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biopet.biopet
Commits
ec59d68a
Commit
ec59d68a
authored
Apr 27, 2016
by
Peter van 't Hof
Browse files
Disable gathering
parent
dbc5cfbd
Changes
1
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public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
View file @
ec59d68a
...
...
@@ -15,17 +15,17 @@
*/
package
nl.lumc.sasc.biopet.core
import
java.io.
{
PrintWriter
,
File
,
FileInputStream
}
import
java.io.
{
File
,
FileInputStream
,
PrintWriter
}
import
java.security.MessageDigest
import
nl.lumc.sasc.biopet.utils.Logging
import
org.broadinstitute.gatk.utils.commandline.
{
Output
,
Input
}
import
org.broadinstitute.gatk.utils.commandline.
{
Gather
,
Input
,
Output
}
import
org.broadinstitute.gatk.utils.runtime.ProcessSettings
import
org.ggf.drmaa.JobTemplate
import
scala.collection.mutable
import
scala.io.Source
import
scala.sys.process.
{
Process
,
ProcessLogger
}
import
scala.sys.process.
{
Process
,
ProcessLogger
}
import
scala.collection.JavaConversions._
/** Biopet command line trait to auto check executable and cluster values */
...
...
@@ -36,6 +36,7 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
var
deps
:
List
[
File
]
=
Nil
@Output
@Gather
(
enabled
=
false
)
var
outputFiles
:
List
[
File
]
=
Nil
var
executable
:
String
=
_
...
...
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