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biopet.biopet
Commits
64de449b
Commit
64de449b
authored
Feb 07, 2017
by
Peter van 't Hof
Browse files
Fixing gears merge step
parent
0894771f
Changes
2
Hide whitespace changes
Inline
Side-by-side
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
View file @
64de449b
...
...
@@ -84,13 +84,13 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
protected
def
executeFlexiprep
(
r1
:
List
[
File
],
r2
:
List
[
File
])
:
(
File
,
Option
[
File
])
=
{
val
read1
:
File
=
if
(
r1
.
size
==
1
)
r1
.
head
else
{
val
outputFile
=
new
File
(
outputDir
,
"merged.R1.fq.gz"
)
Zcat
(
this
,
r1
)
|
new
Gzip
(
this
)
>
outputFile
add
(
Zcat
(
this
,
r1
)
|
new
Gzip
(
this
)
>
outputFile
)
outputFile
}
val
read2
:
Option
[
File
]
=
if
(
r2
.
size
<=
1
)
r2
.
headOption
else
{
val
outputFile
=
new
File
(
outputDir
,
"merged.R2.fq.gz"
)
Zcat
(
this
,
r2
)
|
new
Gzip
(
this
)
>
outputFile
add
(
Zcat
(
this
,
r2
)
|
new
Gzip
(
this
)
>
outputFile
)
Some
(
outputFile
)
}
...
...
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMapping.scala
View file @
64de449b
...
...
@@ -67,7 +67,10 @@ trait MultisampleMappingTrait extends MultiSampleQScript
Some
(
report
)
}
override
def
defaults
:
Map
[
String
,
Any
]
=
super
.
defaults
++
Map
(
"reordersam"
->
Map
(
"allow_incomplete_dict_concordance"
->
true
))
override
def
defaults
:
Map
[
String
,
Any
]
=
super
.
defaults
++
Map
(
"reordersam"
->
Map
(
"allow_incomplete_dict_concordance"
->
true
),
"gears"
->
Map
(
"skip_flexiprep"
->
true
)
)
override
def
fixedValues
:
Map
[
String
,
Any
]
=
super
.
fixedValues
++
Map
(
"gearssingle"
->
Map
(
"skip_flexiprep"
->
true
))
...
...
@@ -99,6 +102,8 @@ trait MultisampleMappingTrait extends MultiSampleQScript
lazy
val
inputR1
:
Option
[
File
]
=
MultisampleMapping
.
fileMustBeAbsolute
(
config
(
"R1"
))
lazy
val
inputR2
:
Option
[
File
]
=
MultisampleMapping
.
fileMustBeAbsolute
(
config
(
"R2"
))
lazy
val
qcFastqR1
=
mapping
.
map
(
_
.
flexiprep
.
fastqR1Qc
)
lazy
val
qcFastqR2
=
mapping
.
flatMap
(
_
.
flexiprep
.
fastqR2Qc
)
lazy
val
inputBam
:
Option
[
File
]
=
MultisampleMapping
.
fileMustBeAbsolute
(
if
(
inputR1
.
isEmpty
)
config
(
"bam"
)
else
None
)
lazy
val
bamToFastq
:
Boolean
=
config
(
"bam_to_fastq"
,
default
=
false
)
lazy
val
correctReadgroups
:
Boolean
=
config
(
"correct_readgroups"
,
default
=
false
)
...
...
@@ -274,8 +279,8 @@ trait MultisampleMappingTrait extends MultiSampleQScript
add
(
gears
)
case
"all"
=>
val
gears
=
new
GearsSingle
(
qscript
)
gears
.
fastqR1
=
libraries
.
flatMap
(
_
.
_2
.
input
R1
).
toList
gears
.
fastqR2
=
libraries
.
flatMap
(
_
.
_2
.
input
R2
).
toList
gears
.
fastqR1
=
libraries
.
flatMap
(
_
.
_2
.
qcFastq
R1
).
toList
gears
.
fastqR2
=
libraries
.
flatMap
(
_
.
_2
.
qcFastq
R2
).
toList
gears
.
sampleId
=
Some
(
sampleId
)
gears
.
outputDir
=
new
File
(
sampleDir
,
"gears"
)
add
(
gears
)
...
...
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