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biopet.biopet
Commits
e3fd97af
Commit
e3fd97af
authored
Jan 08, 2016
by
Peter van 't Hof
Browse files
Fix output file for tophat step
parent
d91e8f6f
Changes
1
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public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
e3fd97af
...
...
@@ -380,7 +380,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
// merge with mapped file
val
mergeSamFile
=
MergeSamFiles
(
this
,
List
(
tophat
.
outputAcceptedHits
,
sorter
.
output
),
tophat
.
output_dir
,
"coordinate"
)
new
File
(
tophat
.
output_dir
,
"fixed_merged.bam"
),
sortOrder
=
"coordinate"
)
mergeSamFile
.
createIndex
=
true
mergeSamFile
.
isIntermediate
=
true
add
(
mergeSamFile
)
...
...
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