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biopet.biopet
Commits
a2ebfada
Commit
a2ebfada
authored
Jul 15, 2014
by
Peter van 't Hof
Browse files
Fix outputDir for flexiprep
parent
21b032c9
Changes
1
Hide whitespace changes
Inline
Side-by-side
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
a2ebfada
...
...
@@ -123,6 +123,7 @@ class Mapping(val root:Configurable) extends QScript with BiopetQScript {
var
fastq_R1
:
File
=
input_R1
var
fastq_R2
:
File
=
if
(
paired
)
input_R2
else
""
val
flexiprep
=
new
Flexiprep
(
this
)
flexiprep
.
outputDir
=
outputDir
+
"flexiprep/"
var
bamFiles
:
List
[
File
]
=
Nil
var
fastq_R1_output
:
List
[
File
]
=
Nil
var
fastq_R2_output
:
List
[
File
]
=
Nil
...
...
@@ -136,7 +137,7 @@ class Mapping(val root:Configurable) extends QScript with BiopetQScript {
if
(
chunking
)
for
(
t
<-
1
to
numberChunks
)
{
chunks
+=
(
"chunk_"
+
t
->
(
removeGz
(
outputDir
+
"chunk_"
+
t
+
"/"
+
fastq_R1
.
getName
),
if
(
paired
)
removeGz
(
outputDir
+
"chunk_"
+
t
+
"/"
+
fastq_R2
.
getName
)
else
""
))
}
else
chunks
+=
(
""
->
(
fastq_R1
,
fastq_R2
))
}
else
chunks
+=
(
flexiprep
.
outputDir
->
(
fastq_R1
,
fastq_R2
))
if
(
chunking
)
{
val
fastSplitter_R1
=
new
FastqSplitter
(
this
)
...
...
@@ -162,7 +163,6 @@ class Mapping(val root:Configurable) extends QScript with BiopetQScript {
if
(!
skipFlexiprep
)
{
flexiprep
.
input_R1
=
fastq_R1
if
(
paired
)
flexiprep
.
input_R2
=
fastq_R2
flexiprep
.
outputDir
=
outputDir
+
"flexiprep/"
flexiprep
.
init
flexiprep
.
runInitialJobs
//flexiprep.biopetScript
...
...
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