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Mirrors
biopet.biopet
Commits
34a00edf
Commit
34a00edf
authored
Feb 10, 2015
by
Sander Bollen
Browse files
Fixing config values
parent
9dbde99d
Changes
3
Hide whitespace changes
Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
View file @
34a00edf
...
...
@@ -24,98 +24,98 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
override
def
versionCommand
=
executable
+
" "
+
vep_script
+
" --help"
//Boolean vars
var
v
:
Boolean
=
config
(
"v"
)
var
q
:
Boolean
=
config
(
"q"
)
var
offline
:
Boolean
=
config
(
"offline"
)
var
no_progress
:
Boolean
=
config
(
"no_progress"
)
var
everything
:
Boolean
=
config
(
"everything"
)
var
force
:
Boolean
=
config
(
"force"
)
var
no_stats
:
Boolean
=
config
(
"no_stats"
)
var
stats_text
:
Boolean
=
config
(
"stats_text"
)
var
html
:
Boolean
=
config
(
"html"
)
var
cache
:
Boolean
=
config
(
"cache"
)
var
humdiv
:
Boolean
=
config
(
"humdiv"
)
var
regulatory
:
Boolean
=
config
(
"regulatory"
)
var
cell_type
:
Boolean
=
config
(
"cell_type"
)
var
phased
:
Boolean
=
config
(
"phased"
)
var
allele_number
:
Boolean
=
config
(
"allele_number"
)
var
numbers
:
Boolean
=
config
(
"numbers"
)
var
domains
:
Boolean
=
config
(
"domains"
)
var
no_escape
:
Boolean
=
config
(
"no_escape"
)
var
hgvs
:
Boolean
=
config
(
"hgvs"
)
var
protein
:
Boolean
=
config
(
"protein"
)
var
symbol
:
Boolean
=
config
(
"symbol"
)
var
ccds
:
Boolean
=
config
(
"ccds"
)
var
uniprot
:
Boolean
=
config
(
"uniprot"
)
var
tsl
:
Boolean
=
config
(
"tsl"
)
var
canonical
:
Boolean
=
config
(
"canonical"
)
var
biotype
:
Boolean
=
config
(
"biotype"
)
var
xref_refseq
:
Boolean
=
config
(
"xref_refseq"
)
var
check_existing
:
Boolean
=
config
(
"check_existing"
)
var
check_alleles
:
Boolean
=
config
(
"check_alleles"
)
var
check_svs
:
Boolean
=
config
(
"svs"
)
var
gmaf
:
Boolean
=
config
(
"gmaf"
)
var
maf_1kg
:
Boolean
=
config
(
"maf_1kg"
)
var
maf_esp
:
Boolean
=
config
(
"maf_esp"
)
var
old_map
:
Boolean
=
config
(
"old_maf"
)
var
pubmed
:
Boolean
=
config
(
"pubmed"
)
var
failed
:
Boolean
=
config
(
"failed"
)
var
v
:
Boolean
=
config
(
"v"
,
default
=
true
)
var
q
:
Boolean
=
config
(
"q"
,
default
=
false
)
var
offline
:
Boolean
=
config
(
"offline"
,
default
=
false
)
var
no_progress
:
Boolean
=
config
(
"no_progress"
,
default
=
false
)
var
everything
:
Boolean
=
config
(
"everything"
,
default
=
true
)
var
force
:
Boolean
=
config
(
"force"
,
default
=
false
)
var
no_stats
:
Boolean
=
config
(
"no_stats"
,
default
=
false
)
var
stats_text
:
Boolean
=
config
(
"stats_text"
,
default
=
false
)
var
html
:
Boolean
=
config
(
"html"
,
default
=
false
)
var
cache
:
Boolean
=
config
(
"cache"
,
default
=
false
)
var
humdiv
:
Boolean
=
config
(
"humdiv"
,
default
=
false
)
var
regulatory
:
Boolean
=
config
(
"regulatory"
,
default
=
false
)
var
cell_type
:
Boolean
=
config
(
"cell_type"
,
default
=
false
)
var
phased
:
Boolean
=
config
(
"phased"
,
default
=
false
)
var
allele_number
:
Boolean
=
config
(
"allele_number"
,
default
=
false
)
var
numbers
:
Boolean
