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biopet.biopet
Commits
0c1c8db6
Commit
0c1c8db6
authored
Mar 05, 2015
by
Peter van 't Hof
Browse files
Added scala docs for bwa
parent
e98f7409
Changes
5
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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/Bwa.scala
View file @
0c1c8db6
...
...
@@ -3,6 +3,8 @@ package nl.lumc.sasc.biopet.extensions.bwa
import
nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
/**
* General bwa extension
*
* Created by pjvan_thof on 1/16/15.
*/
abstract
class
Bwa
extends
BiopetCommandLineFunction
{
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
View file @
0c1c8db6
...
...
@@ -6,6 +6,10 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Output
,
Input
}
/**
* Extension for bwa aln
*
* Based on version 0.7.12-r1039
*
* Created by pjvan_thof on 1/16/15.
*/
class
BwaAln
(
val
root
:
Configurable
)
extends
Bwa
{
...
...
@@ -44,6 +48,7 @@ class BwaAln(val root: Configurable) extends Bwa {
override
val
defaultVmem
=
"5G"
override
val
defaultThreads
=
8
/** Returns command to execute */
def
cmdLine
=
required
(
executable
)
+
required
(
"aln"
)
+
optional
(
"-n"
,
n
)
+
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
View file @
0c1c8db6
...
...
@@ -22,6 +22,11 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.core.summary.Summarizable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
/**
* Extension for bwa mem
*
* Based on version 0.7.12-r1039
*/
class
BwaMem
(
val
root
:
Configurable
)
extends
Bwa
{
@Input
(
doc
=
"Fastq file R1"
,
shortName
=
"R1"
)
var
R1
:
File
=
_
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
View file @
0c1c8db6
...
...
@@ -10,7 +10,6 @@ import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
*
* based on executable version 0.7.10-r789
*
* @param root Configurable
*/
class
BwaSampe
(
val
root
:
Configurable
)
extends
Bwa
{
@Input
(
doc
=
"Fastq file R1"
,
required
=
true
)
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala
View file @
0c1c8db6
...
...
@@ -6,7 +6,10 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Output
,
Input
}
/**
* Created by pjvan_thof on 1/16/15.
* BWA samse wrapper
*
* based on executable version 0.7.10-r789
*
*/
class
BwaSamse
(
val
root
:
Configurable
)
extends
Bwa
{
@Input
(
doc
=
"Fastq file"
,
required
=
true
)
...
...
@@ -24,6 +27,7 @@ class BwaSamse(val root: Configurable) extends Bwa {
var
n
:
Option
[
Int
]
=
config
(
"n"
)
var
r
:
String
=
_
/** Returns command to execute */
def
cmdLine
=
required
(
executable
)
+
required
(
"samse"
)
+
optional
(
"-n"
,
n
)
+
...
...
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