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biopet.biopet
Commits
fb215ab1
Commit
fb215ab1
authored
Feb 05, 2015
by
Peter van 't Hof
Browse files
Fix bug on vmem
parent
c008141f
Changes
1
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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
View file @
fb215ab1
...
...
@@ -15,13 +15,11 @@
*/
package
nl.lumc.sasc.biopet.core
//import java.io.BufferedInputStream
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.queue.QException
import
org.broadinstitute.gatk.queue.function.CommandLineFunction
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Argument
}
//import scala.io.Source
import
scala.sys.process.
{
Process
,
ProcessLogger
}
import
scala.util.matching.Regex
import
java.io.FileInputStream
...
...
@@ -62,7 +60,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
vmem
=
config
(
"vmem"
)
if
(
vmem
.
isEmpty
&&
defaultVmem
.
nonEmpty
)
vmem
=
Some
(
defaultVmem
)
}
if
(
vmem
!=
null
)
jobResourceRequests
:+=
"h_vmem="
+
vmem
if
(
vmem
.
isDefined
)
jobResourceRequests
:+=
"h_vmem="
+
vmem
.
get
jobName
=
configName
+
":"
+
(
if
(
firstOutput
!=
null
)
firstOutput
.
getName
else
jobOutputFile
)
super
.
freezeFieldValues
()
...
...
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