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biopet.biopet
Commits
35bd64d6
Commit
35bd64d6
authored
Oct 03, 2016
by
Peter van 't Hof
Browse files
Make output name required
parent
e7437482
Changes
2
Hide whitespace changes
Inline
Side-by-side
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsCentrifuge.scala
View file @
35bd64d6
...
@@ -23,10 +23,7 @@ class GearsCentrifuge(val root: Configurable) extends QScript with SummaryQScrip
...
@@ -23,10 +23,7 @@ class GearsCentrifuge(val root: Configurable) extends QScript with SummaryQScrip
def
init
()
:
Unit
=
{
def
init
()
:
Unit
=
{
require
(
fastqR1
!=
null
)
require
(
fastqR1
!=
null
)
if
(
outputName
==
null
)
outputName
=
fastqR1
.
getName
require
(
outputName
!=
null
)
.
stripSuffix
(
".gz"
)
.
stripSuffix
(
".fq"
)
.
stripSuffix
(
".fastq"
)
}
}
def
biopetScript
()
:
Unit
=
{
def
biopetScript
()
:
Unit
=
{
...
...
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsKraken.scala
View file @
35bd64d6
...
@@ -41,10 +41,7 @@ class GearsKraken(val root: Configurable) extends QScript with SummaryQScript wi
...
@@ -41,10 +41,7 @@ class GearsKraken(val root: Configurable) extends QScript with SummaryQScript wi
def
init
()
:
Unit
=
{
def
init
()
:
Unit
=
{
require
(
fastqR1
!=
null
)
require
(
fastqR1
!=
null
)
if
(
outputName
==
null
)
outputName
=
fastqR1
.
getName
require
(
outputName
!=
null
)
.
stripSuffix
(
".gz"
)
.
stripSuffix
(
".fq"
)
.
stripSuffix
(
".fastq"
)
}
}
lazy
val
krakenConvertToFasta
:
Boolean
=
config
(
"kraken_discard_quality"
,
default
=
false
)
lazy
val
krakenConvertToFasta
:
Boolean
=
config
(
"kraken_discard_quality"
,
default
=
false
)
...
...
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