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biopet.biopet
Commits
e667ee49
Commit
e667ee49
authored
Aug 03, 2015
by
Peter van 't Hof
Browse files
Review changes
parent
bc53f7e3
Changes
1
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public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
View file @
e667ee49
...
...
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.pipelines.gears
import
htsjdk.samtools.SamReaderFactory
import
nl.lumc.sasc.biopet.FullVersion
import
nl.lumc.sasc.biopet.core.
{
PipelineCommand
,
MultiSampleQScript
}
import
nl.lumc.sasc.biopet.core.
{
PipelineCommand
,
MultiSampleQScript
}
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.extensions.Ln
import
nl.lumc.sasc.biopet.extensions.kraken.
{
Kraken
,
KrakenReport
}
...
...
@@ -58,9 +58,7 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs
def
summaryFile
=
new
File
(
outputDir
,
"gears.summary.json"
)
/** Settings of pipeline for summary */
def
summarySettings
=
Map
(
"version"
->
FullVersion
)
def
summarySettings
=
Map
()
/** Files for the summary */
def
summaryFiles
=
Map
()
...
...
@@ -294,18 +292,18 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs
qscript
.
add
(
samToFastq
)
// sync the fastq records
val
fastq
s
ync
=
new
FastqSync
(
qscript
)
fastq
s
ync
.
refFastq
=
samToFastq
.
fastqR1
fastq
s
ync
.
inputFastq1
=
samToFastq
.
fastqR1
fastq
s
ync
.
inputFastq2
=
samToFastq
.
fastqR2
fastq
s
ync
.
outputFastq1
=
createFile
(
".unmapsynced.R1.fastq.gz"
)
fastq
s
ync
.
outputFastq2
=
createFile
(
".unmapsynced.R2.fastq.gz"
)
fastq
s
ync
.
outputStats
=
createFile
(
".syncstats.json"
)
qscript
.
add
(
fastq
s
ync
)
val
fastq
S
ync
=
new
FastqSync
(
qscript
)
fastq
S
ync
.
refFastq
=
samToFastq
.
fastqR1
fastq
S
ync
.
inputFastq1
=
samToFastq
.
fastqR1
fastq
S
ync
.
inputFastq2
=
samToFastq
.
fastqR2
fastq
S
ync
.
outputFastq1
=
createFile
(
".unmapsynced.R1.fastq.gz"
)
fastq
S
ync
.
outputFastq2
=
createFile
(
".unmapsynced.R2.fastq.gz"
)
fastq
S
ync
.
outputStats
=
createFile
(
".syncstats.json"
)
qscript
.
add
(
fastq
S
ync
)
// start kraken
val
krakenAnalysis
=
new
Kraken
(
qscript
)
krakenAnalysis
.
input
=
List
(
fastq
s
ync
.
outputFastq1
,
fastq
s
ync
.
outputFastq2
)
krakenAnalysis
.
input
=
List
(
fastq
S
ync
.
outputFastq1
,
fastq
S
ync
.
outputFastq2
)
krakenAnalysis
.
output
=
createFile
(
".krkn.raw"
)
krakenAnalysis
.
paired
=
true
krakenAnalysis
.
classified_out
=
Option
(
createFile
(
".krkn.classified.fastq"
))
...
...
@@ -319,7 +317,6 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs
krakenReport
.
show_zeros
=
true
krakenReport
.
output
=
createFile
(
".krkn.full"
)
qscript
.
add
(
krakenReport
)
}
}
}
...
...
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