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biopet.biopet
Commits
cd175ab7
Commit
cd175ab7
authored
Jun 26, 2014
by
Peter van 't Hof
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Added config report
parent
71a74799
Changes
1
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10 additions
and
2 deletions
+10
-2
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
...c/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+10
-2
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biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
View file @
cd175ab7
package
nl.lumc.sasc.biopet.core
//import org.broadinstitute.sting.queue.QScript
import
java.io.File
import
java.io.PrintWriter
import
nl.lumc.sasc.biopet.core.config._
import
org.broadinstitute.sting.commandline._
import
org.broadinstitute.sting.queue.QSettings
import
org.broadinstitute.sting.queue.function.QFunction
trait
BiopetQScript
extends
Configurable
{
...
...
@@ -15,13 +16,20 @@ trait BiopetQScript extends Configurable {
var
outputFiles
:
Map
[
String
,
File
]
=
Map
()
var
qSettings
:
QSettings
def
init
def
biopetScript
final
def
script
()
{
init
biopetScript
// TODO: Config report
val
configReport
=
globalConfig
.
getReport
val
configReportFile
=
new
File
(
outputDir
+
qSettings
.
runName
+
".configreport.txt"
)
val
writer
=
new
PrintWriter
(
configReportFile
)
writer
.
write
(
configReport
)
writer
.
close
()
for
(
line
<-
configReport
.
split
(
"\n"
))
logger
.
debug
(
line
)
}
def
add
(
functions
:
QFunction*
)
// Gets implemeted at org.broadinstitute.sting.queue.QScript
...
...
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