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biopet.biopet
Commits
481a7a96
Commit
481a7a96
authored
Feb 03, 2015
by
Peter van 't Hof
Browse files
Skip extractIfNeeded on R2 when not paired
parent
2838b39a
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
481a7a96
...
...
@@ -146,8 +146,10 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
chunks
+=
(
chunkDir
->
(
removeGz
(
chunkDir
+
input_R1
.
getName
),
if
(
paired
)
removeGz
(
chunkDir
+
input_R2
.
get
.
getName
)
else
""
))
}
else
chunks
+=
(
outputDir
->
(
flexiprep
.
extractIfNeeded
(
input_R1
,
flexiprep
.
outputDir
),
flexiprep
.
extractIfNeeded
(
input_R2
.
getOrElse
(
null
),
flexiprep
.
outputDir
)))
else
chunks
+=
(
outputDir
->
(
flexiprep
.
extractIfNeeded
(
input_R1
,
flexiprep
.
outputDir
),
if
(
paired
)
flexiprep
.
extractIfNeeded
(
input_R2
.
get
,
flexiprep
.
outputDir
)
else
""
)
)
if
(
chunking
)
{
val
fastSplitter_R1
=
new
FastqSplitter
(
this
)
...
...
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