=
config
(
"numbers"
,
default
=
false
)
var
domains
:
Boolean
=
config
(
"domains"
,
default
=
false
)
var
no_escape
:
Boolean
=
config
(
"no_escape"
,
default
=
false
)
var
hgvs
:
Boolean
=
config
(
"hgvs"
,
default
=
false
)
var
protein
:
Boolean
=
config
(
"protein"
,
default
=
false
)
var
symbol
:
Boolean
=
config
(
"symbol"
,
default
=
false
)
var
ccds
:
Boolean
=
config
(
"ccds"
,
default
=
false
)
var
uniprot
:
Boolean
=
config
(
"uniprot"
,
default
=
false
)
var
tsl
:
Boolean
=
config
(
"tsl"
,
default
=
false
)
var
canonical
:
Boolean
=
config
(
"canonical"
,
default
=
false
)
var
biotype
:
Boolean
=
config
(
"biotype"
,
default
=
false
)
var
xref_refseq
:
Boolean
=
config
(
"xref_refseq"
,
default
=
false
)
var
check_existing
:
Boolean
=
config
(
"check_existing"
,
default
=
false
)
var
check_alleles
:
Boolean
=
config
(
"check_alleles"
,
default
=
false
)
var
check_svs
:
Boolean
=
config
(
"svs"
,
default
=
false
)
var
gmaf
:
Boolean
=
config
(
"gmaf"
,
default
=
false
)
var
maf_1kg
:
Boolean
=
config
(
"maf_1kg"
,
default
=
false
)
var
maf_esp
:
Boolean
=
config
(
"maf_esp"
,
default
=
false
)
var
old_map
:
Boolean
=
config
(
"old_maf"
,
default
=
false
)
var
pubmed
:
Boolean
=
config
(
"pubmed"
,
default
=
false
)
var
failed
:
Boolean
=
config
(
"failed"
,
default
=
false
)
var
vcf
:
Boolean
=
config
(
"vcf"
,
default
=
true
)
var
json
:
Boolean
=
config
(
"json"
)
var
gvf
:
Boolean
=
config
(
"gvf"
)
var
check_ref
:
Boolean
=
config
(
"check_ref"
)
var
coding_only
:
Boolean
=
config
(
"coding_only"
)
var
no_intergenic
:
Boolean
=
config
(
"no_intergenic"
)
var
pick
:
Boolean
=
config
(
"pick"
)
var
pick_allele
:
Boolean
=
config
(
"pick_allele"
)
var
flag_pick
:
Boolean
=
config
(
"flag_pick"
)
var
flag_pick_allele
:
Boolean
=
config
(
"flag_pick_allele"
)
var
per_gene
:
Boolean
=
config
(
"per_gene"
)
var
most_severe
:
Boolean
=
config
(
"most_severe"
)
var
summary
:
Boolean
=
config
(
"summary"
)
var
filter_common
:
Boolean
=
config
(
"filter_common"
)
var
check_frequency
:
Boolean
=
config
(
"check_frequency"
)
var
allow_non_variant
:
Boolean
=
config
(
"allow_non_variant"
)
var
database
:
Boolean
=
config
(
"database"
)
var
genomes
:
Boolean
=
config
(
"genomes"
)
var
gencode_basic
:
Boolean
=
config
(
"gencode_basic"
)
var
refseq
:
Boolean
=
config
(
"refseq"
)
var
merged
:
Boolean
=
config
(
"merged"
)
var
all_refseq
:
Boolean
=
config
(
"all_refseq"
)
var
lrg
:
Boolean
=
config
(
"lrg"
)
var
no_whole_genome
:
Boolean
=
config
(
"no_whole_genome"
)
var
skip_db_check
:
Boolean
=
config
(
"skip_db_check"
)
var
json
:
Boolean
=
config
(
"json"
,
default
=
false
)
var
gvf
:
Boolean
=
config
(
"gvf"
,
default
=
false
)
var
check_ref
:
Boolean
=
config
(
"check_ref"
,
default
=
false
)
var
coding_only
:
Boolean
=
config
(
"coding_only"
,
default
=
false
)
var
no_intergenic
:
Boolean
=
config
(
"no_intergenic"
,
default
=
false
)
var
pick
:
Boolean
=
config
(
"pick"
,
default
=
false
)
var
pick_allele
:
Boolean
=
config
(
"pick_allele"
,
default
=
false
)
var
flag_pick
:
Boolean
=
config
(
