Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Mirrors
biopet.biopet
Commits
8afdecfc
Commit
8afdecfc
authored
Jan 20, 2016
by
Peter van 't Hof
Browse files
Fix compile issue
parent
ae8146ba
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/CombineReads.scala
View file @
8afdecfc
...
...
@@ -50,10 +50,10 @@ class CombineReads(val root: Configurable) extends QScript with SummaryQScript w
if
((
forwardPrimers
:::
reversePrimers
).
nonEmpty
)
{
val
cutadapt
=
new
Cutadapt
(
this
)
cutadapt
.
fastq
_i
nput
=
flash
.
combinedFastq
cutadapt
.
fastq
_o
utput
=
this
.
combinedFastq
cutadapt
.
stats
_o
utput
=
swapExt
(
outputDir
,
cutadapt
.
fastq
_o
utput
,
".fastq.gz"
,
".stats"
)
(
forwardPrimers
:::
reversePrimers
).
foreach
(
cutadapt
.
opt_
anywhere
+=
_
)
cutadapt
.
fastq
I
nput
=
flash
.
combinedFastq
cutadapt
.
fastq
O
utput
=
this
.
combinedFastq
cutadapt
.
stats
O
utput
=
swapExt
(
outputDir
,
cutadapt
.
fastq
O
utput
,
".fastq.gz"
,
".stats"
)
(
forwardPrimers
:::
reversePrimers
).
foreach
(
cutadapt
.
anywhere
+=
_
)
add
(
cutadapt
)
addSummarizable
(
cutadapt
,
"cutadapt"
)
}
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment