Skip to content
GitLab
Menu
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
0379df8e
Commit
0379df8e
authored
Nov 28, 2014
by
wyleung
Browse files
Fixing names of variables and apply sambamba markduplicates on the merged bam of yamsvp
parent
a927d433
Changes
3
Hide whitespace changes
Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaIndex.scala
View file @
0379df8e
...
...
@@ -22,10 +22,10 @@ class SambambaIndex(val root: Configurable) extends Sambamba {
object
SambambaIndex
{
def
apply
(
root
:
Configurable
,
input
:
File
,
output
:
File
)
:
SambambaIndex
=
{
val
flagstat
=
new
SambambaIndex
(
root
)
flagstat
.
input
=
input
flagstat
.
output
=
output
return
flagstat
val
indexer
=
new
SambambaIndex
(
root
)
indexer
.
input
=
input
indexer
.
output
=
output
return
indexer
}
def
apply
(
root
:
Configurable
,
input
:
File
,
outputDir
:
String
)
:
SambambaIndex
=
{
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMarkdup.scala
View file @
0379df8e
...
...
@@ -35,10 +35,10 @@ class SambambaMarkdup(val root: Configurable) extends Sambamba {
object
SambambaMarkdup
{
def
apply
(
root
:
Configurable
,
input
:
File
,
output
:
File
)
:
SambambaMarkdup
=
{
val
flagstat
=
new
SambambaMarkdup
(
root
)
flagstat
.
input
=
input
flagstat
.
output
=
output
return
flagstat
val
markdup
=
new
SambambaMarkdup
(
root
)
markdup
.
input
=
input
markdup
.
output
=
output
return
markdup
}
def
apply
(
root
:
Configurable
,
input
:
File
,
outputDir
:
String
)
:
SambambaMarkdup
=
{
...
...
public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
View file @
0379df8e
...
...
@@ -9,7 +9,7 @@ import nl.lumc.sasc.biopet.core.MultiSampleQScript
import
nl.lumc.sasc.biopet.core.PipelineCommand
import
nl.lumc.sasc.biopet.extensions.Ln
import
nl.lumc.sasc.biopet.extensions.sambamba.
{
SambambaIndex
,
SambambaMerge
}
import
nl.lumc.sasc.biopet.extensions.sambamba.
{
SambambaIndex
,
SambambaMerge
,
SambambaMarkdup
}
import
nl.lumc.sasc.biopet.extensions.svcallers.pindel.Pindel
import
nl.lumc.sasc.biopet.extensions.svcallers.
{
Breakdancer
,
Delly
,
CleverCaller
}
...
...
@@ -79,19 +79,25 @@ class Yamsvp(val root: Configurable) extends QScript with MultiSampleQScript {
val
mergeSamFiles
=
new
SambambaMerge
(
root
)
mergeSamFiles
.
input
=
libraryBamfiles
mergeSamFiles
.
output
=
alignmentDir
+
sampleID
+
".merged.bam"
add
(
mergeSamFiles
)
add
(
mergeSamFiles
,
isIntermediate
=
true
)
mergeSamFiles
.
output
}
else
null
val
bamIndex
=
SambambaIndex
(
root
,
bamFile
)
add
(
bamIndex
)
// TODO: Check whether sambamba reaches release version v0.5.0 which includes
// automatic indexing of the bam file.
val
bamMarkDup
=
SambambaMarkdup
(
root
,
bamFile
)
add
(
bamMarkDup
)
val
analysisBam
:
File
=
bamMarkDup
.
output
val
analysisBamIndex
=
SambambaIndex
(
root
,
analysisBam
)
add
(
analysisBamIndex
)
/// bamfile will be used as input for the SV callers. First run Clever
// val cleverVCF : File = sampleDir + "/" + sampleID + ".clever.vcf"
val
cleverDir
=
svcallingDir
+
sampleID
+
".clever/"
val
clever
=
CleverCaller
(
this
,
bamFile
,
this
.
reference
,
svcallingDir
,
cleverDir
)
clever
.
deps
=
List
(
b
amIndex
.
output
)
val
clever
=
CleverCaller
(
this
,
analysisBam
,
this
.
reference
,
svcallingDir
,
cleverDir
)
clever
.
deps
=
List
(
analysisB
amIndex
.
output
)
sampleOutput
.
vcf
+=
(
"clever"
->
List
(
clever
.
outputvcf
))
add
(
clever
)
...
...
@@ -99,7 +105,7 @@ class Yamsvp(val root: Configurable) extends QScript with MultiSampleQScript {
add
(
clever_vcf
)
val
breakdancerDir
=
svcallingDir
+
sampleID
+
".breakdancer/"
val
breakdancer
=
Breakdancer
(
this
,
bamFile
,
this
.
reference
,
breakdancerDir
)
val
breakdancer
=
Breakdancer
(
this
,
analysisBam
,
this
.
reference
,
breakdancerDir
)
sampleOutput
.
vcf
+=
(
"breakdancer"
->
List
(
breakdancer
.
outputvcf
))
addAll
(
breakdancer
.
functions
)
...
...
@@ -107,7 +113,7 @@ class Yamsvp(val root: Configurable) extends QScript with MultiSampleQScript {
add
(
bd_vcf
)
val
dellyDir
=
svcallingDir
+
sampleID
+
".delly/"
val
delly
=
Delly
(
this
,
bamFile
,
dellyDir
)
val
delly
=
Delly
(
this
,
analysisBam
,
dellyDir
)
sampleOutput
.
vcf
+=
(
"delly"
->
List
(
delly
.
outputvcf
))
addAll
(
delly
.
functions
)
...
...
@@ -116,7 +122,7 @@ class Yamsvp(val root: Configurable) extends QScript with MultiSampleQScript {
// for pindel we should use per library config collected into one config file
// val pindelDir = svcallingDir + sampleID + ".pindel/"
// val pindel = Pindel(this,
bamFile
, this.reference, pindelDir)
// val pindel = Pindel(this,
analysisBam
, this.reference, pindelDir)
// sampleOutput.vcf += ("pindel" -> List(pindel.outputvcf))
// addAll(pindel.functions)
//
...
...
@@ -139,7 +145,10 @@ class Yamsvp(val root: Configurable) extends QScript with MultiSampleQScript {
if
(
runConfig
.
contains
(
"R1"
))
{
val
mapping
=
new
Mapping
(
this
)
mapping
.
aligner
=
config
(
"aligner"
,
default
=
"stampy"
)
// TODO: check and test config[aligner] in json
// yamsvp/aligner -> value
// this setting causes error if not defined?
mapping
.
aligner
=
config
(
"aligner"
,
default
=
"bwa"
)
mapping
.
skipFlexiprep
=
false
mapping
.
skipMarkduplicates
=
true
// we do the dedup marking using Sambamba
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Attach a 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