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biopet.biopet
Commits
12da6e96
Commit
12da6e96
authored
Jul 16, 2015
by
Sander van der Zeeuw
Browse files
Fix symlinking of the final bai file
parent
e88b3068
Changes
2
Hide whitespace changes
Inline
Side-by-side
public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
View file @
12da6e96
...
...
@@ -720,12 +720,12 @@ class Gentrap(val root: Configurable) extends QScript
if
(
inFiles
.
size
==
1
)
{
val
jobBam
=
new
Ln
(
qscript
)
jobBam
.
input
=
inFiles
.
head
jobBam
.
input
=
inFiles
.
head
.
getAbsoluteFile
jobBam
.
output
=
outFile
val
jobIdx
=
new
Ln
(
qscript
)
jobIdx
.
input
=
swapExt
(
jobBam
.
input
,
".bam"
,
".bai"
)
jobIdx
.
output
=
swapExt
(
jobBam
.
output
,
".bam"
,
".bai"
)
jobIdx
.
input
=
swapExt
(
libraries
.
values
.
head
.
libDir
,
jobBam
.
input
,
".bam"
,
".bai"
)
jobIdx
.
output
=
swapExt
(
sampleDir
,
jobBam
.
output
,
".bam"
,
".bai"
)
CombineFileJobSet
(
jobBam
,
Some
(
jobIdx
))
}
else
{
...
...
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
12da6e96
...
...
@@ -268,7 +268,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
add
(
Ln
(
this
,
swapExt
(
outputDir
,
bamFile
,
".bam"
,
".bai"
),
swapExt
(
outputDir
,
finalBamFile
,
".bam"
,
".bai"
)))
add
(
Ln
(
this
,
bamFile
,
finalBamFile
))
outputFiles
+=
(
"finalBamFile"
->
bam
File
)
outputFiles
+=
(
"finalBamFile"
->
finalBamFile
.
getAbsolute
File
)
if
(
config
(
"generate_wig"
,
default
=
false
).
asBoolean
)
addAll
(
Bam2Wig
(
this
,
finalBamFile
).
functions
)
...
...
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