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biopet.biopet
Commits
89753299
Commit
89753299
authored
Dec 10, 2015
by
Peter van 't Hof
Browse files
Added flexiprep
parent
790eb131
Changes
2
Hide whitespace changes
Inline
Side-by-side
public/gears/pom.xml
View file @
89753299
...
...
@@ -38,6 +38,11 @@
<artifactId>
BiopetCore
</artifactId>
<version>
${project.version}
</version>
</dependency>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Flexiprep
</artifactId>
<version>
${project.version}
</version>
</dependency>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
BiopetToolsExtensions
</artifactId>
...
...
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
View file @
89753299
...
...
@@ -19,6 +19,7 @@ import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import
nl.lumc.sasc.biopet.core.BiopetQScript.InputFile
import
nl.lumc.sasc.biopet.core.
{
PipelineCommand
,
SampleLibraryTag
}
import
nl.lumc.sasc.biopet.extensions.seqtk.SeqtkSeq
import
nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.queue.QScript
...
...
@@ -88,14 +89,21 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
case
_
=>
throw
new
IllegalArgumentException
(
"Missing input files"
)
}
lazy
val
fastaR1
=
fastqToFasta
(
r1
,
outputName
+
".R1"
)
lazy
val
fastaR2
=
r2
.
map
(
fastqToFasta
(
_
,
outputName
+
".R2"
))
val
flexiprep
=
new
Flexiprep
(
this
)
flexiprep
.
input_R1
=
r1
flexiprep
.
input_R2
=
r2
flexiprep
.
init
()
flexiprep
.
biopetScript
()
addAll
(
flexiprep
.
functions
)
lazy
val
fastaR1
=
fastqToFasta
(
flexiprep
.
fastqR1Qc
,
outputName
+
".R1"
)
lazy
val
fastaR2
=
flexiprep
.
fastqR2Qc
.
map
(
fastqToFasta
(
_
,
outputName
+
".R2"
))
if
(
gearsUseKraken
)
{
val
kraken
=
new
GearsKraken
(
this
)
kraken
.
outputDir
=
new
File
(
outputDir
,
"kraken"
)
kraken
.
fastqR1
=
r1
kraken
.
fastqR2
=
r2
kraken
.
fastqR1
=
flexiprep
.
fastqR1Qc
kraken
.
fastqR2
=
flexiprep
.
fastqR2Qc
kraken
.
outputName
=
outputName
kraken
.
init
()
kraken
.
biopetScript
()
...
...
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