflatstats.out"
)
add
(
refflatStats
)
...
...
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