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biopet.biopet
Commits
7d179c4e
Commit
7d179c4e
authored
Apr 20, 2017
by
Peter van 't Hof
Committed by
GitHub
Apr 20, 2017
Browse files
Merge pull request #84 from biopet/fix-BIOPET-659
Fixing scatter jobs
parents
11260a4c
190b7590
Changes
2
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biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
View file @
7d179c4e
...
...
@@ -54,7 +54,7 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
}
writer
.
println
(
"set -eubf"
)
writer
.
println
(
"set -o pipefail"
)
writer
.
println
(
this
.
commandLine
)
writer
.
println
(
lines
.
mkString
(
"\n"
)
)
jobDelayTime
.
foreach
(
x
=>
writer
.
println
(
s
"sleep $x"
))
writer
.
close
()
}
...
...
@@ -99,7 +99,13 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
beforeGraph
()
internalBeforeGraph
()
if
(
jobOutputFile
!=
null
)
this
.
commandDirectory
=
this
.
jobOutputFile
.
getAbsoluteFile
.
getParentFile
if
(
jobOutputFile
!=
null
)
{
this
.
commandDirectory
=
this
.
jobOutputFile
.
getAbsoluteFile
.
getParentFile
this
match
{
case
s
:
ScatterGatherableFunction
=>
s
.
scatterGatherDirectory
=
new
File
(
this
.
commandDirectory
,
".scatter"
)
case
_
=>
}
}
super
.
freezeFieldValues
()
}
...
...
gatk
@
677d7574
Compare
86ee6287
...
677d7574
Subproject commit
86ee6287b66562544e701f9ffa7cbbf0af9f3eba
Subproject commit
677d757419f515779766b10149b0e92eff71e5b2
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