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biopet.biopet
Commits
d7e3156a
Commit
d7e3156a
authored
Nov 17, 2014
by
Peter van 't Hof
Browse files
Fix reference name
parent
ef67b6a8
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
View file @
d7e3156a
...
...
@@ -37,8 +37,8 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
gatkPipeline
.
biopetScript
addAll
(
gatkPipeline
.
functions
)
val
refVariants
=
addGenerateFasta
(
null
,
outputDir
+
"reference/"
,
"reference"
)
val
refVariantSnps
=
addGenerateFasta
(
null
,
outputDir
+
"reference/"
,
"reference"
,
snpsOnly
=
true
)
val
refVariants
=
addGenerateFasta
(
null
,
outputDir
+
"reference/"
,
outputName
=
"reference"
)
val
refVariantSnps
=
addGenerateFasta
(
null
,
outputDir
+
"reference/"
,
outputName
=
"reference"
,
snpsOnly
=
true
)
runSamplesJobs
()
...
...
@@ -105,8 +105,8 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
sampleOutput
.
libraries
=
runLibraryJobs
(
sampleConfig
)
sampleOutput
.
output
=
addGenerateFasta
(
sampleID
,
sampleDir
,
sampleID
)
sampleOutput
.
outputSnps
=
addGenerateFasta
(
sampleID
,
sampleDir
,
sampleID
,
snpsOnly
=
true
)
sampleOutput
.
output
=
addGenerateFasta
(
sampleID
,
sampleDir
)
sampleOutput
.
outputSnps
=
addGenerateFasta
(
sampleID
,
sampleDir
,
snpsOnly
=
true
)
return
sampleOutput
}
...
...
@@ -122,18 +122,18 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
return
libraryOutput
}
def
addGenerateFasta
(
sampleName
:
String
,
outputDir
:
String
,
outputName
:
String
,
def
addGenerateFasta
(
sampleName
:
String
,
outputDir
:
String
,
outputName
:
String
=
null
,
snpsOnly
:
Boolean
=
false
)
:
FastaOutput
=
{
val
bastyGenerateFasta
=
new
BastyGenerateFasta
(
this
)
bastyGenerateFasta
.
outputName
=
if
(
outputName
!=
null
)
outputName
else
sampleName
bastyGenerateFasta
.
inputVcf
=
gatkPipeline
.
multisampleVariantcalling
.
scriptOutput
.
finalVcfFile
if
(
gatkPipeline
.
samplesOutput
.
contains
(
sampleName
))
{
bastyGenerateFasta
.
bamFile
=
gatkPipeline
.
samplesOutput
(
sampleName
).
variantcalling
.
bamFiles
.
head
}
bastyGenerateFasta
.
outputVariants
=
outputDir
+
sample
Name
+
".variants"
+
(
if
(
snpsOnly
)
".snps_only"
else
""
)
+
".fasta"
bastyGenerateFasta
.
outputConsensus
=
outputDir
+
sample
Name
+
".consensus"
+
(
if
(
snpsOnly
)
".snps_only"
else
""
)
+
".fasta"
bastyGenerateFasta
.
outputConsensusVariants
=
outputDir
+
sample
Name
+
".consensus_variants"
+
(
if
(
snpsOnly
)
".snps_only"
else
""
)
+
".fasta"
bastyGenerateFasta
.
outputVariants
=
outputDir
+
bastyGenerateFasta
.
output
Name
+
".variants"
+
(
if
(
snpsOnly
)
".snps_only"
else
""
)
+
".fasta"
bastyGenerateFasta
.
outputConsensus
=
outputDir
+
bastyGenerateFasta
.
output
Name
+
".consensus"
+
(
if
(
snpsOnly
)
".snps_only"
else
""
)
+
".fasta"
bastyGenerateFasta
.
outputConsensusVariants
=
outputDir
+
bastyGenerateFasta
.
output
Name
+
".consensus_variants"
+
(
if
(
snpsOnly
)
".snps_only"
else
""
)
+
".fasta"
bastyGenerateFasta
.
sampleName
=
sampleName
bastyGenerateFasta
.
outputName
=
if
(
outputName
!=
null
)
outputName
else
sampleName
bastyGenerateFasta
.
snpsOnly
=
snpsOnly
add
(
bastyGenerateFasta
)
return
FastaOutput
(
bastyGenerateFasta
.
outputVariants
,
bastyGenerateFasta
.
outputConsensus
,
bastyGenerateFasta
.
outputConsensusVariants
)
...
...
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