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biopet.biopet
Commits
a0e16b2f
Commit
a0e16b2f
authored
Aug 04, 2014
by
Peter van 't Hof
Browse files
Fix on outputdir for flexiprep
parent
7c1fa255
Changes
1
Hide whitespace changes
Inline
Side-by-side
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
a0e16b2f
...
...
@@ -155,6 +155,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
for
((
chunk
,
fastqfile
)
<-
chunks
)
{
var
R1
=
fastqfile
.
_1
var
R2
=
fastqfile
.
_2
val
chunkDir
=
if
(
chunking
)
outputDir
+
chunk
+
"/"
else
outputDir
if
(!
skipFlexiprep
)
{
flexiprep
.
input_R1
=
fastq_R1
if
(
paired
)
flexiprep
.
input_R2
=
fastq_R2
...
...
@@ -162,14 +163,14 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
flexiprep
.
init
flexiprep
.
runInitialJobs
//flexiprep.biopetScript
val
flexiout
=
flexiprep
.
runTrimClip
(
R1
,
R2
,
outputDir
+
chunk
,
chunk
)
val
flexiout
=
flexiprep
.
runTrimClip
(
R1
,
R2
,
chunkDir
+
"flexiprep/"
,
chunk
)
logger
.
debug
(
chunk
+
" - "
+
flexiout
)
R1
=
flexiout
.
_1
if
(
paired
)
R2
=
flexiout
.
_2
fastq_R1_output
:+=
R1
fastq_R2_output
:+=
R2
}
val
chunkDir
=
if
(
chunking
)
outputDir
+
chunk
+
"/"
else
outputDir
if
(
aligner
==
"bwa"
)
{
val
bwaCommand
=
new
Bwa
(
this
)
bwaCommand
.
R1
=
R1
...
...
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