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biopet.biopet
Commits
71b12276
Commit
71b12276
authored
Sep 09, 2014
by
Peter van 't Hof
Browse files
Added option for metrics for each chunk
parent
c43bfa2a
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
71b12276
...
...
@@ -186,6 +186,8 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
case
"star-2pass"
=>
addStar2pass
(
R1
,
R2
,
outputBam
,
deps
)
case
_
=>
throw
new
IllegalStateException
(
"Option Alginer: '"
+
aligner
+
"' is not valid"
)
}
if
(
config
(
"chunk_metrics"
,
default
=
false
))
addAll
(
BamMetrics
(
this
,
outputBam
,
chunkDir
+
"metrics/"
).
functions
)
}
if
(!
skipFlexiprep
)
{
flexiprep
.
runFinalize
(
fastq_R1_output
,
fastq_R2_output
)
...
...
@@ -202,7 +204,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
bamFile
=
mergeSamFile
.
output
}
if
(!
skipMetrics
)
addAll
(
BamMetrics
.
apply
(
this
,
bamFile
,
outputDir
+
"metrics/"
).
functions
)
if
(!
skipMetrics
)
addAll
(
BamMetrics
(
this
,
bamFile
,
outputDir
+
"metrics/"
).
functions
)
outputFiles
+=
(
"finalBamFile"
->
bamFile
)
}
...
...
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