Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Mirrors
biopet.biopet
Commits
b747862a
Commit
b747862a
authored
Dec 02, 2016
by
Peter van 't Hof
Browse files
Fixed small issue with dependency
parent
8242e484
Changes
2
Hide whitespace changes
Inline
Side-by-side
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
))
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment