Skip to content
GitLab
Projects
Groups
Snippets
Help
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
B
biopet.biopet
Project overview
Project overview
Details
Activity
Releases
Repository
Repository
Files
Commits
Branches
Tags
Contributors
Graph
Compare
CI / CD
CI / CD
Pipelines
Jobs
Schedules
Operations
Operations
Environments
Analytics
Analytics
CI / CD
Repository
Value Stream
Members
Members
Collapse sidebar
Close sidebar
Activity
Graph
Jobs
Commits
Open sidebar
Mirrors
biopet.biopet
Commits
2c17add4
Commit
2c17add4
authored
Apr 14, 2017
by
Peter van 't Hof
Browse files
Options
Browse Files
Download
Email Patches
Plain Diff
Fixed small issues
parent
2b479c4c
Changes
2
Hide whitespace changes
Inline
Side-by-side
Showing
2 changed files
with
9 additions
and
0 deletions
+9
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMerge.scala
.../lumc/sasc/biopet/extensions/sambamba/SambambaMerge.scala
+7
-0
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMapping.scala
...mc/sasc/biopet/pipelines/mapping/MultisampleMapping.scala
+2
-0
No files found.
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMerge.scala
View file @
2c17add4
...
...
@@ -37,6 +37,13 @@ class SambambaMerge(val parent: Configurable) extends Sambamba {
override
def
defaultThreads
=
4
override
def
defaultCoreMemory
=
4.0
@Output
private
var
indexOutput
:
File
=
_
override
def
beforeGraph
()
:
Unit
=
{
indexOutput
=
new
File
(
output
+
".bai"
)
}
/** Returns command to execute */
def
cmdLine
:
String
=
required
(
executable
)
+
required
(
"merge"
)
+
...
...
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMapping.scala
View file @
2c17add4
...
...
@@ -267,9 +267,11 @@ trait MultisampleMappingTrait extends MultiSampleQScript
val
merge
=
new
SambambaMerge
(
qscript
)
merge
.
input
=
libraries
.
flatMap
(
_
.
_2
.
preProcessBam
).
toList
merge
.
output
=
mergedBam
merge
.
isIntermediate
=
true
add
(
merge
)
}
add
(
SambambaMarkdup
(
qscript
,
mergedBam
,
bamFile
.
get
,
isIntermediate
=
!
keepMergedFiles
))
Ln
(
qscript
,
bamFile
.
get
+
".bai"
,
bamFile
.
get
.
getAbsolutePath
.
stripSuffix
(
".bam"
)
+
".bai"
)
case
_
=>
throw
new
IllegalStateException
(
"This should not be possible, unimplemented MergeStrategy?"
)
}
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a 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