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biopet.biopet
Commits
725ed53a
Commit
725ed53a
authored
Dec 22, 2016
by
Sander Bollen
Browse files
Merge branch 'fix-BIOPET-504' into 'develop'
Added output files Tiny fix See merge request !503
parents
409c5382
a1b738e0
Changes
2
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shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala
View file @
725ed53a
...
...
@@ -181,7 +181,7 @@ class Shiva(val root: Configurable) extends QScript with MultisampleMappingTrait
override
def
addMultiSampleJobs
()
=
{
super
.
addMultiSampleJobs
()
addAll
(
dbsnpVcfFile
.
map
(
Shiva
.
makeValidateVcfJobs
(
this
,
_
,
referenceFasta
())).
getOrElse
(
Nil
))
addAll
(
dbsnpVcfFile
.
map
(
Shiva
.
makeValidateVcfJobs
(
this
,
_
,
referenceFasta
()
,
new
File
(
outputDir
,
".validate"
)
)).
getOrElse
(
Nil
))
multisampleVariantCalling
.
foreach
(
vc
=>
{
vc
.
outputDir
=
new
File
(
outputDir
,
"variantcalling"
)
...
...
@@ -264,16 +264,18 @@ object Shiva extends PipelineCommand {
// This is used to only execute 1 validation per vcf file
private
var
validateVcfSeen
:
Set
[(
File
,
File
)]
=
Set
()
def
makeValidateVcfJobs
(
root
:
Configurable
,
vcfFile
:
File
,
referenceFile
:
File
)
:
List
[
QFunction
]
=
{
def
makeValidateVcfJobs
(
root
:
Configurable
,
vcfFile
:
File
,
referenceFile
:
File
,
outputDir
:
File
)
:
List
[
QFunction
]
=
{
if
(
validateVcfSeen
.
contains
((
vcfFile
,
referenceFile
)))
Nil
else
{
validateVcfSeen
++=
Set
((
vcfFile
,
referenceFile
))
val
validateVcf
=
new
ValidateVcf
(
root
)
validateVcf
.
inputVcf
=
vcfFile
validateVcf
.
reference
=
referenceFile
validateVcf
.
jobOutputFile
=
new
File
(
outputDir
,
vcfFile
.
getAbsolutePath
+
".validateVcf.out"
)
val
checkValidateVcf
=
new
CheckValidateVcf
checkValidateVcf
.
inputLogFile
=
validateVcf
.
jobOutputFile
checkValidateVcf
.
jobOutputFile
=
new
File
(
outputDir
,
vcfFile
.
getAbsolutePath
+
".checkValidateVcf.out"
)
List
(
validateVcf
,
checkValidateVcf
)
}
...
...
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcalling.scala
View file @
725ed53a
...
...
@@ -85,7 +85,7 @@ class ShivaVariantcalling(val root: Configurable) extends QScript
require
(
inputBams
.
nonEmpty
,
"No input bams found"
)
require
(
callers
.
nonEmpty
,
"must select at least 1 variantcaller, choices are: "
+
callersList
.
map
(
_
.
name
).
mkString
(
", "
))
addAll
(
dbsnpVcfFile
.
map
(
Shiva
.
makeValidateVcfJobs
(
this
,
_
,
referenceFasta
())).
getOrElse
(
Nil
))
addAll
(
dbsnpVcfFile
.
map
(
Shiva
.
makeValidateVcfJobs
(
this
,
_
,
referenceFasta
()
,
new
File
(
outputDir
,
".validate"
)
)).
getOrElse
(
Nil
))
val
cv
=
new
CombineVariants
(
qscript
)
cv
.
out
=
finalFile
...
...
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