Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Mirrors
biopet.biopet
Commits
8a6f4376
Commit
8a6f4376
authored
Mar 14, 2016
by
Peter van 't Hof
Browse files
Fix free vars
parent
d65a12e7
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala
View file @
8a6f4376
...
...
@@ -41,22 +41,22 @@ class Freebayes(val root: Configurable) extends BiopetCommandLineFunction with R
var
bamList
:
Option
[
File
]
=
config
(
"bam_list"
)
@Input
(
required
=
false
)
var
targets
:
Option
[
File
]
=
config
(
"targets"
)
var
targets
:
Option
[
File
]
=
config
(
"targets"
,
freeVar
=
false
)
@Input
(
required
=
false
)
var
samples
:
Option
[
File
]
=
config
(
"samples"
)
var
samples
:
Option
[
File
]
=
config
(
"samples"
,
freeVar
=
false
)
@Input
(
required
=
false
)
var
populations
:
Option
[
File
]
=
config
(
"populations"
)
var
populations
:
Option
[
File
]
=
config
(
"populations"
,
freeVar
=
false
)
@Input
(
required
=
false
)
var
cnvMap
:
Option
[
File
]
=
config
(
"cnv_map"
)
var
cnvMap
:
Option
[
File
]
=
config
(
"cnv_map"
,
freeVar
=
false
)
@Input
(
required
=
false
)
var
trace
:
Option
[
File
]
=
config
(
"trace"
)
var
trace
:
Option
[
File
]
=
config
(
"trace"
,
freeVar
=
false
)
@Input
(
required
=
false
)
var
failedAlleles
:
Option
[
File
]
=
config
(
"failed_alleles"
)
var
failedAlleles
:
Option
[
File
]
=
config
(
"failed_alleles"
,
freeVar
=
false
)
@Input
(
required
=
false
)
var
observationBias
:
Option
[
File
]
=
config
(
"observation_bias"
)
...
...
@@ -65,14 +65,14 @@ class Freebayes(val root: Configurable) extends BiopetCommandLineFunction with R
var
contaminationEstimates
:
Option
[
File
]
=
config
(
"contamination_estimates"
)
@Input
(
required
=
false
)
var
variantInput
:
Option
[
File
]
=
config
(
"variant_input"
)
var
variantInput
:
Option
[
File
]
=
config
(
"variant_input"
,
freeVar
=
false
)
@Input
(
required
=
false
)
var
haplotypeBasisAlleles
:
Option
[
File
]
=
config
(
"haplotype_basis_alleles"
)
var
haplotypeBasisAlleles
:
Option
[
File
]
=
config
(
"haplotype_basis_alleles"
,
freeVar
=
false
)
var
pvar
:
Option
[
Int
]
=
config
(
"pvar"
)
var
theta
:
Option
[
Int
]
=
config
(
"theta"
)
var
ploidy
:
Option
[
Int
]
=
config
(
"ploidy"
)
var
pvar
:
Option
[
Int
]
=
config
(
"pvar"
,
freeVar
=
false
)
var
theta
:
Option
[
Int
]
=
config
(
"theta"
,
freeVar
=
false
)
var
ploidy
:
Option
[
Int
]
=
config
(
"ploidy"
,
freeVar
=
false
)
var
useBestNAlleles
:
Option
[
Int
]
=
config
(
"use_best_n_alleles"
)
var
maxComplexGap
:
Option
[
Int
]
=
config
(
"max_complex_gap"
)
var
minRepeatSize
:
Option
[
Int
]
=
config
(
"min_repeat_size"
)
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment