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biopet.biopet
Commits
7bea64ef
Commit
7bea64ef
authored
Jan 16, 2015
by
Peter van 't Hof
Browse files
Added bwa aln extension
parent
36e763df
Changes
1
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Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
0 → 100644
View file @
7bea64ef
package
nl.lumc.sasc.biopet.extensions.bwa
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Output
,
Input
}
/**
* Created by pjvan_thof on 1/16/15.
*/
class
BwaAln
(
val
root
:
Configurable
)
extends
Bwa
{
@Input
(
doc
=
"Fastq file"
,
required
=
true
)
var
fastq
:
File
=
_
@Input
(
doc
=
"The reference file for the bam files."
,
required
=
true
)
var
reference
:
File
=
config
(
"reference"
,
required
=
true
)
@Output
(
doc
=
"Output file SAM"
,
required
=
false
)
var
output
:
File
=
_
var
n
:
Option
[
Int
]
=
config
(
"n"
)
var
o
:
Option
[
Int
]
=
config
(
"o"
)
var
e
:
Option
[
Int
]
=
config
(
"e"
)
var
i
:
Option
[
Int
]
=
config
(
"i"
)
var
d
:
Option
[
Int
]
=
config
(
"d"
)
var
l
:
Option
[
Int
]
=
config
(
"l"
)
var
k
:
Option
[
Int
]
=
config
(
"k"
)
var
m
:
Option
[
Int
]
=
config
(
"m"
)
var
M
:
Option
[
Int
]
=
config
(
"M"
)
var
O
:
Option
[
Int
]
=
config
(
"O"
)
var
E
:
Option
[
Int
]
=
config
(
"E"
)
var
R
:
Option
[
Int
]
=
config
(
"R"
)
var
q
:
Option
[
Int
]
=
config
(
"q"
)
var
B
:
Option
[
Int
]
=
config
(
"B"
)
var
L
:
Boolean
=
config
(
"L"
,
default
=
false
)
var
N
:
Boolean
=
config
(
"N"
,
default
=
false
)
var
I
:
Boolean
=
config
(
"I"
,
default
=
false
)
var
b
:
Boolean
=
config
(
"b"
,
default
=
false
)
var
n0
:
Boolean
=
config
(
"0"
,
default
=
false
)
var
n1
:
Boolean
=
config
(
"1"
,
default
=
false
)
var
n2
:
Boolean
=
config
(
"2"
,
default
=
false
)
var
Y
:
Boolean
=
config
(
"Y"
,
default
=
false
)
override
val
defaultVmem
=
"5G"
override
val
defaultThreads
=
8
def
cmdLine
=
required
(
executable
)
+
required
(
"aln"
)
+
optional
(
"-n"
,
n
)
+
optional
(
"-o"
,
o
)
+
optional
(
"-e"
,
e
)
+
optional
(
"-i"
,
i
)
+
optional
(
"-d"
,
d
)
+
optional
(
"-l"
,
l
)
+
optional
(
"-k"
,
k
)
+
optional
(
"-m"
,
m
)
+
optional
(
"-M"
,
M
)
+
optional
(
"-O"
,
O
)
+
optional
(
"-E"
,
E
)
+
optional
(
"-R"
,
R
)
+
optional
(
"-q"
,
q
)
+
optional
(
"-B"
,
B
)
+
conditional
(
L
,
"-L"
)
+
conditional
(
N
,
"-N"
)
+
conditional
(
I
,
"-I"
)
+
conditional
(
b
,
"-b"
)
+
conditional
(
n0
,
"-0"
)
+
conditional
(
n1
,
"-1"
)
+
conditional
(
n2
,
"-2"
)
+
conditional
(
Y
,
"-Y"
)
+
required
(
"-f"
,
output
)
+
required
(
reference
)
+
required
(
fastq
)
}
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