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biopet.biopet
Commits
dbab1a53
Commit
dbab1a53
authored
Mar 10, 2015
by
bow
Browse files
Fix wrong threads setting in GSNAP wrapper
parent
e76f0625
Changes
1
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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala
View file @
dbab1a53
...
...
@@ -326,6 +326,10 @@ class Gsnap(val root: Configurable) extends BiopetCommandLineFunction {
override
val
versionRegex
=
""".* version (.*)"""
.
r
override
def
versionCommand
=
executable
+
" --version"
override
def
beforeGraph
:
Unit
=
{
threads
=
nthreads
.
getOrElse
(
1
)
}
def
cmdLine
=
{
required
(
executable
)
+
optional
(
"--dir"
,
dir
)
+
...
...
@@ -371,7 +375,7 @@ class Gsnap(val root: Configurable) extends BiopetCommandLineFunction {
optional
(
"--use-tally"
,
use_tally
)
+
optional
(
"--runlengthdir"
,
runlengthdir
)
+
optional
(
"--use-runlength"
,
use_runlength
)
+
optional
(
"--nthreads"
,
nCoresRequest
)
+
optional
(
"--nthreads"
,
threads
)
+
optional
(
"--gmap-mode"
,
gmap_mode
)
+
optional
(
"--trigger-score-for-gmap"
,
trigger_score_for_gmap
)
+
optional
(
"--gmap-min-match-length"
,
gmap_min_match_length
)
+
...
...
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