Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Mirrors
biopet.biopet
Commits
0ecd6778
Commit
0ecd6778
authored
Feb 04, 2016
by
Peter van 't Hof
Browse files
Added gears to multi mapping
parent
95882d8e
Changes
2
Hide whitespace changes
Inline
Side-by-side
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
0ecd6778
...
...
@@ -264,11 +264,10 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
if
(
config
(
"unmapped_to_gears"
,
default
=
false
).
asBoolean
)
{
val
gears
=
new
GearsSingle
(
this
)
gears
.
bamFile
=
Some
(
finalBamFile
)
gears
.
sampleId
=
sampleId
gears
.
libId
=
libId
gears
.
outputDir
=
new
File
(
outputDir
,
"gears"
)
gears
.
init
()
gears
.
biopetScript
()
addAll
(
gears
.
functions
)
addSummaryQScript
(
gears
)
add
(
gears
)
}
if
(
config
(
"generate_wig"
,
default
=
false
).
asBoolean
)
...
...
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTrait.scala
View file @
0ecd6778
...
...
@@ -8,6 +8,7 @@ import nl.lumc.sasc.biopet.core.{ PipelineCommand, Reference, MultiSampleQScript
import
nl.lumc.sasc.biopet.extensions.Ln
import
nl.lumc.sasc.biopet.extensions.picard.
{
MarkDuplicates
,
MergeSamFiles
,
AddOrReplaceReadGroups
,
SamToFastq
}
import
nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
import
nl.lumc.sasc.biopet.pipelines.gears.GearsSingle
import
nl.lumc.sasc.biopet.utils.Logging
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.queue.QScript
...
...
@@ -199,6 +200,14 @@ trait MultisampleMappingTrait extends MultiSampleQScript
bamMetrics
.
outputDir
=
new
File
(
sampleDir
,
"metrics"
)
add
(
bamMetrics
)
}
if
(
config
(
"unmapped_to_gears"
,
default
=
false
)
&&
libraries
.
flatMap
(
_
.
_2
.
bamFile
).
nonEmpty
)
{
val
gears
=
new
GearsSingle
(
qscript
)
gears
.
bamFile
=
preProcessBam
gears
.
sampleId
=
Some
(
sampleId
)
gears
.
outputDir
=
new
File
(
sampleDir
,
"gears"
)
add
(
gears
)
}
}
}
}
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment