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
a9f86490
Commit
a9f86490
authored
Feb 03, 2015
by
Peter van 't Hof
Browse files
Switch to new multisample part
parent
944b9af0
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/Kopisu.scala
View file @
a9f86490
...
...
@@ -25,31 +25,29 @@ class Kopisu(val root: Configurable) extends QScript with MultiSampleQScript {
@Input
(
doc
=
"Input bamfile"
,
required
=
true
)
var
bamFile
:
File
=
config
(
"bam"
)
class
LibraryOutput
extends
AbstractLibraryOutput
{
}
class
SampleOutput
extends
AbstractSampleOutput
{
}
def
init
()
{
if
(!
outputDir
.
endsWith
(
"/"
))
outputDir
+=
"/"
}
def
biopetScript
()
{
run
Sample
s
Jobs
this
.
addPer
SampleJobs
()
}
// Called for each sample
def
runSingleSampleJobs
(
sampleConfig
:
Map
[
String
,
Any
])
:
SampleOutput
=
{
val
sampleOutput
=
new
SampleOutput
def
makeSample
(
id
:
String
)
=
new
Sample
(
id
)
class
Sample
(
sampleId
:
String
)
extends
AbstractSample
(
sampleId
)
{
def
makeLibrary
(
id
:
String
)
=
new
Library
(
id
)
class
Library
(
libraryId
:
String
)
extends
AbstractLibrary
(
libraryId
)
{
def
addJobs
()
:
Unit
=
{
}
}
def
addJobs
()
:
Unit
=
{
return
sampleOutput
}
}
// Called for each run from a sample
def
runSingleLibraryJobs
(
runConfig
:
Map
[
String
,
Any
],
sampleConfig
:
Map
[
String
,
Any
])
:
LibraryOutput
=
{
val
libraryOutput
=
new
LibraryOutput
return
libraryOutput
def
addMultiSampleJobs
()
:
Unit
=
{
}
}
...
...
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