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biopet.biopet
Commits
bbe9311d
Commit
bbe9311d
authored
Aug 26, 2014
by
Peter van 't Hof
Browse files
Fix on final jobs
parent
cd66d051
Changes
1
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Inline
Side-by-side
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
View file @
bbe9311d
...
...
@@ -76,7 +76,9 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
val
out
=
if
(
paired
)
runTrimClip
(
outputFiles
(
"fastq_input_R1"
),
outputFiles
(
"fastq_input_R2"
),
outputDir
)
else
runTrimClip
(
outputFiles
(
"fastq_input_R1"
),
outputDir
)
runFinalize
(
List
(
outputFiles
(
"output_R1"
)),
if
(
outputFiles
.
contains
(
"output_R2"
))
List
(
outputFiles
(
"output_R2"
))
else
List
())
val
R1_files
=
for
((
k
,
v
)
<-
outputFiles
if
k
.
endsWith
(
"output_R1"
))
yield
v
val
R2_files
=
for
((
k
,
v
)
<-
outputFiles
if
k
.
endsWith
(
"output_R2"
))
yield
v
runFinalize
(
R1_files
.
toList
,
R2_files
.
toList
)
}
def
runInitialJobs
()
{
...
...
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