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biopet.biopet
Commits
67db8906
Commit
67db8906
authored
Dec 18, 2015
by
Peter van 't Hof
Browse files
Fix sample IDs
parent
43100197
Changes
1
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Inline
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public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
View file @
67db8906
...
...
@@ -40,9 +40,9 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
@Argument
(
required
=
false
)
var
outputName
:
String
=
_
val
krakenScript
=
if
(
config
(
"gears_use_kraken"
,
default
=
true
))
Some
(
new
GearsKraken
(
this
))
else
None
val
qiimeRatx
=
if
(
config
(
"gear_use_qiime_rtax"
,
default
=
false
))
Some
(
new
GearsQiimeRtax
(
this
))
else
None
val
qiimeClosed
=
if
(
config
(
"gear_use_qiime_closed"
,
default
=
false
))
Some
(
new
GearsQiimeClosed
(
this
))
else
None
lazy
val
krakenScript
=
if
(
config
(
"gears_use_kraken"
,
default
=
true
))
Some
(
new
GearsKraken
(
this
))
else
None
lazy
val
qiimeRatx
=
if
(
config
(
"gear_use_qiime_rtax"
,
default
=
false
))
Some
(
new
GearsQiimeRtax
(
this
))
else
None
lazy
val
qiimeClosed
=
if
(
config
(
"gear_use_qiime_closed"
,
default
=
false
))
Some
(
new
GearsQiimeClosed
(
this
))
else
None
/** Executed before running the script */
def
init
()
:
Unit
=
{
...
...
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