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biopet.biopet
Commits
e294fd51
Commit
e294fd51
authored
Aug 11, 2014
by
Peter van 't Hof
Browse files
Move init jobs for flexiprep out of chunks
parent
d26a67ab
Changes
1
Hide whitespace changes
Inline
Side-by-side
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
e294fd51
...
...
@@ -124,7 +124,15 @@ 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/"
if
(!
skipFlexiprep
)
{
flexiprep
.
outputDir
=
outputDir
+
"flexiprep/"
flexiprep
.
input_R1
=
fastq_R1
if
(
paired
)
flexiprep
.
input_R2
=
fastq_R2
flexiprep
.
sampleName
=
this
.
RGSM
flexiprep
.
libraryName
=
this
.
RGLB
flexiprep
.
init
flexiprep
.
runInitialJobs
}
var
bamFiles
:
List
[
File
]
=
Nil
var
fastq_R1_output
:
List
[
File
]
=
Nil
var
fastq_R2_output
:
List
[
File
]
=
Nil
...
...
@@ -166,13 +174,6 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
var
deps
:
List
[
File
]
=
Nil
val
chunkDir
=
if
(
chunking
)
outputDir
+
chunk
+
"/"
else
outputDir
if
(!
skipFlexiprep
)
{
flexiprep
.
input_R1
=
fastq_R1
if
(
paired
)
flexiprep
.
input_R2
=
fastq_R2
flexiprep
.
sampleName
=
this
.
RGSM
flexiprep
.
libraryName
=
this
.
RGLB
flexiprep
.
init
flexiprep
.
runInitialJobs
//flexiprep.biopetScript
val
flexiout
=
flexiprep
.
runTrimClip
(
R1
,
R2
,
chunkDir
+
"flexiprep/"
,
chunk
)
logger
.
debug
(
chunk
+
" - "
+
flexiout
)
R1
=
flexiout
.
_1
...
...
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