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biopet.biopet
Commits
dd80f227
Commit
dd80f227
authored
Nov 26, 2016
by
Peter van 't Hof
Browse files
Fix compile error
parent
d609b6cb
Changes
2
Hide whitespace changes
Inline
Side-by-side
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala
View file @
dd80f227
...
...
@@ -14,12 +14,12 @@
*/
package
nl.lumc.sasc.biopet.core
import
java.io.
{
File
,
PrintWriter
}
import
java.io.
{
File
,
PrintWriter
}
import
nl.lumc.sasc.biopet.core.summary.WriteSummary
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.utils.
{
ConfigUtils
,
Logging
}
import
org.broadinstitute.gatk.queue.function.
{
CommandLineFunction
,
QFunction
}
import
nl.lumc.sasc.biopet.utils.
{
ConfigUtils
,
Logging
}
import
org.broadinstitute.gatk.queue.function.
{
CommandLineFunction
,
QFunction
}
import
scala.collection.mutable
import
scala.collection.mutable.ListBuffer
...
...
@@ -127,8 +127,9 @@ object WriteDependencies extends Logging with Configurable {
}.
toIterator
.
toMap
mainJobsFile
.
foreach
{
file
=>
val
mainJobs
=
jobs
.
filter
(
_
.
_2
(
"main_job"
)
==
true
).
map
{
case
(
name
,
job
)
=>
name
->
(
job
+
(
"depends_on_jobs"
->
getMainDependencies
(
name
,
jobs
)))
val
mainJobs
=
jobs
.
filter
(
_
.
_2
(
"main_job"
)
==
true
).
map
{
case
(
name
,
job
)
=>
name
->
(
job
+
(
"depends_on_jobs"
->
getMainDependencies
(
name
,
jobs
)))
}
val
writer
=
new
PrintWriter
(
file
)
...
...
@@ -150,7 +151,7 @@ object WriteDependencies extends Logging with Configurable {
def
getMainDependencies
(
jobName
:
String
,
jobsMap
:
Map
[
String
,
Map
[
String
,
Any
]])
:
List
[
String
]
=
{
val
job
=
jobsMap
(
jobName
)
val
dependencies
=
job
(
"depends_on_jobs"
)
match
{
case
l
:
List
[
_
]
=>
l
.
map
(
_
.
toString
)
case
l
:
List
[
_
]
=>
l
.
map
(
_
.
toString
)
}
dependencies
.
flatMap
{
dep
=>
jobsMap
(
dep
)(
"main_job"
)
match
{
...
...
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsCentrifuge.scala
View file @
dd80f227
...
...
@@ -52,7 +52,7 @@ class GearsCentrifuge(val root: Configurable) extends QScript with SummaryQScrip
centrifugeKreport
.
centrifugeOutputFiles
:+=
fifo
centrifugeKreport
.
output
=
new
File
(
outputDir
,
s
"$outputName.$name.kreport"
)
centrifugeKreport
.
onlyUnique
=
unique
val
pipe
=
new
BiopetFifoPipe
(
this
,
List
(
centrifugeKreport
,
Zcat
(
this
,
centrifugeOutput
,
fifo
)))
)
val
pipe
=
new
BiopetFifoPipe
(
this
,
List
(
centrifugeKreport
,
Zcat
(
this
,
centrifugeOutput
,
fifo
)))
pipe
.
mainFunction
=
true
add
(
pipe
)
...
...
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