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biopet.biopet
Commits
608c6349
Commit
608c6349
authored
Nov 07, 2016
by
Peter van 't Hof
Browse files
Fixed file names
parent
d0a06da2
Changes
1
Hide whitespace changes
Inline
Side-by-side
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Delly.scala
View file @
608c6349
...
...
@@ -34,11 +34,13 @@ class Delly(val root: Configurable) extends SvCaller {
val
catVariants
=
new
CatVariants
(
this
)
catVariants
.
outputFile
=
new
File
(
dellyDir
,
sample
+
".delly.vcf"
)
catVariants
.
isIntermediate
=
true
if
(
del
)
{
val
delly
=
new
DellyCaller
(
this
)
delly
.
input
=
bamFile
delly
.
analysistype
=
"DEL"
delly
.
isIntermediate
=
true
delly
.
outputvcf
=
new
File
(
dellyDir
,
sample
+
".delly.del.vcf"
)
add
(
delly
)
...
...
@@ -48,6 +50,7 @@ class Delly(val root: Configurable) extends SvCaller {
val
delly
=
new
DellyCaller
(
this
)
delly
.
input
=
bamFile
delly
.
analysistype
=
"DUP"
delly
.
isIntermediate
=
true
delly
.
outputvcf
=
new
File
(
dellyDir
,
sample
+
".delly.dup.vcf"
)
add
(
delly
)
...
...
@@ -57,6 +60,7 @@ class Delly(val root: Configurable) extends SvCaller {
val
delly
=
new
DellyCaller
(
this
)
delly
.
input
=
bamFile
delly
.
analysistype
=
"INV"
delly
.
isIntermediate
=
true
delly
.
outputvcf
=
new
File
(
dellyDir
,
sample
+
".delly.inv.vcf"
)
add
(
delly
)
...
...
@@ -66,6 +70,7 @@ class Delly(val root: Configurable) extends SvCaller {
val
delly
=
new
DellyCaller
(
this
)
delly
.
input
=
bamFile
delly
.
analysistype
=
"TRA"
delly
.
isIntermediate
=
true
delly
.
outputvcf
=
new
File
(
dellyDir
,
sample
+
".delly.tra.vcf"
)
add
(
delly
)
...
...
@@ -78,7 +83,7 @@ class Delly(val root: Configurable) extends SvCaller {
val
compressedVCF
=
new
SortVcf
(
this
)
compressedVCF
.
input
=
catVariants
.
outputFile
compressedVCF
.
output
=
catVariants
+
".gz"
compressedVCF
.
output
=
catVariants
.
outputFile
+
".gz"
add
(
compressedVCF
)
addVCF
(
sample
,
compressedVCF
.
output
)
...
...
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