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biopet.biopet
Commits
a50fc782
Commit
a50fc782
authored
Oct 03, 2016
by
Peter van 't Hof
Browse files
Output centrifuge as gz files
parent
a8a0e1b0
Changes
1
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Inline
Side-by-side
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsCentrifuge.scala
View file @
a50fc782
...
...
@@ -2,7 +2,8 @@ package nl.lumc.sasc.biopet.pipelines.gears
import
nl.lumc.sasc.biopet.core.SampleLibraryTag
import
nl.lumc.sasc.biopet.core.summary.SummaryQScript
import
nl.lumc.sasc.biopet.extensions.centrifuge.
{
Centrifuge
,
CentrifugeKreport
}
import
nl.lumc.sasc.biopet.extensions.Gzip
import
nl.lumc.sasc.biopet.extensions.centrifuge.
{
Centrifuge
,
CentrifugeKreport
}
import
nl.lumc.sasc.biopet.extensions.tools.KrakenReportToJson
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.queue.QScript
...
...
@@ -27,15 +28,17 @@ class GearsCentrifuge(val root: Configurable) extends QScript with SummaryQScrip
}
def
biopetScript
()
:
Unit
=
{
val
centrifugeOutput
=
new
File
(
outputDir
,
s
"$outputName.centrifuge.gz"
)
val
centrifuge
=
new
Centrifuge
(
this
)
centrifuge
.
inputR1
=
fastqR1
centrifuge
.
inputR2
=
fastqR2
centrifuge
.
output
=
new
File
(
outputDir
,
s
"$outputName.centrifuge"
)
centrifuge
.
report
=
Some
(
new
File
(
outputDir
,
s
"$outputName.centrifuge.report"
))
add
(
centrifuge
)
val
cmd
=
centrifuge
|
new
Gzip
(
this
)
>
centrifugeOutput
cmd
.
threadsCorrection
=
-
1
add
(
cmd
)
makeKreport
(
List
(
centrifuge
.
o
utput
),
"centrifuge"
,
unique
=
false
)
makeKreport
(
List
(
centrifuge
.
o
utput
),
"centrifuge_unique"
,
unique
=
true
)
makeKreport
(
List
(
centrifuge
O
utput
),
"centrifuge"
,
unique
=
false
)
makeKreport
(
List
(
centrifuge
O
utput
),
"centrifuge_unique"
,
unique
=
true
)
addSummaryJobs
()
}
...
...
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