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biopet.biopet
Commits
27236df5
Commit
27236df5
authored
Jan 11, 2016
by
Wai Yi Leung
Browse files
Merge branch 'fix-tophat' into 'develop'
Fix output file for tophat step Still needs testing See merge request !300
parents
d91e8f6f
203a0c98
Changes
4
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protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala
View file @
27236df5
...
...
@@ -21,7 +21,7 @@ class Shiva(val root: Configurable) extends QScript with ShivaTrait {
def
this
()
=
this
(
null
)
/** Make variantcalling submodule, this with the gatk modes in there */
override
def
makeVariantcalling
(
multisample
:
Boolean
=
false
)
:
ShivaVariantcallingTrait
=
{
override
def
makeVariantcalling
(
multisample
:
Boolean
=
false
)
=
{
if
(
multisample
)
new
ShivaVariantcalling
(
qscript
)
{
override
def
namePrefix
=
"multisample"
override
def
configName
=
"shivavariantcalling"
...
...
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2.scala
View file @
27236df5
...
...
@@ -2,10 +2,10 @@ package nl.lumc.sasc.biopet.extensions.bowtie
import
java.io.File
import
nl.lumc.sasc.biopet.core.
{
BiopetCommandLineFunction
,
Reference
,
Version
}
import
nl.lumc.sasc.biopet.core.
{
BiopetCommandLineFunction
,
Reference
,
Version
}
import
nl.lumc.sasc.biopet.utils.Logging
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
/**
* Extension for bowtie 2
...
...
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
27236df5
...
...
@@ -20,7 +20,7 @@ import java.util.Date
import
nl.lumc.sasc.biopet.core._
import
nl.lumc.sasc.biopet.core.summary.SummaryQScript
import
nl.lumc.sasc.biopet.extensions.bowtie.
{
Bowtie2
,
Bowtie
}
import
nl.lumc.sasc.biopet.extensions.bowtie.
{
Bowtie2
,
Bowtie
}
import
nl.lumc.sasc.biopet.extensions.bwa.
{
BwaAln
,
BwaMem
,
BwaSampe
,
BwaSamse
}
import
nl.lumc.sasc.biopet.extensions.gmap.Gsnap
import
nl.lumc.sasc.biopet.extensions.picard.
{
AddOrReplaceReadGroups
,
MarkDuplicates
,
MergeSamFiles
,
ReorderSam
,
SortSam
}
...
...
@@ -380,7 +380,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
// merge with mapped file
val
mergeSamFile
=
MergeSamFiles
(
this
,
List
(
tophat
.
outputAcceptedHits
,
sorter
.
output
),
tophat
.
output_dir
,
"coordinate"
)
new
File
(
tophat
.
output_dir
,
"fixed_merged.bam"
),
sortOrder
=
"coordinate"
)
mergeSamFile
.
createIndex
=
true
mergeSamFile
.
isIntermediate
=
true
add
(
mergeSamFile
)
...
...
@@ -395,6 +395,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
add
(
ar
.
_1
)
ar
.
_2
}
/** Adds stampy jobs */
def
addStampy
(
R1
:
File
,
R2
:
Option
[
File
],
output
:
File
)
:
File
=
{
...
...
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
View file @
27236df5
...
...
@@ -36,10 +36,10 @@ trait ShivaTrait extends MultisampleMappingTrait with Reference with TargetRegio
}
/** Method to make the variantcalling submodule of shiva */
def
makeVariantcalling
(
multisample
:
Boolean
=
false
)
:
ShivaVariantcallingTrait
=
{
def
makeVariantcalling
(
multisample
:
Boolean
=
false
)
:
ShivaVariantcallingTrait
with
QScript
=
{
if
(
multisample
)
new
ShivaVariantcalling
(
qscript
)
{
override
def
namePrefix
=
"multisample"
override
def
configName
=
"shivavariantcalling"
override
def
configName
:
String
=
"shivavariantcalling"
override
def
configPath
:
List
[
String
]
=
super
.
configPath
:::
"multisample"
::
Nil
}
else
new
ShivaVariantcalling
(
qscript
)
{
...
...
@@ -69,7 +69,7 @@ trait ShivaTrait extends MultisampleMappingTrait with Reference with TargetRegio
}
else
None
/** This will add jobs for this library */
override
def
addJobs
=
{
override
def
addJobs
()
=
{
super
.
addJobs
()
variantcalling
.
foreach
(
vc
=>
{
...
...
@@ -78,10 +78,7 @@ trait ShivaTrait extends MultisampleMappingTrait with Reference with TargetRegio
vc
.
outputDir
=
new
File
(
libDir
,
"variantcalling"
)
if
(
preProcessBam
.
isDefined
)
vc
.
inputBams
=
Map
(
sampleId
->
preProcessBam
.
get
)
else
vc
.
inputBams
=
Map
(
sampleId
->
bamFile
.
get
)
vc
.
init
()
vc
.
biopetScript
()
addAll
(
vc
.
functions
)
addSummaryQScript
(
vc
)
add
(
vc
)
})
}
}
...
...
@@ -99,10 +96,7 @@ trait ShivaTrait extends MultisampleMappingTrait with Reference with TargetRegio
vc
.
sampleId
=
Some
(
sampleId
)
vc
.
outputDir
=
new
File
(
sampleDir
,
"variantcalling"
)
vc
.
inputBams
=
Map
(
sampleId
->
bam
)
vc
.
init
()
vc
.
biopetScript
()
addAll
(
vc
.
functions
)
addSummaryQScript
(
vc
)
add
(
vc
)
})
}
}
...
...
@@ -122,34 +116,25 @@ trait ShivaTrait extends MultisampleMappingTrait with Reference with TargetRegio
}
else
None
/** This will add the mutisample variantcalling */
override
def
addMultiSampleJobs
=
{
override
def
addMultiSampleJobs
()
=
{
super
.
addMultiSampleJobs
()
multisampleVariantCalling
.
foreach
(
vc
=>
{
vc
.
outputDir
=
new
File
(
outputDir
,
"variantcalling"
)
vc
.
inputBams
=
samples
.
flatMap
{
case
(
sampleId
,
sample
)
=>
sample
.
preProcessBam
.
map
(
sampleId
->
_
)
}
vc
.
init
()
vc
.
biopetScript
()
addAll
(
vc
.
functions
)
addSummaryQScript
(
vc
)
add
(
vc
)
annotation
.
foreach
{
toucan
=>
toucan
.
outputDir
=
new
File
(
outputDir
,
"annotation"
)
toucan
.
inputVCF
=
vc
.
finalFile
toucan
.
init
()
toucan
.
biopetScript
()
addAll
(
toucan
.
functions
)
addSummaryQScript
(
toucan
)
add
(
toucan
)
}
})
svCalling
.
foreach
(
sv
=>
{
sv
.
outputDir
=
new
File
(
outputDir
,
"sv_calling"
)
sv
.
inputBams
=
samples
.
flatMap
{
case
(
sampleId
,
sample
)
=>
sample
.
preProcessBam
.
map
(
sampleId
->
_
)
}
sv
.
init
()
sv
.
biopetScript
()
addAll
(
sv
.
functions
)
addSummaryQScript
(
sv
)
add
(
sv
)
})
}
...
...
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