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biopet.biopet
Commits
5de27e08
Commit
5de27e08
authored
Apr 14, 2017
by
Peter van 't Hof
Committed by
GitHub
Apr 14, 2017
Browse files
Merge branch 'develop' into fix-BIOPET-649
parents
988d35a6
8fa9668a
Changes
2
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flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
View file @
5de27e08
...
...
@@ -206,7 +206,9 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
val
foundAdapters
=
modules
.
get
(
"Adapter Content"
).
map
{
x
=>
val
header
=
x
.
lines
.
head
.
split
(
"\t"
).
tail
.
zipWithIndex
val
lines
=
x
.
lines
.
tail
.
map
(
_
.
split
(
"\t"
).
tail
)
val
found
=
header
.
filter
(
h
=>
lines
.
exists
(
x
=>
x
(
h
.
_2
).
toFloat
>
0
)).
map
(
_
.
_1
)
val
found
=
header
.
filter
(
h
=>
lines
.
exists
(
x
=>
x
(
h
.
_2
).
toFloat
>
adapterCutoff
))
.
map
(
_
.
_1
)
adapterSet
.
filter
(
x
=>
found
.
contains
(
x
.
name
))
}
...
...
@@ -214,6 +216,8 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
}
else
Set
()
}
val
adapterCutoff
:
Float
=
config
(
"adapter_cutoff"
,
default
=
0.001
)
@Output
private
var
outputFiles
:
List
[
File
]
=
Nil
...
...
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCallerGvcf.scala
View file @
5de27e08
...
...
@@ -36,11 +36,6 @@ class HaplotypeCallerGvcf(val parent: Configurable) extends Variantcaller {
override
def
fixedValues
=
Map
(
"haplotypecaller"
->
Map
(
"emitRefConfidence"
->
"GVCF"
))
override
def
defaults
=
Map
(
"haplotypecaller"
->
Map
(
"variant_index_type"
->
"LINEAR"
,
"variant_index_parameter"
->
128000
)
)
def
biopetScript
()
{
gVcfFiles
=
for
((
sample
,
inputBam
)
<-
inputBams
)
yield
{
val
hc
=
gatk
.
HaplotypeCaller
(
this
,
List
(
inputBam
),
new
File
(
outputDir
,
sample
+
".gvcf.vcf.gz"
))
...
...
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