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biopet.biopet
Commits
aa8fe3fd
Commit
aa8fe3fd
authored
Mar 11, 2015
by
bow
Browse files
Fix test failure caused by incorrectly named function
parent
675718da
Changes
2
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public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/RawBaseCounter.scala
View file @
aa8fe3fd
...
...
@@ -61,6 +61,7 @@ class RawBaseCounter(val root: Configurable) extends BiopetCommandLineFunction {
private
def
bedtoolsCovHist
=
new
BiopetCommandLineFunction
{
var
bam
:
File
=
null
override
val
configName
=
"bedtoolscoverage"
override
val
root
:
Configurable
=
wrapper
.
root
executable
=
config
(
"exe"
,
default
=
"coverageBed"
,
freeVar
=
false
)
override
def
cmdLine
:
String
=
required
(
executable
)
+
...
...
public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
View file @
aa8fe3fd
...
...
@@ -197,7 +197,7 @@ object GentrapTest {
// mapping executables
"star"
,
"bowtie"
,
"samtools"
,
"gsnap"
,
"tophat"
,
// gentrap executables
"cufflinks"
,
"htseqcount"
,
"grep"
,
"pdflatex"
,
"rscript"
,
"tabix"
,
"bgzip"
,
"cufflinks"
,
"htseqcount"
,
"grep"
,
"pdflatex"
,
"rscript"
,
"tabix"
,
"bgzip"
,
"bedtoolscoverage"
,
// bam2wig executables
"igvtools"
,
"wigtobigwig"
).
map
{
case
exe
=>
exe
->
Map
(
"exe"
->
"test"
)
}.
toMap
...
...
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