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
cfae9015
Commit
cfae9015
authored
Aug 25, 2014
by
Peter van 't Hof
Browse files
OutputName change
parent
7624b929
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
View file @
cfae9015
...
...
@@ -22,11 +22,11 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
var
dbsnp
:
File
=
_
@Argument
(
doc
=
"OutputName"
,
required
=
false
)
var
outputName
:
String
=
"hc"
var
outputName
:
String
=
_
@Output
(
doc
=
"OutputFile"
,
required
=
false
)
var
outputFile
:
File
=
_
var
gvcfMode
=
true
var
singleGenotyping
=
false
...
...
@@ -35,7 +35,9 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
if
(!
singleGenotyping
)
singleGenotyping
=
config
(
"singlegenotyping"
)
if
(
reference
==
null
)
reference
=
config
(
"reference"
,
required
=
true
)
if
(
dbsnp
==
null
)
dbsnp
=
config
(
"dbsnp"
)
if
(
outputFile
==
null
)
outputFile
=
outputDir
+
outputName
+
(
if
(
gvcfMode
)
".gvcf.vcf"
else
".vcf"
)
if
(
outputFile
==
null
)
outputFile
=
outputDir
+
(
if
(
outputName
!=
null
&&
!
outputName
.
endsWith
(
"."
))
outputName
+
"."
else
outputName
)
+
(
if
(
gvcfMode
)
"hc.gvcf.vcf"
else
".vcf"
)
if
(
outputDir
==
null
)
throw
new
IllegalStateException
(
"Missing Output directory on gatk module"
)
else
if
(!
outputDir
.
endsWith
(
"/"
))
outputDir
+=
"/"
}
...
...
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