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biopet.biopet
Commits
df582f1a
Commit
df582f1a
authored
Jul 25, 2017
by
Peter van 't Hof
Committed by
GitHub
Jul 25, 2017
Browse files
Merge pull request #167 from biopet/fix-BIOPET-755
Small fixes for Gentrap
parents
23bdc5b2
931771fe
Changes
4
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biopet-core/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/RefflatStats.scala
View file @
df582f1a
...
...
@@ -44,6 +44,8 @@ class RefflatStats(val parent: Configurable) extends ToolCommandFunction with Re
@Output
(
required
=
true
)
var
intronOutput
:
File
=
_
override
def
defaultCoreMemory
=
5.0
override
def
beforeGraph
()
:
Unit
=
{
super
.
beforeGraph
()
if
(
reference
==
null
)
reference
=
referenceFasta
()
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala
View file @
df582f1a
...
...
@@ -80,8 +80,13 @@ class Star(val parent: Configurable)
var
genomeSAindexNbases
:
Option
[
Long
]
=
config
(
"genomesaindexnbases"
)
var
genomeSAsparseD
:
Option
[
Int
]
=
config
(
"genomesasparsed"
)
private
def
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 @
df582f1a
...
...
@@ -31,16 +31,17 @@ object ValidateAnnotation extends ToolCommand {
gtfFiles
:
List
[
File
]
=
Nil
)
class
OptParser
extends
AbstractOptParser
[
Args
](
commandName
)
{
opt
[
File
](
'r'
,
"refflatFile"
)
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"
)
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"
)
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"
)
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"
}
...
...
gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/Measurement.scala
View file @
df582f1a
...
...
@@ -54,7 +54,7 @@ trait Measurement extends SummaryQScript with Reference { qscript: QScript =>
require
(
bamFiles
.
nonEmpty
)
}
lazy
val
mergeCountFiles
:
Boolean
=
config
(
"merge_count_files"
,
default
=
true
)
lazy
val
mergeCountFiles
:
Boolean
=
config
(
"merge_count_files"
,
default
=
bamFiles
.
size
>
1
)
private
var
extraSummaryFiles
:
Map
[
String
,
File
]
=
Map
()
...
...
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