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
ef5ea6ce
Commit
ef5ea6ce
authored
Oct 29, 2015
by
Peter van 't Hof
Browse files
Added bammetrics when start from bam file
parent
3d73d611
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
View file @
ef5ea6ce
...
...
@@ -197,6 +197,16 @@ trait ShivaTrait extends MultiSampleQScript with Reference {
val
bamLn
=
Ln
(
qscript
,
oldBamFile
,
bamFile
.
get
)
bamLn
.
deps
:+=
baiLn
.
output
add
(
bamLn
)
val
bamMetrics
=
new
BamMetrics
(
qscript
)
bamMetrics
.
sampleId
=
Some
(
sampleId
)
bamMetrics
.
libId
=
Some
(
libId
)
bamMetrics
.
inputBam
=
bamFile
.
get
bamMetrics
.
outputDir
=
new
File
(
libDir
,
"metrics"
)
bamMetrics
.
init
()
bamMetrics
.
biopetScript
()
addAll
(
bamMetrics
.
functions
)
addSummaryQScript
(
bamMetrics
)
}
}
}
...
...
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