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
a83a6a3f
Commit
a83a6a3f
authored
Mar 09, 2016
by
Peter van 't Hof
Browse files
Changed the cutadapt so the config will always load, even when fastqc data is no yet avilable
parent
6dda3f45
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala
View file @
a83a6a3f
...
...
@@ -48,7 +48,7 @@ class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetComman
override
def
defaultThreads
=
3
val
seqtk
=
new
SeqtkSeq
(
root
)
var
clip
:
Option
[
Cutadapt
]
=
None
var
clip
:
Option
[
Cutadapt
]
=
if
(!
flexiprep
.
skipClip
)
Some
(
new
Cutadapt
(
root
,
fastqc
))
else
None
var
trim
:
Option
[
Sickle
]
=
None
lazy
val
outputCommand
:
BiopetCommandLineFunction
=
if
(
compress
)
{
val
gzip
=
Gzip
(
root
)
...
...
@@ -101,7 +101,7 @@ class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetComman
clip
=
if
(!
flexiprep
.
skipClip
)
{
val
foundAdapters
=
fastqc
.
foundAdapters
.
map
(
_
.
seq
)
if
(
foundAdapters
.
nonEmpty
)
{
val
cutadapt
=
new
Cutadapt
(
root
,
fastqc
)
val
cutadapt
=
clip
.
getOrElse
(
new
Cutadapt
(
root
,
fastqc
)
)
cutadapt
.
fastqInput
=
seqtk
.
output
cutadapt
.
fastqOutput
=
new
File
(
output
.
getParentFile
,
input
.
getName
+
".cutadapt.fq"
)
cutadapt
.
statsOutput
=
new
File
(
flexiprep
.
outputDir
,
s
"${flexiprep.sampleId.getOrElse("
x
")}-${flexiprep.libId.getOrElse("
x
")}.$read.clip.stats"
)
...
...
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