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biopet.biopet
Commits
72aa3362
Commit
72aa3362
authored
Sep 29, 2015
by
Wai Yi Leung
Browse files
Add todo to GEARS pipeline.
parent
f2a3ee03
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
View file @
72aa3362
...
...
@@ -85,6 +85,8 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript { qscrip
fastqSync
.
inputFastq1
=
samToFastq
.
fastqR1
fastqSync
.
inputFastq2
=
samToFastq
.
fastqR2
fastqSync
.
outputFastq1
=
new
File
(
outputDir
,
s
"$outputName.unmapped.R1.sync.fq.gz"
)
// TODO: need some sanity check on whether R2 is really containing reads (e.g. Single End libraries)
fastqSync
.
outputFastq2
=
new
File
(
outputDir
,
s
"$outputName.unmapped.R2.sync.fq.gz"
)
fastqSync
.
outputStats
=
new
File
(
outputDir
,
s
"$outputName.sync.stats.json"
)
add
(
fastqSync
)
...
...
@@ -96,7 +98,9 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript { qscrip
val
krakenAnalysis
=
new
Kraken
(
qscript
)
krakenAnalysis
.
input
=
fastqFiles
krakenAnalysis
.
output
=
new
File
(
outputDir
,
s
"$outputName.krkn.raw"
)
krakenAnalysis
.
paired
=
true
krakenAnalysis
.
paired
=
(
fastqFiles
.
length
==
2
)
krakenAnalysis
.
classified_out
=
Option
(
new
File
(
outputDir
,
s
"$outputName.krkn.classified.fastq"
))
krakenAnalysis
.
unclassified_out
=
Option
(
new
File
(
outputDir
,
s
"$outputName.krkn.unclassified.fastq"
))
add
(
krakenAnalysis
)
...
...
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