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
9aad81a3
Commit
9aad81a3
authored
Nov 08, 2014
by
Peter van 't Hof
Browse files
Fix memory
parent
bc3e6582
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
View file @
9aad81a3
...
...
@@ -15,7 +15,7 @@ import scala.collection.SortedMap
import
scala.collection.mutable.
{
Map
,
Set
}
import
nl.lumc.sasc.biopet.core.config.Configurable
import
scala.collection.JavaConversions._
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
,
Argument
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
class
MergeAlleles
(
val
root
:
Configurable
)
extends
BiopetJavaCommandLineFunction
{
javaMainClass
=
getClass
.
getName
...
...
@@ -23,12 +23,14 @@ class MergeAlleles(val root: Configurable) extends BiopetJavaCommandLineFunction
@Input
(
doc
=
"Input vcf files"
,
shortName
=
"input"
,
required
=
true
)
var
input
:
List
[
File
]
=
Nil
@Output
(
doc
=
"Output
fastq
file
s
"
,
shortName
=
"output"
,
required
=
true
)
@Output
(
doc
=
"Output
vcf
file"
,
shortName
=
"output"
,
required
=
true
)
var
output
:
File
=
_
@Argument
var
reference
:
File
=
config
(
"reference"
)
override
val
defaultVmem
=
"8G"
memoryLimit
=
Option
(
4
)
override
def
commandLine
=
super
.
commandLine
+
repeat
(
"-I"
,
input
)
+
required
(
"-o"
,
output
)
+
...
...
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