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biopet.biopet
Commits
995c55bb
Commit
995c55bb
authored
Nov 22, 2016
by
Peter van 't Hof
Browse files
fix BIOPET-464
parent
85708a4a
Changes
1
Hide whitespace changes
Inline
Side-by-side
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
View file @
995c55bb
...
...
@@ -141,12 +141,20 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs
class
Library
(
libId
:
String
)
extends
AbstractLibrary
(
libId
)
{
lazy
val
flexiprep
=
new
Flexiprep
(
qscript
)
flexiprep
.
sampleId
=
Some
(
sampleId
)
flexiprep
.
libId
=
Some
(
libId
)
flexiprep
.
inputR1
=
config
(
"R1"
)
flexiprep
.
inputR2
=
config
(
"R2"
)
flexiprep
.
outputDir
=
new
File
(
libDir
,
"flexiprep"
)
lazy
val
inputR1
:
File
=
config
(
"R1"
)
lazy
val
inputR2
:
Option
[
File
]
=
config
(
"R2"
)
lazy
val
skipFlexiprep
:
Boolean
=
config
(
"skip_flexiprep"
,
default
=
false
)
lazy
val
flexiprep
=
if
(
skipFlexiprep
)
None
else
Some
(
new
Flexiprep
(
qscript
))
flexiprep
.
foreach
(
_
.
sampleId
=
Some
(
sampleId
))
flexiprep
.
foreach
(
_
.
libId
=
Some
(
libId
))
flexiprep
.
foreach
(
_
.
inputR1
=
inputR1
)
flexiprep
.
foreach
(
_
.
inputR2
=
inputR2
)
flexiprep
.
foreach
(
_
.
outputDir
=
new
File
(
libDir
,
"flexiprep"
))
lazy
val
qcR1
:
File
=
flexiprep
.
map
(
_
.
fastqR1Qc
).
getOrElse
(
inputR1
)
lazy
val
qcR2
:
Option
[
File
]
=
flexiprep
.
map
(
_
.
fastqR2Qc
).
getOrElse
(
inputR2
)
val
libraryGears
:
Boolean
=
config
(
"library_gears"
,
default
=
false
)
...
...
@@ -154,17 +162,17 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs
/** Function that add library jobs */
protected
def
addJobs
()
:
Unit
=
{
inputFiles
:+=
InputFile
(
flexiprep
.
inputR1
,
config
(
"R1_md5"
))
flexiprep
.
inputR2
.
foreach
(
inputFiles
:+=
InputFile
(
_
,
config
(
"R2_md5"
)))
add
(
flexiprep
)
inputFiles
:+=
InputFile
(
inputR1
,
config
(
"R1_md5"
))
inputR2
.
foreach
(
inputFiles
:+=
InputFile
(
_
,
config
(
"R2_md5"
)))
flexiprep
.
foreach
(
add
(
_
)
)
gearsSingle
.
foreach
{
gs
=>
gs
.
sampleId
=
Some
(
sampleId
)
gs
.
libId
=
Some
(
libId
)
gs
.
outputDir
=
libDir
gs
.
fastqR1
=
List
(
addDownsample
(
flexiprep
.
fastqR1Qc
,
gs
.
outputDir
))
gs
.
fastqR2
=
flexiprep
.
fastqR2Qc
.
map
(
addDownsample
(
_
,
gs
.
outputDir
)).
toList
gs
.
fastqR1
=
List
(
addDownsample
(
qcR1
,
gs
.
outputDir
))
gs
.
fastqR2
=
qcR2
.
map
(
addDownsample
(
_
,
gs
.
outputDir
)).
toList
add
(
gs
)
}
}
...
...
@@ -187,11 +195,11 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs
val
flexipreps
=
libraries
.
values
.
map
(
_
.
flexiprep
).
toList
val
mergeR1
:
File
=
new
File
(
sampleDir
,
s
"$sampleId.R1.fq.gz"
)
add
(
Zcat
(
qscript
,
flexipreps
.
map
(
_
.
fastqR1Qc
)
)
|
new
Gzip
(
qscript
)
>
mergeR1
)
add
(
Zcat
(
qscript
,
libraries
.
values
.
map
(
_
.
qcR1
).
toList
)
|
new
Gzip
(
qscript
)
>
mergeR1
)
val
mergeR2
=
if
(
flexipreps
.
exists
(
_
.
pair
ed
))
Some
(
new
File
(
sampleDir
,
s
"$sampleId.R2.fq.gz"
))
else
None
val
mergeR2
=
if
(
libraries
.
values
.
exists
(
_
.
inputR2
.
isDefin
ed
))
Some
(
new
File
(
sampleDir
,
s
"$sampleId.R2.fq.gz"
))
else
None
mergeR2
.
foreach
{
file
=>
add
(
Zcat
(
qscript
,
flexipreps
.
flatMap
(
_
.
fastqR2Qc
)
)
|
new
Gzip
(
qscript
)
>
file
)
add
(
Zcat
(
qscript
,
libraries
.
values
.
flatMap
(
_
.
qcR2
).
toList
)
|
new
Gzip
(
qscript
)
>
file
)
}
gearsSingle
.
fastqR1
=
List
(
addDownsample
(
mergeR1
,
gearsSingle
.
outputDir
))
...
...
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