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biopet.biopet
Commits
af8d9361
Commit
af8d9361
authored
Dec 16, 2015
by
Peter van 't Hof
Browse files
Simplify modules
parent
5c344be9
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
View file @
af8d9361
...
...
@@ -83,9 +83,7 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
extract
.
outputDir
=
outputDir
extract
.
bamFile
=
bam
extract
.
outputName
=
outputName
extract
.
init
()
extract
.
biopetScript
()
addAll
(
extract
.
functions
)
add
(
extract
)
(
extract
.
fastqUnmappedR1
,
Some
(
extract
.
fastqUnmappedR2
))
case
_
=>
throw
new
IllegalArgumentException
(
"Missing input files"
)
}
...
...
@@ -94,10 +92,7 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
flexiprep
.
input_R1
=
r1
flexiprep
.
input_R2
=
r2
flexiprep
.
outputDir
=
new
File
(
outputDir
,
"flexiprep"
)
flexiprep
.
init
()
flexiprep
.
biopetScript
()
addAll
(
flexiprep
.
functions
)
addSummaryQScript
(
flexiprep
)
add
(
flexiprep
)
if
(
gearsUseKraken
)
{
val
kraken
=
new
GearsKraken
(
this
)
...
...
@@ -105,10 +100,7 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
kraken
.
fastqR1
=
flexiprep
.
fastqR1Qc
kraken
.
fastqR2
=
flexiprep
.
fastqR2Qc
kraken
.
outputName
=
outputName
kraken
.
init
()
kraken
.
biopetScript
()
addAll
(
kraken
.
functions
)
addSummaryQScript
(
kraken
)
add
(
kraken
)
}
if
(
gearsUserQiimeRtax
)
{
...
...
@@ -116,9 +108,7 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
qiimeRatx
.
outputDir
=
new
File
(
outputDir
,
"qiime_rtax"
)
qiimeRatx
.
fastqR1
=
flexiprep
.
fastqR1Qc
qiimeRatx
.
fastqR2
=
flexiprep
.
fastqR2Qc
qiimeRatx
.
init
()
qiimeRatx
.
biopetScript
()
addAll
(
qiimeRatx
.
functions
)
add
(
qiimeRatx
)
}
if
(
gearsUserQiimeClosed
)
{
...
...
@@ -126,9 +116,7 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
qiimeClosed
.
outputDir
=
new
File
(
outputDir
,
"qiime_rtax"
)
qiimeClosed
.
fastqR1
=
flexiprep
.
fastqR1Qc
qiimeClosed
.
fastqR2
=
flexiprep
.
fastqR2Qc
qiimeClosed
.
init
()
qiimeClosed
.
biopetScript
()
addAll
(
qiimeClosed
.
functions
)
add
(
qiimeClosed
)
}
addSummaryJobs
()
...
...
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