"flag_pick"
,
default
=
false
)
var
flag_pick_allele
:
Boolean
=
config
(
"flag_pick_allele"
,
default
=
false
)
var
per_gene
:
Boolean
=
config
(
"per_gene"
,
default
=
false
)
var
most_severe
:
Boolean
=
config
(
"most_severe"
,
default
=
false
)
var
summary
:
Boolean
=
config
(
"summary"
,
default
=
false
)
var
filter_common
:
Boolean
=
config
(
"filter_common"
,
default
=
false
)
var
check_frequency
:
Boolean
=
config
(
"check_frequency"
,
default
=
false
)
var
allow_non_variant
:
Boolean
=
config
(
"allow_non_variant"
,
default
=
false
)
var
database
:
Boolean
=
config
(
"database"
,
default
=
false
)
var
genomes
:
Boolean
=
config
(
"genomes"
,
default
=
false
)
var
gencode_basic
:
Boolean
=
config
(
"gencode_basic"
,
default
=
false
)
var
refseq
:
Boolean
=
config
(
"refseq"
,
default
=
false
)
var
merged
:
Boolean
=
config
(
"merged"
,
default
=
false
)
var
all_refseq
:
Boolean
=
config
(
"all_refseq"
,
default
=
false
)
var
lrg
:
Boolean
=
config
(
"lrg"
,
default
=
false
)
var
no_whole_genome
:
Boolean
=
config
(
"no_whole_genome"
,
default
=
false
)
var
skip_db_check
:
Boolean
=
config
(
"skip_db_check"
,
default
=
false
)
// Textual args
var
vep_config
:
String
=
config
(
"config"
)
var
species
:
String
=
config
(
"species"
)
var
assembly
:
String
=
config
(
"assembly"
)
var
format
:
String
=
config
(
"format"
)
var
dir
:
String
=
config
(
"dir"
)
var
dir_cache
:
String
=
config
(
"dir_cache"
)
var
dir_plugins
:
String
=
config
(
"dir_plugins"
)
var
fasta
:
File
=
config
(
"fasta"
)
var
sift
:
String
=
config
(
"sift"
)
var
polyphen
:
String
=
config
(
"polyphen"
)
var
custom
:
String
=
config
(
"custom"
)
var
plugin
:
List
[
String
]
=
config
(
"plugin"
)
var
individual
:
String
=
config
(
"individual"
)
var
fields
:
String
=
config
(
"fields"
)
var
convert
:
String
=
config
(
"convert"
)
var
terms
:
String
=
config
(
"terms"
)
var
chr
:
String
=
config
(
"chr"
)
var
pick_order
:
String
=
config
(
"pick_order"
)
var
freq_pop
:
String
=
config
(
"check_pop"
)
var
freq_gt_lt
:
String
=
config
(
"freq_gt_lt"
)
var
freq_filter
:
String
=
config
(
"freq_filter"
)
var
filter
:
String
=
config
(
"filter"
)
var
host
:
String
=
config
(
"host"
)
var
user
:
String
=
config
(
"user"
)
var
password
:
String
=
config
(
"password"
)
var
registry
:
String
=
config
(
"registry"
)
var
build
:
String
=
config
(
"build"
)
var
compress
:
String
=
config
(
"compress"
)
var
cache_region_size
:
String
=
config
(
"cache_region_size"
)
var
vep_config
:
Option
[
String
]
=
config
(
"config"
)
var
species
:
Option
[
String
]
=
config
(
"species"
)
var
assembly
:
Option
[
String
]
=
config
(
"assembly"
)
var
format
:
Option
[
String
]
=
config
(
"format"
)
var
dir
:
Option
[
String
]
=
config
(
"dir"
)
var
dir_cache
:
Option
[
String
]
=
config
(
"dir_cache"
)
var
dir_plugins
:
Option
[
String
]
=
config
(
"dir_plugins"
)
var
fasta
:
Option
[
String
]
=
config
(
"fasta"
)
var
sift
:
Option
[
String
]
=
config
(
"sift"
)
var
polyphen
:
Option
[
String
]
=
config
(
"polyphen"
)
var
custom
:
Option
[
String
]
=
config
(
"custom"
)
var
