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
72a96f7e
Commit
72a96f7e
authored
Oct 30, 2015
by
Wai Yi Leung
Browse files
Adding Gears to summary output of Mapping
parent
3cd8150f
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
72a96f7e
...
...
@@ -19,18 +19,17 @@ 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
}
import
nl.lumc.sasc.biopet.extensions.picard.
{
AddOrReplaceReadGroups
,
MarkDuplicates
,
MergeSamFiles
,
ReorderSam
,
SortSam
}
import
nl.lumc.sasc.biopet.extensions.tools.FastqSplitter
import
nl.lumc.sasc.biopet.extensions.
{
Gsnap
,
Tophat
,
_
}
import
nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
import
nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
import
nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
import
nl.lumc.sasc.biopet.pipelines.gears.Gears
import
nl.lumc.sasc.biopet.pipelines.mapping.scripts.TophatRecondition
import
nl.lumc.sasc.biopet.extensions.tools.FastqSplitter
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.queue.QScript
import
scala.math._
...
...
@@ -266,6 +265,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
gears
.
init
()
gears
.
biopetScript
()
addAll
(
gears
.
functions
)
addSummaryQScript
(
gears
)
}
if
(
config
(
"generate_wig"
,
default
=
false
).
asBoolean
)
...
...
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