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biopet.biopet
Commits
33f456b9
Commit
33f456b9
authored
Jan 28, 2015
by
Peter van 't Hof
Browse files
Renaming values
parent
413f0bd1
Changes
5
Hide whitespace changes
Inline
Side-by-side
protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
View file @
33f456b9
...
...
@@ -34,14 +34,14 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
class
Sample
(
sampleId
:
String
)
extends
AbstractSample
(
sampleId
)
{
def
makeLibrary
(
id
:
String
)
=
new
Library
(
id
)
class
Library
(
libraryId
:
String
)
extends
AbstractLibrary
(
libraryId
)
{
protected
def
add
Lib
Jobs
Internal
()
:
Unit
=
{}
protected
def
addJobs
()
:
Unit
=
{}
}
var
output
:
FastaOutput
=
_
var
outputSnps
:
FastaOutput
=
_
protected
def
add
SampleJobsInternal
()
:
Unit
=
{
run
LibsJobs
()
protected
def
add
Jobs
()
:
Unit
=
{
add
LibsJobs
()
output
=
addGenerateFasta
(
sampleId
,
sampleDir
)
outputSnps
=
addGenerateFasta
(
sampleId
,
sampleDir
,
snpsOnly
=
true
)
}
...
...
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
View file @
33f456b9
...
...
@@ -54,7 +54,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
gatkVariantcalling
.
sampleID
=
sampleId
gatkVariantcalling
.
outputDir
=
libDir
protected
def
add
Lib
Jobs
Internal
()
:
Unit
=
{
protected
def
addJobs
()
:
Unit
=
{
val
bamFile
:
Option
[
File
]
=
if
(
config
.
contains
(
"R1"
))
{
mapping
.
input_R1
=
config
(
"R1"
)
mapping
.
input_R2
=
config
(
"R2"
)
...
...
@@ -126,8 +126,8 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
gatkVariantcalling
.
sampleID
=
sampleId
gatkVariantcalling
.
outputDir
=
sampleDir
+
"/variantcalling/"
protected
def
add
SampleJobsInternal
()
:
Unit
=
{
run
LibsJobs
()
protected
def
add
Jobs
()
:
Unit
=
{
add
LibsJobs
()
gatkVariantcalling
.
inputBams
=
libraries
.
map
(
_
.
_2
.
mapping
.
finalBamFile
).
toList
gatkVariantcalling
.
preProcesBams
=
false
if
(!
singleSampleCalling
)
{
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
View file @
33f456b9
...
...
@@ -47,10 +47,10 @@ trait MultiSampleQScript extends BiopetQScript {
val
config
=
new
ConfigFunctions
(
defaultSample
=
sampleId
,
defaultLibrary
=
libraryId
)
/** Adds the library jobs */
final
def
add
Lib
Jobs
()
:
Unit
=
{
final
def
add
AndTrack
Jobs
()
:
Unit
=
{
currentSample
=
Some
(
sampleId
)
currentLib
=
Some
(
libraryId
)
add
Lib
Jobs
Internal
()
addJobs
()
currentLib
=
None
currentSample
=
None
}
...
...
@@ -62,7 +62,7 @@ trait MultiSampleQScript extends BiopetQScript {
def
libDir
=
sampleDir
+
"lib_"
+
libraryId
+
File
.
separator
/** Function that add library jobs */
protected
def
add
Lib
Jobs
Internal
()
protected
def
addJobs
()
}
/** Library type, need implementation in pipeline */
...
...
@@ -84,19 +84,19 @@ trait MultiSampleQScript extends BiopetQScript {
}
/** Adds sample jobs */
final
def
add
Sample
Jobs
()
:
Unit
=
{
final
def
add
AndTrack
Jobs
()
:
Unit
=
{
currentSample
=
Some
(
sampleId
)
add
SampleJobsInternal
()
add
Jobs
()
currentSample
=
None
}
/** Function to add sample jobs */
protected
def
add
SampleJobsInternal
()
protected
def
add
Jobs
()
/** function runs all libraries in one call */
protected
final
def
run
LibsJobs
()
:
Unit
=
{
protected
final
def
add
LibsJobs
()
:
Unit
=
{
for
((
libraryId
,
library
)
<-
libraries
)
{
library
.
add
Lib
Jobs
()
library
.
add
AndTrack
Jobs
()
}
}
...
...
@@ -132,7 +132,7 @@ trait MultiSampleQScript extends BiopetQScript {
/** Runs runSingleSampleJobs method for each sample */
final
def
addSamplesJobs
()
{
for
((
sampleId
,
sample
)
<-
samples
)
{
sample
.
add
Sample
Jobs
()
sample
.
add
AndTrack
Jobs
()
}
}
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/MultisamplePipelineTemplate.scala
View file @
33f456b9
...
...
@@ -27,12 +27,12 @@ class MultisamplePipelineTemplate(val root: Configurable) extends QScript with M
def
makeLibrary
(
id
:
String
)
=
new
Library
(
id
)
class
Library
(
libraryId
:
String
)
extends
AbstractLibrary
(
libraryId
)
{
protected
def
add
Lib
Jobs
Internal
()
:
Unit
=
{
protected
def
addJobs
()
:
Unit
=
{
// Library jobs
}
}
protected
def
add
SampleJobsInternal
()
:
Unit
=
{
protected
def
add
Jobs
()
:
Unit
=
{
// Sample jobs
}
}
...
...
public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
View file @
33f456b9
...
...
@@ -74,7 +74,7 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
mapping
.
libraryId
=
libraryId
mapping
.
sampleId
=
sampleId
protected
def
add
Lib
Jobs
Internal
()
:
Unit
=
{
protected
def
addJobs
()
:
Unit
=
{
flexiprep
.
outputDir
=
libDir
+
"flexiprep/"
flexiprep
.
input_R1
=
inputFastq
flexiprep
.
init
...
...
@@ -102,8 +102,8 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
}
}
protected
def
add
SampleJobsInternal
()
:
Unit
=
{
run
LibsJobs
()
protected
def
add
Jobs
()
:
Unit
=
{
add
LibsJobs
()
val
libraryBamfiles
=
libraries
.
map
(
_
.
_2
.
mapping
.
finalBamFile
).
toList
val
libraryFastqFiles
=
libraries
.
map
(
_
.
_2
.
prefixFastq
).
toList
...
...
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