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biopet.biopet
Commits
699c7baf
Commit
699c7baf
authored
Oct 02, 2015
by
Peter van 't Hof
Browse files
Removed zcat step
parent
2156f192
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
699c7baf
...
...
@@ -184,12 +184,8 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
chunkDir
->
(
new
File
(
chunkDir
,
input_R1
.
getName
),
if
(
paired
)
Some
(
new
File
(
chunkDir
,
input_R2
.
get
.
getName
))
else
None
)
}).
toMap
}
else
if
(
skipFlexiprep
)
{
Map
(
outputDir
->
(
extractIfNeeded
(
input_R1
,
flexiprep
.
outputDir
),
if
(
paired
)
Some
(
extractIfNeeded
(
input_R2
.
get
,
outputDir
))
else
None
)
)
}
else
Map
(
outputDir
->
(
flexiprep
.
input_R1
,
flexiprep
.
input_R2
))
}
else
if
(
skipFlexiprep
)
Map
(
outputDir
->
(
input_R1
,
(
if
(
paired
)
input_R2
else
None
)))
else
Map
(
outputDir
->
(
flexiprep
.
input_R1
,
flexiprep
.
input_R2
))
}
if
(
chunking
)
{
...
...
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