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biopet.biopet
Commits
c15b307b
Commit
c15b307b
authored
Sep 24, 2015
by
Peter van 't Hof
Browse files
removed qscript key
parent
6598b281
Changes
1
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Inline
Side-by-side
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
View file @
c15b307b
...
...
@@ -77,7 +77,7 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript { qscrip
new
File
(
outputDir
,
s
"$outputName.unmapped.R2.fq.gz"
)
)
samToFastq
.
isIntermediate
=
true
qscript
.
add
(
samToFastq
)
add
(
samToFastq
)
// sync the fastq records
val
fastqSync
=
new
FastqSync
(
qscript
)
...
...
@@ -87,7 +87,7 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript { qscrip
fastqSync
.
outputFastq1
=
new
File
(
outputDir
,
s
"$outputName.unmapped.R1.sync.fq.gz"
)
fastqSync
.
outputFastq2
=
new
File
(
outputDir
,
s
"$outputName.unmapped.R2.sync.fq.gz"
)
fastqSync
.
outputStats
=
new
File
(
outputDir
,
s
"$outputName.sync.stats.json"
)
qscript
.
add
(
fastqSync
)
add
(
fastqSync
)
List
(
fastqSync
.
outputFastq1
,
fastqSync
.
outputFastq2
)
}.
getOrElse
(
List
(
fastqFileR1
,
fastqFileR2
).
flatten
)
...
...
@@ -99,7 +99,7 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript { qscrip
krakenAnalysis
.
paired
=
true
krakenAnalysis
.
classified_out
=
Option
(
new
File
(
outputDir
,
s
"$outputName.krkn.classified.fastq"
))
krakenAnalysis
.
unclassified_out
=
Option
(
new
File
(
outputDir
,
s
"$outputName.krkn.unclassified.fastq"
))
qscript
.
add
(
krakenAnalysis
)
add
(
krakenAnalysis
)
// create kraken summary file
...
...
@@ -107,7 +107,7 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript { qscrip
krakenReport
.
input
=
krakenAnalysis
.
output
krakenReport
.
show_zeros
=
true
krakenReport
.
output
=
new
File
(
outputDir
,
s
"$outputName.krkn.full"
)
qscript
.
add
(
krakenReport
)
add
(
krakenReport
)
addSummaryJobs
()
}
...
...
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