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biopet.biopet
Commits
d90761b6
Commit
d90761b6
authored
Aug 07, 2014
by
Peter van 't Hof
Browse files
Added metrics pipeline
parent
72ac9801
Changes
1
Hide whitespace changes
Inline
Side-by-side
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
d90761b6
...
...
@@ -201,7 +201,9 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
bamFile
=
new
File
(
outputDir
+
outputName
+
".dedup.bam"
)
add
(
MarkDuplicates
(
this
,
bamFiles
,
bamFile
))
}
else
if
(
skipMarkduplicates
&&
chunking
)
bamFile
=
addMergeBam
(
bamFiles
,
new
File
(
outputDir
+
outputName
+
".bam"
),
outputDir
)
addAll
(
BamMetrics
.
apply
(
this
,
bamFile
,
outputDir
+
"metrics/"
).
functions
)
outputFiles
+=
(
"finalBamFile"
->
bamFile
)
}
...
...
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