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biopet.biopet
Commits
47e33420
Commit
47e33420
authored
Apr 26, 2016
by
Peter van 't Hof
Browse files
Make dict required for all gatk tools
parent
5b09944b
Changes
1
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protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CommandLineGATK.scala
View file @
47e33420
...
...
@@ -2,9 +2,9 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import
java.io.File
import
nl.lumc.sasc.biopet.core.
{
BiopetJavaCommandLineFunction
,
Reference
,
Version
}
import
nl.lumc.sasc.biopet.core.
{
BiopetJavaCommandLineFunction
,
Reference
,
Version
}
import
org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Gather
,
Input
,
Output
}
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Gather
,
Input
,
Output
}
trait
CommandLineGATK
extends
BiopetJavaCommandLineFunction
with
Reference
with
Version
{
analysisName
=
"CommandLineGATK"
...
...
@@ -320,6 +320,8 @@ trait CommandLineGATK extends BiopetJavaCommandLineFunction with Reference with
override
def
versionExitcode
=
List
(
0
,
1
)
def
versionCommand
=
executable
+
" -jar "
+
jarFile
+
" -version"
override
def
dictRequired
=
true
override
def
beforeGraph
()
{
super
.
beforeGraph
()
if
(
reference_sequence
!=
null
)
reference_sequence
=
referenceFasta
()
...
...
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