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biopet.biopet
Commits
532f837c
Commit
532f837c
authored
Jul 25, 2017
by
pjvan_thof
Browse files
Adding default gtf file to STAR
parent
250e63be
Changes
2
Hide whitespace changes
Inline
Side-by-side
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
View file @
532f837c
...
...
@@ -80,8 +80,13 @@ class Star(val parent: Configurable)
var
genomeSAindexNbases
:
Option
[
Long
]
=
config
(
"genomesaindexnbases"
)
var
genomeSAsparseD
:
Option
[
Int
]
=
config
(
"genomesasparsed"
)
val
defaultGtf
:
Option
[
File
]
=
config
(
"annotation_gtf"
)
@Input
(
required
=
false
)
var
sjdbGTFfile
:
Option
[
File
]
=
config
(
"sjdbgtfile"
)
var
sjdbGTFfile
:
Option
[
File
]
=
defaultGtf
match
{
case
Some
(
file
)
=>
config
(
"sjdbgtfile"
,
default
=
file
)
case
_
=>
config
(
"sjdbgtfile"
)
}
var
sjdbGTFchrPrefix
:
Option
[
String
]
=
config
(
"sjdbgtfchrprefix"
)
var
sjdbGTFfeatureExon
:
Option
[
String
]
=
config
(
"sjdbgtffeatureexon"
)
var
sjdbGTFtagExonParentTranscript
:
Option
[
String
]
=
config
(
"sjdbgtftagexonparenttranscript"
)
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/ValidateAnnotation.scala
View file @
532f837c
...
...
@@ -31,16 +31,17 @@ object ValidateAnnotation extends ToolCommand {
gtfFiles
:
List
[
File
]
=
Nil
)
class
OptParser
extends
AbstractOptParser
[
Args
](
commandName
)
{
opt
[
File
](
'r'
,
"refflatFile"
)
unbounded
()
maxOccurs
1
valueName
"<file>"
action
{
(
x
,
c
)
=>
opt
[
File
](
'r'
,
"refflatFile"
)
unbounded
()
maxOccurs
1
valueName
"<file>"
action
{
(
x
,
c
)
=>
c
.
copy
(
refflatFile
=
Some
(
x
))
}
text
"Refflat file to check"
opt
[
File
](
'g'
,
"gtfFile"
)
unbounded
()
valueName
"<file>"
action
{
(
x
,
c
)
=>
opt
[
File
](
'g'
,
"gtfFile"
)
unbounded
()
valueName
"<file>"
action
{
(
x
,
c
)
=>
c
.
copy
(
gtfFiles
=
x
::
c
.
gtfFiles
)
}
text
"Gtf files to check"
opt
[
File
](
'R'
,
"reference"
)
unbounded
()
required
()
maxOccurs
1
valueName
"<file>"
action
{
(
x
,
c
)
=>
c
.
copy
(
reference
=
x
)
opt
[
File
](
'R'
,
"reference"
)
unbounded
()
required
()
maxOccurs
1
valueName
"<file>"
action
{
(
x
,
c
)
=>
c
.
copy
(
reference
=
x
)
}
text
"Reference fasta to check vcf file against"
opt
[
Unit
](
"disableFail"
)
unbounded
()
maxOccurs
1
valueName
"<file>"
action
{
(
_
,
c
)
=>
opt
[
Unit
](
"disableFail"
)
unbounded
()
maxOccurs
1
valueName
"<file>"
action
{
(
_
,
c
)
=>
c
.
copy
(
failOnError
=
false
)
}
text
"Do not fail on error. The tool will still exit when encountering an error, but will do so with exit code 0"
}
...
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