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biopet.biopet
Commits
80e8742a
Commit
80e8742a
authored
Apr 06, 2017
by
Peter van 't Hof
Browse files
Only suply bqsr files when printreads is not executed
parent
cb17d470
Changes
1
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Inline
Side-by-side
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala
View file @
80e8742a
...
...
@@ -50,6 +50,8 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra
"unifiedgenotyper"
->
Map
(
"stand_call_conf"
->
30
,
"stand_emit_conf"
->
0
)
)
lazy
val
usePrintReads
:
Boolean
=
config
(
"use_printreads"
,
default
=
true
)
/** Method to make the variantcalling namespace of shiva */
def
makeVariantcalling
(
multisample
:
Boolean
,
sample
:
Option
[
String
]
=
None
,
...
...
@@ -94,7 +96,6 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra
logger
.
warn
(
"No Known site found, skipping base recalibration, file: "
+
inputBam
)
c
&&
br
.
knownSites
.
nonEmpty
}
lazy
val
usePrintReads
:
Boolean
=
if
(
useBaseRecalibration
)
config
(
"use_printreads"
,
default
=
true
)
else
false
lazy
val
useAnalyzeCovariates
:
Boolean
=
if
(
useBaseRecalibration
)
config
(
"use_analyze_covariates"
,
default
=
true
)
else
false
lazy
val
bqsrFile
:
Option
[
File
]
=
if
(
useBaseRecalibration
)
Some
(
createFile
(
"baserecal"
))
else
None
...
...
@@ -115,7 +116,6 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra
"library_variantcalling"
->
variantcalling
.
isDefined
,
"use_indel_realigner"
->
useIndelRealigner
,
"use_base_recalibration"
->
useBaseRecalibration
,
"use_print_reads"
->
usePrintReads
,
"useAnalyze_covariates"
->
useAnalyzeCovariates
)
...
...
@@ -242,7 +242,8 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra
multisampleVariantCalling
.
foreach
(
vc
=>
{
vc
.
outputDir
=
new
File
(
outputDir
,
"variantcalling"
)
vc
.
inputBams
=
samples
.
flatMap
{
case
(
sampleId
,
sample
)
=>
sample
.
preProcessBam
.
map
(
sampleId
->
_
)
}
vc
.
inputBqsrFiles
=
samples
.
flatMap
{
case
(
sampleId
,
sample
)
=>
sample
.
bqsrFile
.
map
(
sampleId
->
_
)
}
if
(!
usePrintReads
)
vc
.
inputBqsrFiles
=
samples
.
flatMap
{
case
(
sampleId
,
sample
)
=>
sample
.
bqsrFile
.
map
(
sampleId
->
_
)
}
add
(
vc
)
annotation
.
foreach
{
toucan
=>
...
...
@@ -272,7 +273,8 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra
"sv_calling"
->
svCalling
.
isDefined
,
"cnv_calling"
->
cnvCalling
.
isDefined
,
"regions_of_interest"
->
roiBedFiles
.
map
(
_
.
getName
.
stripSuffix
(
".bed"
)),
"amplicon_bed"
->
ampliconBedFile
.
map
(
_
.
getName
.
stripSuffix
(
".bed"
))
"amplicon_bed"
->
ampliconBedFile
.
map
(
_
.
getName
.
stripSuffix
(
".bed"
)),
"use_print_reads"
->
usePrintReads
)
/** Adds indel realignment jobs */
...
...
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