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biopet.biopet
Commits
5d3b5448
Commit
5d3b5448
authored
Jul 24, 2017
by
Peter van 't Hof
Committed by
GitHub
Jul 24, 2017
Browse files
Merge pull request #162 from biopet/fix-BIOPET-745
Fixing some failing tests
parents
d452d397
2ca6260e
Changes
2
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Inline
Side-by-side
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
View file @
5d3b5448
...
...
@@ -284,6 +284,9 @@ object BammetricsReport extends ReportBuilder {
.
getOrElse
(
throw
new
IllegalStateException
(
"Sample must be there"
))
val
libraryName
=
library
.
flatMap
(
l
=>
Await
.
result
(
summary
.
getLibraryName
(
l
),
Duration
.
Inf
))
if
(
yKeyList
.
find
(
x
=>
map
.
contains
(
x
)
&&
map
(
x
).
isDefined
).
isEmpty
)
{
""
}
val
yKey
=
yKeyList
.
find
(
x
=>
map
.
contains
(
x
)
&&
map
(
x
).
isDefined
).
get
val
xKey
=
xKeyList
.
find
(
x
=>
map
.
contains
(
x
)
&&
map
(
x
).
isDefined
).
get
Map
(
...
...
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMapping.scala
View file @
5d3b5448
...
...
@@ -120,8 +120,8 @@ trait MultisampleMappingTrait extends MultiSampleQScript with Reference { qscrip
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
qcFastqR1
:
Option
[
File
]
=
mapping
.
map
(
_
.
flexiprep
.
fastqR1Qc
)
lazy
val
qcFastqR2
:
Option
[
File
]
=
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
)
...
...
@@ -229,17 +229,19 @@ trait MultisampleMappingTrait extends MultiSampleQScript with Reference { qscrip
qscript
.
add
(
aorrg
)
}
}
else
add
(
Ln
.
linkBamFile
(
qscript
,
inputBam
.
get
,
bamFile
.
get
)
:
_
*
)
}
if
(!
bamToFastq
)
{
val
bamMetrics
=
new
BamMetrics
(
qscript
)
bamMetrics
.
sampleId
=
Some
(
sampleId
)
bamMetrics
.
libId
=
Some
(
libId
)
bamMetrics
.
inputBam
=
bamFile
.
get
bamMetrics
.
outputDir
=
new
File
(
libDir
,
"metrics"
)
bamMetrics
.
paired
=
inputR2
.
isDefined
bamMetrics
.
paired
=
inputR2
.
isDefined
||
inputBam
.
isDefined
add
(
bamMetrics
)
if
(
config
(
"execute_bam2wig"
,
default
=
true
))
add
(
Bam2Wig
(
qscript
,
bamFile
.
get
))
}
if
(
config
(
"execute_bam2wig"
,
default
=
true
))
add
(
Bam2Wig
(
qscript
,
bamFile
.
get
))
}
else
logger
.
warn
(
s
"Sample '$sampleId' does not have any input files"
)
}
}
...
...
@@ -340,7 +342,8 @@ trait MultisampleMappingTrait extends MultiSampleQScript with Reference { qscrip
bamMetrics
.
sampleId
=
Some
(
sampleId
)
bamMetrics
.
inputBam
=
if
(
metricsPreprogressBam
)
preProcessBam
.
get
else
bamFile
.
get
bamMetrics
.
outputDir
=
new
File
(
sampleDir
,
"metrics"
)
bamMetrics
.
paired
=
libraries
.
exists
(
_
.
_2
.
inputR1
.
isDefined
)
bamMetrics
.
paired
=
libraries
.
exists
(
x
=>
x
.
_2
.
inputR1
.
isDefined
||
x
.
_2
.
inputBam
.
isDefined
)
add
(
bamMetrics
)
if
(
config
(
"execute_bam2wig"
,
default
=
true
))
add
(
Bam2Wig
(
qscript
,
preProcessBam
.
get
))
...
...
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