Skip to content
GitLab
Menu
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
73d6d6d7
Commit
73d6d6d7
authored
Mar 22, 2017
by
Peter van 't Hof
Browse files
Adding final files for sample and library variantcaling to summary
(cherry picked from commit 7b205dd)
parent
a278b762
Changes
1
Hide whitespace changes
Inline
Side-by-side
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala
View file @
73d6d6d7
...
...
@@ -77,6 +77,8 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra
/** Class to generate jobs for a library */
class
Library
(
libId
:
String
)
extends
super
.
Library
(
libId
)
{
override
def
summaryFiles
=
super
.
summaryFiles
++
variantcalling
.
map
(
"final"
->
_
.
finalFile
)
lazy
val
useIndelRealigner
:
Boolean
=
config
(
"use_indel_realigner"
,
default
=
true
)
lazy
val
useBaseRecalibration
:
Boolean
=
{
val
c
:
Boolean
=
config
(
"use_base_recalibration"
,
default
=
true
)
...
...
@@ -141,6 +143,8 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra
bamFile
.
map
(
swapExt
(
sampleDir
,
_
,
".bam"
,
".realign.bam"
))
}
else
bamFile
override
def
summaryFiles
=
super
.
summaryFiles
++
variantcalling
.
map
(
"final"
->
_
.
finalFile
)
/** This will add sample jobs */
override
def
addJobs
()
:
Unit
=
{
super
.
addJobs
()
...
...
Write
Preview
Supports
Markdown
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