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
3f7a6044
Commit
3f7a6044
authored
Nov 29, 2015
by
Peter van 't Hof
Browse files
Fixed md5sums
parent
32692078
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
View file @
3f7a6044
...
...
@@ -67,15 +67,16 @@ trait ShivaVariantcallingTrait extends SummaryQScript
/** Variantcallers requested by the config */
protected
val
configCallers
:
Set
[
String
]
=
config
(
"variantcallers"
)
protected
val
callers
:
List
[
Variantcaller
]
=
{
(
for
(
name
<-
configCallers
)
yield
{
if
(!
callersList
.
exists
(
_
.
name
==
name
))
Logging
.
addError
(
s
"variantcaller '$name' does not exist, possible to use: "
+
callersList
.
map
(
_
.
name
).
mkString
(
", "
))
callersList
.
find
(
_
.
name
==
name
)
}).
flatten
.
toList
.
sortBy
(
_
.
prio
)
}
/** This will add jobs for this pipeline */
def
biopetScript
()
:
Unit
=
{
for
(
cal
<-
configCallers
)
{
if
(!
callersList
.
exists
(
_
.
name
==
cal
))
Logging
.
addError
(
"variantcaller '"
+
cal
+
"' does not exist, possible to use: "
+
callersList
.
map
(
_
.
name
).
mkString
(
", "
))
}
val
callers
=
callersList
.
filter
(
x
=>
configCallers
.
contains
(
x
.
name
)).
sortBy
(
_
.
prio
)
require
(
inputBams
.
nonEmpty
,
"No input bams found"
)
require
(
callers
.
nonEmpty
,
"must select at least 1 variantcaller, choices are: "
+
callersList
.
map
(
_
.
name
).
mkString
(
", "
))
...
...
@@ -168,7 +169,6 @@ trait ShivaVariantcallingTrait extends SummaryQScript
/** Files for the summary */
def
summaryFiles
:
Map
[
String
,
File
]
=
{
val
callers
:
Set
[
String
]
=
config
(
"variantcallers"
)
callersList
.
filter
(
x
=>
callers
.
contains
(
x
.
name
)).
map
(
x
=>
x
.
name
->
x
.
outputFile
).
toMap
+
(
"final"
->
finalFile
)
callers
.
map
(
x
=>
x
.
name
->
x
.
outputFile
).
toMap
+
(
"final"
->
finalFile
)
}
}
\ No newline at end of file
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