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biopet.biopet
Commits
d125c2f3
Commit
d125c2f3
authored
Feb 16, 2015
by
Peter van 't Hof
Browse files
Fix on index ln methods
parent
d8464ae3
Changes
2
Hide whitespace changes
Inline
Side-by-side
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
View file @
d125c2f3
...
...
@@ -66,12 +66,13 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
else
if
(
files
.
size
==
1
)
{
val
bamFile
=
new
File
(
outputDir
,
files
.
head
.
getName
)
if
(
bamFile
!=
files
.
head
)
{
val
oldIndex
:
File
=
files
.
head
.
getAbsolutePath
.
stripSuffix
(
".bam"
)
+
".bai"
val
newIndex
:
File
=
bamFile
.
getAbsolutePath
.
stripSuffix
(
".bam"
)
+
".bai"
add
(
Ln
(
this
,
oldIndex
,
newIndex
))
val
oldIndex
:
File
=
new
File
(
files
.
head
.
getAbsolutePath
.
stripSuffix
(
".bam"
)
+
".bai"
)
val
newIndex
:
File
=
swapExt
(
outputDir
,
bamFile
,
".bam"
,
".bai"
)
val
baiLn
=
Ln
(
this
,
oldIndex
,
newIndex
)
add
(
baiLn
)
val
bamLn
=
Ln
(
this
,
files
.
head
,
bamFile
)
bamLn
.
deps
:+=
newIndex
bamLn
.
deps
:+=
baiLn
.
out
add
(
bamLn
)
}
List
(
bamFile
)
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala
View file @
d125c2f3
...
...
@@ -30,7 +30,7 @@ class Ln(val root: Configurable) extends InProcessFunction with Configurable {
@Output
(
doc
=
"Link destination"
)
var
out
:
File
=
_
@
Output
@
Input
(
required
=
false
)
var
deps
:
List
[
File
]
=
Nil
var
relative
:
Boolean
=
true
...
...
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