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
c19baaeb
Commit
c19baaeb
authored
Nov 14, 2014
by
sajvanderzeeuw
Browse files
Fix singleSample commandline function
parent
4805a430
Changes
2
Hide whitespace changes
Inline
Side-by-side
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
View file @
c19baaeb
...
...
@@ -13,12 +13,11 @@ trait MultiSampleQScript extends BiopetQScript {
def
getLibrary
(
key
:
String
)
=
libraries
(
key
)
}
var
samplesConfig
:
Map
[
String
,
Any
]
=
Map
(
)
var
samplesConfig
:
Map
[
String
,
Any
]
=
config
(
"samples"
)
var
samplesOutput
:
Map
[
String
,
SampleOutput
]
=
Map
()
def
globalSampleDir
:
String
=
outputDir
+
"samples/"
final
def
runSamplesJobs
()
{
samplesConfig
=
config
(
"samples"
)
if
(
samplesConfig
==
null
)
samplesConfig
=
Map
()
if
(
Config
.
global
.
contains
(
"samples"
))
for
((
key
,
value
)
<-
samplesConfig
)
{
var
sample
=
Configurable
.
any2map
(
value
)
...
...
@@ -32,7 +31,11 @@ trait MultiSampleQScript extends BiopetQScript {
def
runSingleSampleJobs
(
sampleConfig
:
Map
[
String
,
Any
])
:
SampleOutput
def
runSingleSampleJobs
(
sample
:
String
)
:
SampleOutput
=
{
return
runSingleSampleJobs
(
Configurable
.
any2map
(
samplesConfig
(
sample
)))
var
map
=
Configurable
.
any2map
(
samplesConfig
(
sample
))
if
(
map
.
contains
(
"ID"
)
&&
map
(
"ID"
)
!=
sample
)
throw
new
IllegalStateException
(
"ID in config not the same as the key"
)
else
map
+=
(
"ID"
->
sample
)
return
runSingleSampleJobs
(
map
)
}
final
def
runLibraryJobs
(
sampleConfig
:
Map
[
String
,
Any
])
:
Map
[
String
,
LibraryOutput
]
=
{
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
View file @
c19baaeb
...
...
@@ -18,7 +18,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
def
this
()
=
this
(
null
)
@Argument
(
doc
=
"Only Sample"
,
shortName
=
"sample"
,
required
=
false
)
val
onlySample
:
String
=
""
val
onlySample
:
List
[
String
]
=
Nil
@Argument
(
doc
=
"Skip Genotyping step"
,
shortName
=
"skipgenotyping"
,
required
=
false
)
var
skipGenotyping
:
Boolean
=
false
...
...
@@ -115,7 +115,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
recalibration
.
biopetScript
}
}
}
else
runSingleSampleJobs
(
onlyS
ample
)
}
else
for
(
sample
<-
onlySample
)
runSingleSampleJobs
(
s
ample
)
}
// Called for each sample
...
...
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