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biopet.biopet
Commits
ff5e56e1
Commit
ff5e56e1
authored
Nov 10, 2016
by
Peter van 't Hof
Browse files
Switch to fifo pipe
parent
785d5a26
Changes
1
Hide whitespace changes
Inline
Side-by-side
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsCentrifuge.scala
View file @
ff5e56e1
package
nl.lumc.sasc.biopet.pipelines.gears
import
nl.lumc.sasc.biopet.core.SampleLibraryTag
import
nl.lumc.sasc.biopet.core.
{
BiopetFifoPipe
,
SampleLibraryTag
}
import
nl.lumc.sasc.biopet.core.summary.SummaryQScript
import
nl.lumc.sasc.biopet.extensions.
{
Gzip
,
Zcat
}
import
nl.lumc.sasc.biopet.extensions.centrifuge.
{
Centrifuge
,
CentrifugeKreport
}
...
...
@@ -46,10 +46,12 @@ class GearsCentrifuge(val root: Configurable) extends QScript with SummaryQScrip
}
protected
def
makeKreport
(
name
:
String
,
unique
:
Boolean
)
:
Unit
=
{
val
fifo
=
new
File
(
outputDir
,
s
"$outputName.$name.fifo"
)
val
centrifugeKreport
=
new
CentrifugeKreport
(
this
)
centrifugeKreport
.
centrifugeOutputFiles
:+=
fifo
centrifugeKreport
.
output
=
new
File
(
outputDir
,
s
"$outputName.$name.kreport"
)
centrifugeKreport
.
onlyUnique
=
unique
add
(
centrifugeOutput
:<:
Zcat
(
this
)
|
centrifuge
Kreport
)
add
(
new
BiopetFifoPipe
(
this
,
List
(
centrifugeKreport
,
Zcat
(
this
,
centrifuge
Output
,
fifo
)))
)
val
krakenReportJSON
=
new
KrakenReportToJson
(
this
)
krakenReportJSON
.
inputReport
=
centrifugeKreport
.
output
...
...
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