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biopet.biopet
Commits
ab50cd4f
Commit
ab50cd4f
authored
Mar 04, 2015
by
Peter van 't Hof
Browse files
Switch Basty to Shiva
parent
04b80825
Changes
1
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protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
View file @
ab50cd4f
...
...
@@ -11,6 +11,7 @@ import nl.lumc.sasc.biopet.core.PipelineCommand
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.extensions.
{
RunGubbins
,
Cat
,
Raxml
}
import
nl.lumc.sasc.biopet.pipelines.gatk.GatkPipeline
import
nl.lumc.sasc.biopet.pipelines.shiva.Shiva
import
nl.lumc.sasc.biopet.tools.BastyGenerateFasta
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
org.broadinstitute.gatk.queue.QScript
...
...
@@ -21,15 +22,14 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
case
class
FastaOutput
(
variants
:
File
,
consensus
:
File
,
consensusVariants
:
File
)
def
variantcallers
=
List
(
"freebayes"
)
override
def
defaults
=
ConfigUtils
.
mergeMaps
(
Map
(
"ploidy"
->
1
,
"use_haplotypecaller"
->
false
,
"use_unifiedgenotyper"
->
true
,
"joint_variantcalling"
->
true
,
"single_sample_calling"
->
false
"variantscallers"
->
variantcallers
),
super
.
defaults
)
va
r
gatkPipeline
:
GatkPipeline
=
new
GatkPipeline
(
qscript
)
va
l
shiva
=
new
Shiva
(
qscript
)
def
summaryFile
:
File
=
new
File
(
outputDir
,
"Sage.summary.json"
)
...
...
@@ -69,14 +69,14 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
}
def
init
()
{
gatkPipeline
.
outputDir
=
outputDir
gatkPipeline
.
init
shiva
.
outputDir
=
outputDir
shiva
.
init
}
def
biopetScript
()
{
gatkPipeline
.
biopetScript
addAll
(
gatkPipeline
.
functions
)
addSummaryQScript
(
gatkPipeline
)
shiva
.
biopetScript
addAll
(
shiva
.
functions
)
addSummaryQScript
(
shiva
)
addSamplesJobs
()
}
...
...
@@ -168,9 +168,9 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
snpsOnly
:
Boolean
=
false
)
:
FastaOutput
=
{
val
bastyGenerateFasta
=
new
BastyGenerateFasta
(
this
)
bastyGenerateFasta
.
outputName
=
if
(
outputName
!=
null
)
outputName
else
sampleName
bastyGenerateFasta
.
inputVcf
=
gatkPipeline
.
multisampleV
ariantcalling
.
scriptOutpu
t
.
final
Vcf
File
if
(
gatkPipeline
.
samples
.
contains
(
sampleName
))
{
bastyGenerateFasta
.
bamFile
=
gatkPipeline
.
samples
(
sampleName
).
gatkVariantcalling
.
scriptOutput
.
bamFiles
.
head
bastyGenerateFasta
.
inputVcf
=
shiva
.
v
ariantcalling
.
ge
t
.
finalFile
if
(
shiva
.
samples
.
contains
(
sampleName
))
{
bastyGenerateFasta
.
bamFile
=
shiva
.
samples
(
sampleName
).
preProcessBam
.
get
}
bastyGenerateFasta
.
outputVariants
=
new
File
(
outputDir
,
bastyGenerateFasta
.
outputName
+
".variants"
+
(
if
(
snpsOnly
)
".snps_only"
else
""
)
+
".fasta"
)
bastyGenerateFasta
.
outputConsensus
=
new
File
(
outputDir
,
bastyGenerateFasta
.
outputName
+
".consensus"
+
(
if
(
snpsOnly
)
".snps_only"
else
""
)
+
".fasta"
)
...
...
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