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biopet.biopet
Commits
07c70b86
Commit
07c70b86
authored
Jun 16, 2015
by
Wai Yi Leung
Browse files
Code style change and avoid "empty" File definition
parent
9f572fe3
Changes
1
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Inline
Side-by-side
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTrait.scala
View file @
07c70b86
...
...
@@ -31,7 +31,7 @@ import nl.lumc.sasc.biopet.tools.FastqSync
import
org.broadinstitute.gatk.queue.QScript
import
org.broadinstitute.gatk.queue.function.QFunction
import
scala.collection.JavaConversions._
//import scala.language.reflectiveCalls
/**
* This is a trait for the Gears pipeline
* The ShivaTrait is used as template for this pipeline
...
...
@@ -246,23 +246,23 @@ trait GearsTrait extends MultiSampleQScript with SummaryQScript { qscript =>
private
def
makeCombineJob
(
inFiles
:
List
[
File
],
outFile
:
File
,
mergeSortOrder
:
String
=
"coordinate"
)
:
Ln
=
{
require
(
inFiles
.
nonEmpty
,
"At least one input files for combine job"
)
va
r
input
:
File
=
new
File
(
""
)
if
(
inFiles
.
size
==
1
)
{
input
=
inFiles
.
head
}
else
{
val
mergedBam
=
createFile
(
".merged.bam"
)
val
job
=
new
MergeSamFiles
(
qscript
)
job
.
in
put
=
inFiles
job
.
output
=
mergedBam
job
.
sortOrder
=
mergeSortOrder
input
=
job
.
output
va
l
input
:
File
=
{
if
(
inFiles
.
size
==
1
)
inFiles
.
head
else
{
val
mergedBam
=
createFile
(
".merged.bam"
)
val
job
=
new
MergeSamFiles
(
qscript
)
job
.
input
=
inFiles
job
.
out
put
=
mergedBam
job
.
sortOrder
=
mergeSortOrder
job
.
output
}
}
val
j
ob
=
new
Ln
(
qscript
)
j
ob
.
input
=
input
j
ob
.
output
=
outFile
j
ob
val
linkJ
ob
=
new
Ln
(
qscript
)
linkJ
ob
.
input
=
input
linkJ
ob
.
output
=
outFile
linkJ
ob
}
...
...
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