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biopet.biopet
Commits
c640dc87
Commit
c640dc87
authored
Apr 26, 2016
by
Peter van 't Hof
Browse files
Fixed reference
parent
a39f363c
Changes
1
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protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CommandLineGATK.scala
View file @
c640dc87
...
...
@@ -324,7 +324,7 @@ trait CommandLineGATK extends BiopetJavaCommandLineFunction with Reference with
override
def
beforeGraph
()
{
super
.
beforeGraph
()
if
(
reference_sequence
!
=
null
)
reference_sequence
=
referenceFasta
()
if
(
reference_sequence
=
=
null
)
reference_sequence
=
referenceFasta
()
input_fileIndexes
++=
input_file
.
filter
(
orig
=>
orig
!=
null
&&
orig
.
getName
.
endsWith
(
".bam"
)).
flatMap
(
orig
=>
Array
(
new
File
(
orig
.
getPath
+
".bai"
),
new
File
(
orig
.
getPath
.
stripSuffix
(
".bam"
)
+
".bai"
)))
if
(
num_threads
.
isDefined
)
nCoresRequest
=
num_threads
if
(
num_cpu_threads_per_data_thread
.
isDefined
)
nCoresRequest
=
Some
(
nCoresRequest
.
getOrElse
(
1
)
*
num_cpu_threads_per_data_thread
.
getOrElse
(
1
))
...
...
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