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
7de7e6ee
Commit
7de7e6ee
authored
Dec 13, 2016
by
Sander Bollen
Browse files
Merge branch 'fix-BIOPET-317' into 'develop'
Fixing BIOPET-317 See merge request !489
parents
ba0deb1c
81188921
Changes
1
Hide whitespace changes
Inline
Side-by-side
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
View file @
7de7e6ee
...
...
@@ -269,11 +269,15 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
if
(
fastq_R1
.
length
>
1
)
{
val
zcat
=
new
Zcat
(
this
)
zcat
.
input
=
fastq_R1
add
(
zcat
|
new
Gzip
(
this
)
>
fastqR1Qc
)
val
cmdR1
=
zcat
|
new
Gzip
(
this
)
>
fastqR1Qc
cmdR1
.
isIntermediate
=
!
keepQcFastqFiles
add
(
cmdR1
)
if
(
paired
)
{
val
zcat
=
new
Zcat
(
this
)
zcat
.
input
=
fastq_R2
add
(
zcat
|
new
Gzip
(
this
)
>
fastqR2Qc
.
get
)
val
cmdR2
=
zcat
|
new
Gzip
(
this
)
>
fastqR2Qc
.
get
cmdR2
.
isIntermediate
=
!
keepQcFastqFiles
add
(
cmdR2
)
}
}
...
...
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