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biopet.biopet
Commits
910074b8
Commit
910074b8
authored
Sep 28, 2015
by
Peter van 't Hof
Browse files
Fix for #210
parent
adb6ffe1
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
910074b8
...
...
@@ -244,7 +244,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
case
_
=>
throw
new
IllegalStateException
(
"Option aligner: '"
+
aligner
+
"' is not valid"
)
}
if
(
chunking
&&
numberChunks
.
getOrElse
(
1
)
>
1
&&
config
(
"chunk_metrics"
,
default
=
false
))
addAll
(
BamMetrics
(
this
,
outputBam
,
new
File
(
chunkDir
,
"metrics"
)).
functions
)
addAll
(
BamMetrics
(
this
,
outputBam
,
new
File
(
chunkDir
,
"metrics"
)
,
sampleId
,
libId
).
functions
)
}
if
(!
skipFlexiprep
)
{
flexiprep
.
runFinalize
(
fastq_R1_output
,
fastq_R2_output
)
...
...
@@ -265,7 +265,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
}
if
(!
skipMetrics
)
{
val
bamMetrics
=
BamMetrics
(
this
,
bamFile
,
new
File
(
outputDir
,
"metrics"
))
val
bamMetrics
=
BamMetrics
(
this
,
bamFile
,
new
File
(
outputDir
,
"metrics"
)
,
sampleId
,
libId
)
addAll
(
bamMetrics
.
functions
)
addSummaryQScript
(
bamMetrics
)
}
...
...
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