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biopet.biopet
Commits
3fbbc7b9
Commit
3fbbc7b9
authored
Apr 14, 2017
by
Peter van 't Hof
Browse files
Fixing output files of sambamba markdup
parent
8a0e0c8e
Changes
1
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Inline
Side-by-side
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMarkdup.scala
View file @
3fbbc7b9
...
...
@@ -40,6 +40,13 @@ class SambambaMarkdup(val parent: Configurable) extends Sambamba {
override
def
defaultThreads
=
4
override
def
defaultCoreMemory
=
4.0
@Output
private
var
indexOutput
:
File
=
_
override
def
beforeGraph
()
:
Unit
=
{
indexOutput
=
new
File
(
output
+
".bai"
)
}
/** Returns command to execute */
def
cmdLine
:
String
=
required
(
executable
)
+
required
(
"markdup"
)
+
...
...
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