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biopet.biopet
Commits
6598b281
Commit
6598b281
authored
Sep 24, 2015
by
Peter van 't Hof
Browse files
Added gears as optional step into mapping
parent
bbc185f4
Changes
2
Hide whitespace changes
Inline
Side-by-side
public/mapping/pom.xml
View file @
6598b281
...
...
@@ -43,6 +43,11 @@
<artifactId>
Flexiprep
</artifactId>
<version>
${project.version}
</version>
</dependency>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Gears
</artifactId>
<version>
${project.version}
</version>
</dependency>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
BamMetrics
</artifactId>
...
...
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
6598b281
...
...
@@ -19,6 +19,7 @@ import java.io.File
import
java.util.Date
import
nl.lumc.sasc.biopet.core._
import
nl.lumc.sasc.biopet.pipelines.gears.Gears
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.core.summary.SummaryQScript
import
nl.lumc.sasc.biopet.extensions.bwa.
{
BwaAln
,
BwaMem
,
BwaSampe
,
BwaSamse
}
...
...
@@ -273,6 +274,15 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
add
(
Ln
(
this
,
bamFile
,
finalBamFile
))
outputFiles
+=
(
"finalBamFile"
->
finalBamFile
.
getAbsoluteFile
)
if
(
config
(
"unmapped_to_gears"
,
default
=
false
).
asBoolean
)
{
val
gears
=
new
Gears
(
this
)
gears
.
bamFile
=
Some
(
finalBamFile
)
gears
.
outputDir
=
new
File
(
outputDir
,
"gears"
)
gears
.
init
()
gears
.
biopetScript
()
addAll
(
gears
.
functions
)
}
if
(
config
(
"generate_wig"
,
default
=
false
).
asBoolean
)
addAll
(
Bam2Wig
(
this
,
finalBamFile
).
functions
)
...
...
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