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biopet.biopet
Commits
40802e4e
Commit
40802e4e
authored
Jun 07, 2016
by
Peter van 't Hof
Browse files
Added hisat2build extension
parent
506a51d6
Changes
1
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Inline
Side-by-side
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/hisat/Hisat2Build.scala
0 → 100644
View file @
40802e4e
package
nl.lumc.sasc.biopet.extensions.hisat
import
java.io.File
import
nl.lumc.sasc.biopet.core.
{
BiopetCommandLineFunction
,
Reference
,
Version
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.Input
/**
* Created by pjvan_thof on 7-6-16.
*/
class
Hisat2Build
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
with
Version
{
@Input
(
required
=
true
)
var
inputFasta
:
File
=
_
var
hisat2IndexBase
:
String
=
_
@Input
(
required
=
false
)
var
snp
:
Option
[
File
]
=
config
(
"snp"
)
@Input
(
required
=
false
)
var
haplotype
:
Option
[
File
]
=
config
(
"haplotype"
)
@Input
(
required
=
false
)
var
ss
:
Option
[
File
]
=
config
(
"ss"
)
@Input
(
required
=
false
)
var
exon
:
Option
[
File
]
=
config
(
"exon"
)
executable
=
config
(
"exe"
,
default
=
"hisat2-build"
,
freeVar
=
false
)
def
versionRegex
=
""".*hisat2-align-s version (.*)"""
.
r
override
def
versionExitcode
=
List
(
0
,
1
)
def
versionCommand
=
executable
+
" --version"
var
bmax
:
Option
[
Int
]
=
config
(
"bmax"
)
var
bmaxdivn
:
Option
[
Int
]
=
config
(
"bmaxdivn"
)
var
dcv
:
Option
[
Int
]
=
config
(
"dcv"
)
var
offrate
:
Option
[
Int
]
=
config
(
"offrate"
)
var
ftabchars
:
Option
[
Int
]
=
config
(
"ftabchars"
)
var
localoffrate
:
Option
[
Int
]
=
config
(
"localoffrate"
)
var
localftabchars
:
Option
[
Int
]
=
config
(
"localftabchars"
)
var
seed
:
Option
[
Int
]
=
config
(
"seed"
)
var
large
-
index
:
Boolean
=
config
(
"large-index"
,
default
=
false
)
var
dcv
:
Boolean
=
config
(
"dcv"
,
default
=
false
)
var
memory
-
fitting
:
Boolean
=
config
(
"memory-fitting"
,
default
=
false
)
var
nodc
:
Boolean
=
config
(
"nodc"
,
default
=
false
)
var
noref
:
Boolean
=
config
(
"noref"
,
default
=
false
)
var
justref
:
Boolean
=
config
(
"justref"
,
default
=
false
)
var
quiet
:
Boolean
=
config
(
"quiet"
,
default
=
false
)
override
def
beforeGraph
()
:
Unit
=
{
super
.
beforeGraph
()
val
indexDir
=
new
File
(
hisat2IndexBase
).
getParentFile
val
indexName
=
new
File
(
hisat2IndexBase
).
getName
jobOutputFile
=
new
File
(
indexDir
,
s
".$indexName.hisat2-build.out"
)
}
def
cmdLine
=
required
(
executable
)
+
optional
(
"--bmax"
,
bmax
)
+
optional
(
"--bmaxdivn"
,
bmaxdivn
)
+
optional
(
"--dcv"
,
dcv
)
+
optional
(
"--offrate"
,
offrate
)
+
optional
(
"--ftabchars"
,
ftabchars
)
+
optional
(
"--localoffrate"
,
localoffrate
)
+
optional
(
"--localftabchars"
,
localftabchars
)
+
optional
(
"--seed"
,
seed
)
+
optional
(
"--snp"
,
snp
)
+
optional
(
"--haplotype"
,
haplotype
)
+
optional
(
"--ss"
,
ss
)
+
optional
(
"--exon"
,
exon
)
+
conditional
(
large
-
index
,
"--large-index"
)
+
conditional
(
dcv
,
"--dcv"
)
+
conditional
(
memory
-
fitting
,
"--memory-fitting"
)
+
conditional
(
nodc
,
"--nodc"
)
+
conditional
(
noref
,
"--noref"
)
+
conditional
(
justref
,
"--justref"
)
+
conditional
(
quiet
,
"--quiet"
)
+
required
(
inputFasta
)
+
required
(
hisat2IndexBase
)
}
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