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
bc930d51
Commit
bc930d51
authored
Jan 25, 2017
by
Peter van 't Hof
Browse files
Make centrifuge usable output method
parent
d36878da
Changes
1
Hide whitespace changes
Inline
Side-by-side
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
View file @
bc930d51
...
...
@@ -94,18 +94,21 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
Some
(
outputFile
)
}
if
(!
skipFlexiprep
)
{
val
flexiprep
=
new
Flexiprep
(
this
)
flexiprep
.
inputR1
=
read1
flexiprep
.
inputR2
=
read2
flexiprep
.
sampleId
=
if
(
sampleId
.
isEmpty
)
Some
(
"noSampleName"
)
else
sampleId
flexiprep
.
libId
=
if
(
libId
.
isEmpty
)
Some
(
"noLibName"
)
else
libId
flexiprep
.
outputDir
=
new
File
(
outputDir
,
"flexiprep"
)
add
(
flexiprep
)
(
flexiprep
.
fastqR1Qc
,
flexiprep
.
fastqR2Qc
)
}
else
(
read1
,
read2
)
flexiprep
.
map
{
f
=>
f
.
inputR1
=
read1
f
.
inputR2
=
read2
f
.
sampleId
=
Some
(
sampleId
.
getOrElse
(
"noSampleName"
))
f
.
libId
=
Some
(
libId
.
getOrElse
(
"noLibName"
))
f
.
outputDir
=
new
File
(
outputDir
,
"flexiprep"
)
add
(
f
)
(
f
.
fastqR1Qc
,
f
.
fastqR2Qc
)
}.
getOrElse
((
read1
,
read2
))
}
lazy
protected
val
flexiprep
:
Option
[
Flexiprep
]
=
if
(!
skipFlexiprep
)
{
Some
(
new
Flexiprep
(
this
))
}
else
None
/** Method to add jobs */
def
biopetScript
()
:
Unit
=
{
val
(
r1
,
r2
)
:
(
File
,
Option
[
File
])
=
(
fastqR1
,
fastqR2
,
bamFile
)
match
{
...
...
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