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biopet.biopet
Commits
47b02b54
Commit
47b02b54
authored
Oct 02, 2015
by
Peter van 't Hof
Browse files
Fixed graph issue
parent
5d5c30c1
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
47b02b54
...
...
@@ -177,26 +177,19 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
var
fastq_R1_output
:
List
[
File
]
=
Nil
var
fastq_R2_output
:
List
[
File
]
=
Nil
def
removeGz
(
file
:
File
)
:
File
=
{
val
absPath
=
file
.
getAbsolutePath
if
(
absPath
.
endsWith
(
".gz"
))
new
File
(
absPath
.
substring
(
0
,
absPath
.
lastIndexOf
(
".gz"
)))
else
if
(
absPath
.
endsWith
(
".gzip"
))
new
File
(
absPath
.
substring
(
0
,
absPath
.
lastIndexOf
(
".gzip"
)))
else
file
}
val
chunks
:
Map
[
File
,
(
File
,
Option
[
File
])]
=
{
if
(
chunking
)
{
(
for
(
t
<-
1
to
numberChunks
.
getOrElse
(
1
))
yield
{
val
chunkDir
=
new
File
(
outputDir
,
"chunks"
+
File
.
separator
+
t
)
chunkDir
->
(
removeGz
(
new
File
(
chunkDir
,
input_R1
.
getName
)
)
,
if
(
paired
)
Some
(
removeGz
(
new
File
(
chunkDir
,
input_R2
.
get
.
getName
))
)
else
None
)
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
.
fastqR1Qc
,
flexiprep
.
fastqR2Qc
))
}
else
Map
(
outputDir
->
(
flexiprep
.
input_R1
,
flexiprep
.
input_R2
))
}
if
(
chunking
)
{
...
...
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