plugin
:
List
[
String
]
=
config
(
"plugin"
,
default
=
Nil
)
var
individual
:
Option
[
String
]
=
config
(
"individual"
)
var
fields
:
Option
[
String
]
=
config
(
"fields"
)
var
convert
:
Option
[
String
]
=
config
(
"convert"
)
var
terms
:
Option
[
String
]
=
config
(
"terms"
)
var
chr
:
Option
[
String
]
=
config
(
"chr"
)
var
pick_order
:
Option
[
String
]
=
config
(
"pick_order"
)
var
freq_pop
:
Option
[
String
]
=
config
(
"check_pop"
)
var
freq_gt_lt
:
Option
[
String
]
=
config
(
"freq_gt_lt"
)
var
freq_filter
:
Option
[
String
]
=
config
(
"freq_filter"
)
var
filter
:
Option
[
String
]
=
config
(
"filter"
)
var
host
:
Option
[
String
]
=
config
(
"host"
)
var
user
:
Option
[
String
]
=
config
(
"user"
)
var
password
:
Option
[
String
]
=
config
(
"password"
)
var
registry
:
Option
[
String
]
=
config
(
"registry"
)
var
build
:
Option
[
String
]
=
config
(
"build"
)
var
compress
:
Option
[
String
]
=
config
(
"compress"
)
var
cache_region_size
:
Option
[
String
]
=
config
(
"cache_region_size"
)
// Numeric args
var
fork
:
Option
[
Int
]
=
config
(
"fork"
)
...
...
@@ -129,7 +129,7 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
super
.
afterGraph
if
(!
cache
&&
!
database
)
{
throw
new
IllegalArgumentException
(
"Must supply either cache or database"
)
}
else
if
(
cache
&&
dir
==
null
)
{
}
else
if
(
cache
&&
dir
.
isEmpty
)
{
throw
new
IllegalArgumentException
(
"Must supply dir to cache"
)
}
}
...
...
public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutablePublic.scala
View file @
34a00edf
...
...
@@ -24,7 +24,8 @@ object BiopetExecutablePublic extends BiopetExecutable {
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
yamsvp
.
Yamsvp
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
sage
.
Sage
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
kopisu
.
ConiferPipeline
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
carp
.
Carp
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
carp
.
Carp
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
toucan
.
Toucan
)
def
tools
:
List
[
MainCommand
]
=
List
(
...
...
public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
View file @
34a00edf
...
...
@@ -4,6 +4,7 @@ import nl.lumc.sasc.biopet.core.{ PipelineCommand, BiopetQScript }
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.extensions.VariantEffectPredictor
import
nl.lumc.sasc.biopet.tools.VEPNormalizer
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
org.broadinstitute.gatk.queue.QScript
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Argument
}
...
...
@@ -20,7 +21,11 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript {
}
defaults
++=
Map
(
"varianteffectpredictor"
->
Map
(
"everything"
->
true
))
override
def
defaults
=
ConfigUtils
.
mergeMaps
(
Map
(
"varianteffectpredictor"
->
Map
(
"everything"
->
true
)
),
super
.
defaults
)
//defaults ++= Map("varianteffectpredictor" -> Map("everything" -> true))
def
biopetScript
()
:
Unit
=
{
val
vep
=
new
VariantEffectPredictor
(
this
)
...
...
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