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biopet.biopet
Commits
dd813f33
Commit
dd813f33
authored
Mar 09, 2017
by
Peter van 't Hof
Browse files
Fix format
parent
02b8fdad
Changes
1
Hide whitespace changes
Inline
Side-by-side
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala
View file @
dd813f33
...
...
@@ -123,7 +123,7 @@ class QcCommand(val parent: Configurable, val fastqc: Fastqc, val read: String)
Some
(
cutadapt
)
}
else
None
case
(
None
,
_
)
=>
None
case
(
Some
(
c
),
_
)
=>
case
(
Some
(
c
),
_
)
=>
c
.
fastqInput
=
seqtk
.
output
c
.
fastqOutput
=
new
File
(
output
.
getParentFile
,
input
.
getName
+
".cutadapt.fq"
)
c
.
statsOutput
=
new
File
(
flexiprep
.
outputDir
,
s
"${flexiprep.sampleId.getOrElse("
x
")}-${flexiprep.libId.getOrElse("
x
")}.$read.clip.stats"
)
...
...
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