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biopet.biopet
Commits
00034b55
Commit
00034b55
authored
Mar 10, 2016
by
Wai Yi Leung
Browse files
Merge branch 'fix-cutadapt' into 'develop'
Fixed default value Fixes #294 See merge request !347
parents
74cbd401
a83a6a3f
Changes
2
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public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala
View file @
00034b55
...
...
@@ -85,7 +85,7 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Su
var
trimN
:
Boolean
=
config
(
"trim_n"
,
default
=
false
)
var
prefix
:
Option
[
String
]
=
config
(
"prefix"
)
var
suffix
:
Option
[
String
]
=
config
(
"suffix"
)
var
stripSuffix
:
Set
[
String
]
=
config
(
"strip_suffix"
)
var
stripSuffix
:
Set
[
String
]
=
config
(
"strip_suffix"
,
default
=
Nil
)
var
lengthTag
:
Option
[
String
]
=
config
(
"length_tag"
)
/** Colorspace options */
...
...
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala
View file @
00034b55
...
...
@@ -48,7 +48,7 @@ class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetComman
override
def
defaultThreads
=
3
val
seqtk
=
new
SeqtkSeq
(
root
)
var
clip
:
Option
[
Cutadapt
]
=
None
var
clip
:
Option
[
Cutadapt
]
=
if
(!
flexiprep
.
skipClip
)
Some
(
new
Cutadapt
(
root
,
fastqc
))
else
None
var
trim
:
Option
[
Sickle
]
=
None
lazy
val
outputCommand
:
BiopetCommandLineFunction
=
if
(
compress
)
{
val
gzip
=
Gzip
(
root
)
...
...
@@ -101,7 +101,7 @@ class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetComman
clip
=
if
(!
flexiprep
.
skipClip
)
{
val
foundAdapters
=
fastqc
.
foundAdapters
.
map
(
_
.
seq
)
if
(
foundAdapters
.
nonEmpty
)
{
val
cutadapt
=
new
Cutadapt
(
root
,
fastqc
)
val
cutadapt
=
clip
.
getOrElse
(
new
Cutadapt
(
root
,
fastqc
)
)
cutadapt
.
fastqInput
=
seqtk
.
output
cutadapt
.
fastqOutput
=
new
File
(
output
.
getParentFile
,
input
.
getName
+
".cutadapt.fq"
)
cutadapt
.
statsOutput
=
new
File
(
flexiprep
.
outputDir
,
s
"${flexiprep.sampleId.getOrElse("
x
")}-${flexiprep.libId.getOrElse("
x
")}.$read.clip.stats"
)
...
...
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