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biopet.biopet
Commits
18e080e1
Commit
18e080e1
authored
Aug 19, 2014
by
Peter van 't Hof
Browse files
Moved Flexiprep val to root op mapping class
parent
89121481
Changes
1
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Inline
Side-by-side
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
18e080e1
...
...
@@ -75,6 +75,8 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
var
RGPI
:
Int
=
_
var
paired
:
Boolean
=
false
val
flexiprep
=
new
Flexiprep
(
this
)
def
init
()
{
for
(
file
<-
configfiles
)
globalConfig
.
loadConfigFile
(
file
)
...
...
@@ -123,7 +125,6 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
def
biopetScript
()
{
var
fastq_R1
:
File
=
input_R1
var
fastq_R2
:
File
=
if
(
paired
)
input_R2
else
""
val
flexiprep
=
new
Flexiprep
(
this
)
if
(!
skipFlexiprep
)
{
flexiprep
.
outputDir
=
outputDir
+
"flexiprep/"
flexiprep
.
input_R1
=
fastq_R1
...
...
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