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biopet.biopet
Commits
4e6cf4dc
Commit
4e6cf4dc
authored
Mar 09, 2015
by
bow
Browse files
Add Tophat to Mapping module
parent
1c1d9277
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
4e6cf4dc
...
...
@@ -26,7 +26,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.core.summary.SummaryQScript
import
nl.lumc.sasc.biopet.extensions.
{
Ln
,
Star
,
Stampy
,
Bowtie
}
import
nl.lumc.sasc.biopet.extensions.bwa.
{
BwaSamse
,
BwaSampe
,
BwaAln
,
BwaMem
}
import
nl.lumc.sasc.biopet.extensions.Gsnap
import
nl.lumc.sasc.biopet.extensions.
{
Gsnap
,
Tophat
}
import
nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
import
nl.lumc.sasc.biopet.tools.FastqSplitter
import
nl.lumc.sasc.biopet.extensions.picard.
{
MarkDuplicates
,
SortSam
,
MergeSamFiles
,
AddOrReplaceReadGroups
}
...
...
@@ -209,6 +209,8 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
case
"bwa-aln"
=>
addBwaAln
(
R1
,
R2
,
outputBam
,
deps
)
case
"bowtie"
=>
addBowtie
(
R1
,
R2
,
outputBam
,
deps
)
case
"gsnap"
=>
addGsnap
(
R1
,
R2
,
outputBam
,
deps
)
// TODO: make TopHat here accept multiple input files
case
"tophat"
=>
addTophat
(
R1
,
R2
,
outputBam
,
deps
)
case
"stampy"
=>
addStampy
(
R1
,
R2
,
outputBam
,
deps
)
case
"star"
=>
addStar
(
R1
,
R2
,
outputBam
,
deps
)
case
"star-2pass"
=>
addStar2pass
(
R1
,
R2
,
outputBam
,
deps
)
...
...
@@ -346,6 +348,34 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
sortSam
.
output
}
def
addTophat
(
R1
:
File
,
R2
:
File
,
output
:
File
,
deps
:
List
[
File
])
:
File
=
{
// TODO: merge mapped and unmapped BAM ~ also dealing with validation errors in the unmapped BAM
val
tophat
=
new
Tophat
(
this
)
// FIXME: ideally we should only check for null ~ but apparently it's possible to get a File object with "" as the path
tophat
.
R1
=
tophat
.
R1
:+
R1
if
(
R2
!=
null
&&
R2
.
getPath
!=
""
)
tophat
.
R2
=
tophat
.
R2
:+
R2
tophat
.
output_dir
=
new
File
(
outputDir
,
"tophat_out"
)
// always output BAM
tophat
.
no_convert_bam
=
false
tophat
.
deps
=
deps
// always output BAM
tophat
.
no_convert_bam
=
false
add
(
tophat
)
val
ln
=
new
Ln
(
this
)
ln
.
input
=
tophat
.
outputAcceptedHits
ln
.
output
=
swapExt
(
output
.
getParent
,
output
,
".bam"
,
".raw.bam"
)
add
(
ln
)
val
sortSam
=
new
SortSam
(
this
)
sortSam
.
input
=
ln
.
output
sortSam
.
output
=
output
sortSam
.
sortOrder
=
"coordinate"
sortSam
.
isIntermediate
=
chunking
||
!
skipMarkduplicates
add
(
sortSam
)
sortSam
.
output
}
/**
* Adds stampy jobs
* @param R1
...
...
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