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biopet.biopet
Commits
6c521e70
Commit
6c521e70
authored
May 30, 2016
by
Peter van 't Hof
Browse files
Fixed adapter feeding
parent
0dc6aa4c
Changes
1
Hide whitespace changes
Inline
Side-by-side
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala
View file @
6c521e70
...
...
@@ -34,10 +34,10 @@ class Cutadapt(root: Configurable, fastqc: Fastqc) extends nl.lumc.sasc.biopet.e
adapter
++=
customAdaptersEnd
.
values
.
map
(
_
.
toString
)
val
customAdaptersFront
:
Map
[
String
,
Any
]
=
config
(
"custom_adapters_front"
,
default
=
Map
())
front
++=
customAdapters
End
.
values
.
map
(
_
.
toString
)
front
++=
customAdapters
Front
.
values
.
map
(
_
.
toString
)
val
customAdaptersAny
:
Map
[
String
,
Any
]
=
config
(
"custom_adapters_any"
,
default
=
Map
())
anywhere
++=
customAdapters
End
.
values
.
map
(
_
.
toString
)
anywhere
++=
customAdapters
Any
.
values
.
map
(
_
.
toString
)
/** Clipped adapter names from FastQC */
protected
def
seqToName
:
Map
[
String
,
String
]
=
{
...
...
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