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biopet.biopet
Commits
c2284b8b
Commit
c2284b8b
authored
Sep 08, 2014
by
Peter van 't Hof
Browse files
Fixed chunking output dirs
parent
a827c3b4
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
c2284b8b
...
...
@@ -143,38 +143,33 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
}
var
chunks
:
Map
[
String
,
(
String
,
String
)]
=
Map
()
if
(
chunking
)
for
(
t
<-
1
to
numberChunks
.
getOrElse
(
1
))
{
val
chunkDir
=
"chunks/"
+
t
+
"/"
val
chunkDir
=
outputDir
+
"chunks/"
+
t
+
"/"
chunks
+=
(
chunkDir
->
(
removeGz
(
chunkDir
+
fastq_R1
.
getName
),
if
(
paired
)
removeGz
(
chunkDir
+
fastq_R2
.
getName
)
else
""
))
}
else
chunks
+=
(
"flexiprep/"
->
(
flexiprep
.
extractIfNeeded
(
fastq_R1
,
flexiprep
.
outputDir
),
}
else
chunks
+=
(
outputDir
->
(
flexiprep
.
extractIfNeeded
(
fastq_R1
,
flexiprep
.
outputDir
),
flexiprep
.
extractIfNeeded
(
fastq_R2
,
flexiprep
.
outputDir
)))
if
(
chunking
)
{
val
fastSplitter_R1
=
new
FastqSplitter
(
this
)
fastSplitter_R1
.
input
=
fastq_R1
fastSplitter_R1
.
memoryLimit
=
4
fastSplitter_R1
.
jobResourceRequests
:+=
"h_vmem=8G"
for
((
chunk
,
fastqfile
)
<-
chunks
)
fastSplitter_R1
.
output
:+=
fastqfile
.
_1
for
((
chunkDir
,
fastqfile
)
<-
chunks
)
fastSplitter_R1
.
output
:+=
fastqfile
.
_1
add
(
fastSplitter_R1
)
if
(
paired
)
{
val
fastSplitter_R2
=
new
FastqSplitter
(
this
)
fastSplitter_R2
.
input
=
fastq_R2
fastSplitter_R2
.
memoryLimit
=
4
fastSplitter_R2
.
jobResourceRequests
:+=
"h_vmem=8G"
for
((
chunk
,
fastqfile
)
<-
chunks
)
fastSplitter_R2
.
output
:+=
fastqfile
.
_2
for
((
chunkDir
,
fastqfile
)
<-
chunks
)
fastSplitter_R2
.
output
:+=
fastqfile
.
_2
add
(
fastSplitter_R2
)
}
}
for
((
chunk
,
fastqfile
)
<-
chunks
)
{
for
((
chunk
Dir
,
fastqfile
)
<-
chunks
)
{
var
R1
=
fastqfile
.
_1
var
R2
=
fastqfile
.
_2
var
deps
:
List
[
File
]
=
Nil
val
chunkDir
=
if
(
chunking
)
outputDir
+
chunk
else
outputDir
if
(!
skipFlexiprep
)
{
val
flexiout
=
flexiprep
.
runTrimClip
(
R1
,
R2
,
chunkDir
+
"flexiprep/"
,
chunk
)
logger
.
debug
(
chunk
+
" - "
+
flexiout
)
val
flexiout
=
flexiprep
.
runTrimClip
(
R1
,
R2
,
chunkDir
+
"flexiprep/"
,
chunk
Dir
)
logger
.
debug
(
chunk
Dir
+
" - "
+
flexiout
)
R1
=
flexiout
.
_1
if
(
paired
)
R2
=
flexiout
.
_2
deps
=
flexiout
.
_3
...
...
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