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biopet.biopet
Commits
5f8a8375
Commit
5f8a8375
authored
Feb 03, 2015
by
Peter van 't Hof
Browse files
Implemented addMultisampleJobs method
parent
a9f86490
Changes
5
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Inline
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protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
View file @
5f8a8375
...
...
@@ -41,7 +41,7 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
var
outputSnps
:
FastaOutput
=
_
protected
def
addJobs
()
:
Unit
=
{
addLib
s
Jobs
()
add
Per
LibJobs
()
output
=
addGenerateFasta
(
sampleId
,
sampleDir
)
outputSnps
=
addGenerateFasta
(
sampleId
,
sampleDir
,
snpsOnly
=
true
)
}
...
...
@@ -56,11 +56,13 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
gatkPipeline
.
biopetScript
addAll
(
gatkPipeline
.
functions
)
addPerSampleJobs
()
}
def
addMultiSampleJobs
()
:
Unit
=
{
val
refVariants
=
addGenerateFasta
(
null
,
outputDir
+
"reference/"
,
outputName
=
"reference"
)
val
refVariantSnps
=
addGenerateFasta
(
null
,
outputDir
+
"reference/"
,
outputName
=
"reference"
,
snpsOnly
=
true
)
addSamplesJobs
()
val
catVariants
=
Cat
(
this
,
refVariants
.
variants
::
samples
.
map
(
_
.
_2
.
output
.
variants
).
toList
,
outputDir
+
"fastas/variant.fasta"
)
add
(
catVariants
)
val
catVariantsSnps
=
Cat
(
this
,
refVariantSnps
.
variants
::
samples
.
map
(
_
.
_2
.
outputSnps
.
variants
).
toList
,
outputDir
+
"fastas/variant.snps_only.fasta"
)
...
...
@@ -129,6 +131,7 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
addTreeJobs
(
catVariantsSnps
.
output
,
catConsensusVariantsSnps
.
output
,
outputDir
+
"trees"
+
File
.
separator
+
"snps_only"
,
"snps_only"
)
addTreeJobs
(
catVariants
.
output
,
catConsensusVariants
.
output
,
outputDir
+
"trees"
+
File
.
separator
+
"snps_indels"
,
"snps_indels"
)
}
def
addGenerateFasta
(
sampleName
:
String
,
outputDir
:
String
,
outputName
:
String
=
null
,
...
...
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
View file @
5f8a8375
...
...
@@ -127,7 +127,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
gatkVariantcalling
.
outputDir
=
sampleDir
+
"/variantcalling/"
protected
def
addJobs
()
:
Unit
=
{
addLib
s
Jobs
()
add
Per
LibJobs
()
gatkVariantcalling
.
inputBams
=
libraries
.
map
(
_
.
_2
.
mapping
.
finalBamFile
).
toList
gatkVariantcalling
.
preProcesBams
=
false
if
(!
singleSampleCalling
)
{
...
...
@@ -150,10 +150,11 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
override
def
configPath
:
List
[
String
]
=
super
.
configPath
:::
"multisample"
::
Nil
}
def
biopetScript
()
{
addSamplesJobs
def
biopetScript
()
:
Unit
=
{
addPerSampleJobs
}
//SampleWide jobs
def
addMultiSampleJobs
()
:
Unit
=
{
val
gvcfFiles
:
List
[
File
]
=
if
(
mergeGvcfs
&&
externalGvcfs
.
size
+
samples
.
size
>
1
)
{
val
newFile
=
outputDir
+
"merged.gvcf.vcf.gz"
add
(
CombineGVCFs
(
this
,
externalGvcfs
++
samples
.
map
(
_
.
_2
.
gatkVariantcalling
.
scriptOutput
.
gvcfFile
),
newFile
))
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/MultisamplePipelineTemplate.scala
View file @
5f8a8375
...
...
@@ -37,6 +37,9 @@ class MultisamplePipelineTemplate(val root: Configurable) extends QScript with M
}
}
def
addMultiSampleJobs
()
:
Unit
=
{
}
def
init
()
:
Unit
=
{
}
...
...
public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
View file @
5f8a8375
...
...
@@ -67,7 +67,7 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript {
val
controls
:
List
[
String
]
=
config
(
"control"
,
default
=
Nil
)
def
addJobs
()
:
Unit
=
{
addLib
s
Jobs
()
add
Per
LibJobs
()
val
bamFiles
=
libraries
.
map
(
_
.
_2
.
mapping
.
finalBamFile
).
toList
if
(
bamFiles
.
length
==
1
)
{
add
(
Ln
(
qscript
,
bamFiles
.
head
,
bamFile
))
...
...
@@ -102,8 +102,10 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript {
// Third step is calling peaks on the bam files produced with the mapping pipeline, this will be done with MACS2
logger
.
info
(
"Starting CArP pipeline"
)
addSamplesJobs
addPerSampleJobs
}
def
addMultiSampleJobs
()
:
Unit
=
{
for
((
sampleId
,
sample
)
<-
samples
)
{
for
(
controlId
<-
sample
.
controls
)
{
if
(!
samples
.
contains
(
controlId
))
...
...
public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
View file @
5f8a8375
...
...
@@ -103,7 +103,7 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
}
protected
def
addJobs
()
:
Unit
=
{
addLib
s
Jobs
()
add
Per
LibJobs
()
val
libraryBamfiles
=
libraries
.
map
(
_
.
_2
.
mapping
.
finalBamFile
).
toList
val
libraryFastqFiles
=
libraries
.
map
(
_
.
_2
.
prefixFastq
).
toList
...
...
@@ -151,7 +151,10 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
tagsLibrary
=
cdl
.
output
}
addSamplesJobs
addPerSampleJobs
}
def
addMultiSampleJobs
()
:
Unit
=
{
}
def
addBedtoolsCounts
(
bamFile
:
File
,
outputPrefix
:
String
,
outputDir
:
String
)
{
...
...
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