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biopet.biopet
Commits
b747862a
Commit
b747862a
authored
Dec 02, 2016
by
Peter van 't Hof
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Fixed small issue with dependency
parent
8242e484
Changes
2
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4 additions
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4 deletions
+4
-4
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala
...in/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala
+1
-1
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
...scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
+3
-3
No files found.
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala
View file @
b747862a
...
...
@@ -141,7 +141,7 @@ object WriteDependencies extends Logging with Configurable {
val
jobsDeps
=
jobs
.
map
(
x
=>
x
.
_1
->
(
x
.
_2
(
"depends_on_jobs"
)
match
{
case
l
:
List
[
_
]
=>
l
.
map
(
_
.
toString
)
case
_
=>
throw
new
IllegalStateException
(
"Value 'depends_on_jobs' is not a list"
)
case
_
=>
throw
new
IllegalStateException
(
"Value 'depends_on_jobs' is not a list"
)
}))
val
jobsWriter
=
new
PrintWriter
(
new
File
(
outputDir
,
s
"$prefix.jobs.json"
))
jobsWriter
.
println
(
ConfigUtils
.
mapToJson
(
jobsDeps
).
spaces2
)
...
...
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
View file @
b747862a
...
...
@@ -57,12 +57,12 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
for
(
q
<-
qscript
.
summaryQScripts
)
deps
:+=
q
.
summaryFile
for
((
_
,
l
)
<-
qscript
.
summarizables
;
s
<-
l
)
s
match
{
case
f
:
QFunction
=>
try
{
case
f
:
QFunction
if
qscript.functions.contains
(
f
)
=>
try
{
deps
:+=
f
.
firstOutput
}
catch
{
}
catch
{
case
e
:
NullPointerException
=>
logger
.
warn
(
"Queue values are not init"
)
}
case
_
=>
case
_
=>
}
jobOutputFile
=
new
File
(
out
.
getParentFile
,
".%s.%s.out"
.
format
(
out
.
getName
,
analysisName
))
...
...
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