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
db06f6bc
Commit
db06f6bc
authored
Jul 27, 2015
by
Peter van 't Hof
Browse files
Fix error when no mode selected
parent
844ff098
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/Delly.scala
View file @
db06f6bc
...
...
@@ -73,7 +73,7 @@ class Delly(val root: Configurable) extends QScript with BiopetQScript with Refe
add
(
delly
)
}
// we need to merge the vcf's
va
r
finalVCF
=
if
(
vcfFiles
.
size
>
1
)
{
va
l
finalVCF
=
if
(
vcfFiles
.
size
>
1
)
{
// do merging
// CatVariants is a $org.broadinstitute.gatk.utils.commandline.CommandLineProgram$;
//TODO: convert to biopet extension
...
...
@@ -83,30 +83,28 @@ class Delly(val root: Configurable) extends QScript with BiopetQScript with Refe
variants
.
reference
=
referenceFasta
()
// add the job
add
(
variants
)
this
.
outputvcf
}
else
{
Some
(
outputvcf
)
}
else
if
(
vcfFiles
.
size
==
1
)
{
// TODO: pretify this
val
ln
=
Ln
(
this
,
vcfFiles
.
head
.
_2
,
this
.
outputvcf
,
relative
=
true
)
add
(
ln
)
ln
.
output
}
Some
(
ln
.
output
)
}
else
None
outputFiles
+=
(
"vcf"
->
this
.
outputvcf
)
finalVCF
.
foreach
(
file
=>
outputFiles
+=
(
"vcf"
->
file
)
)
}
private
def
swapExtension
(
inputFile
:
String
)
=
inputFile
.
substring
(
0
,
inputFile
.
lastIndexOf
(
".bam"
))
+
".delly.vcf"
}
object
Delly
extends
PipelineCommand
{
override
val
pipeline
=
"/nl/lumc/sasc/biopet/extensions/svcallers/Delly/Delly.class"
def
apply
(
root
:
Configurable
,
input
:
File
,
runDir
:
File
)
:
Delly
=
{
val
delly
p
ipeline
=
new
Delly
(
root
)
delly
p
ipeline
.
input
=
input
delly
p
ipeline
.
workdir
=
runDir
delly
p
ipeline
.
init
()
delly
p
ipeline
.
biopetScript
()
delly
p
ipeline
val
delly
P
ipeline
=
new
Delly
(
root
)
delly
P
ipeline
.
input
=
input
delly
P
ipeline
.
workdir
=
runDir
delly
P
ipeline
.
init
()
delly
P
ipeline
.
biopetScript
()
delly
P
ipeline
}
}
\ No newline at end of file
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