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biopet.biopet
Commits
6173485e
Commit
6173485e
authored
May 11, 2016
by
Wai Yi Leung
Browse files
Use samplename_suffix to change the sample name
parent
ef811002
Changes
4
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shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Breakdancer.scala
View file @
6173485e
...
...
@@ -33,7 +33,7 @@ class Breakdancer(val root: Configurable) extends SvCaller {
val
bdcfg
=
BreakdancerConfig
(
this
,
bamFile
,
new
File
(
breakdancerSampleDir
,
sample
+
".breakdancer.cfg"
))
val
breakdancer
=
BreakdancerCaller
(
this
,
bdcfg
.
output
,
new
File
(
breakdancerSampleDir
,
sample
+
".breakdancer.tsv"
))
val
bdvcf
=
BreakdancerVCF
(
this
,
breakdancer
.
output
,
new
File
(
breakdancerSampleDir
,
sample
+
".breakdancer.vcf"
),
sample
=
sample
+
"_bd"
)
sample
=
sample
+
sampleNameSuffix
)
val
compressedVCF
=
new
SortVcf
(
this
)
compressedVCF
.
input
=
bdvcf
.
output
...
...
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Clever.scala
View file @
6173485e
...
...
@@ -33,7 +33,7 @@ class Clever(val root: Configurable) extends SvCaller {
val
cleverVCF
=
new
CleverFixVCF
(
this
)
cleverVCF
.
input
=
clever
.
outputvcf
cleverVCF
.
output
=
new
File
(
cleverDir
,
s
".${sample}.clever.vcf"
)
cleverVCF
.
sampleName
=
sample
+
"_cl"
cleverVCF
.
sampleName
=
sample
+
sampleNameSuffix
cleverVCF
.
isIntermediate
=
true
add
(
cleverVCF
)
...
...
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala
View file @
6173485e
...
...
@@ -40,7 +40,7 @@ class Pindel(val root: Configurable) extends SvCaller {
val
configFile
:
File
=
new
File
(
pindelDir
,
sample
+
".pindel.cfg"
)
val
cfg
=
new
PindelConfig
(
this
)
cfg
.
input
=
bamFile
cfg
.
sampleName
=
sample
+
"_pd"
// pindel s
uffix
cfg
.
sampleName
=
sample
+
sampleNameS
uffix
cfg
.
output
=
configFile
add
(
cfg
)
...
...
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/SvCaller.scala
View file @
6173485e
...
...
@@ -30,6 +30,8 @@ trait SvCaller extends QScript with BiopetQScript with Reference {
var
inputBams
:
Map
[
String
,
File
]
=
Map
.
empty
val
sampleNameSuffix
:
String
=
config
(
"samplename_suffix"
,
default
=
""
)
def
outputVCF
(
sample
:
String
)
:
Option
[
File
]
=
{
outputVCFs
.
get
(
sample
)
match
{
case
Some
(
file
)
=>
Some
(
file
)
...
...
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