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biopet.biopet
Commits
705d9cd6
Commit
705d9cd6
authored
Oct 29, 2015
by
Wai Yi Leung
Browse files
Style fixes and config for samtofastq
parent
4cb2adf1
Changes
2
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public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala
View file @
705d9cd6
...
...
@@ -15,7 +15,7 @@
*/
package
nl.lumc.sasc.biopet.extensions.sambamba
import
nl.lumc.sasc.biopet.core.
{
BiopetCommandLineFunction
,
Version
}
import
nl.lumc.sasc.biopet.core.
{
BiopetCommandLineFunction
,
Version
}
/** General Sambamba extension */
abstract
class
Sambamba
extends
BiopetCommandLineFunction
with
Version
{
...
...
@@ -24,7 +24,7 @@ abstract class Sambamba extends BiopetCommandLineFunction with Version {
override
def
subPath
=
"sambamba"
::
super
.
subPath
executable
=
config
(
"exe"
,
default
=
"sambamba"
,
submodule
=
"sambamba"
)
executable
=
config
(
"exe"
,
default
=
"sambamba"
,
submodule
=
"sambamba"
,
freeVar
=
false
)
def
versionCommand
=
executable
def
versionRegex
=
"""sambamba v(.*)"""
.
r
override
def
versionExitcode
=
List
(
0
,
1
)
...
...
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
View file @
705d9cd6
...
...
@@ -63,9 +63,14 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript with Sam
gears
.
summaryFile
=
summaryFile
Some
(
gears
)
}
override
def
defaults
=
Map
(
"samtofastq"
->
Map
(
"validationstringency"
->
"LENIENT"
)
)
/** Method to add jobs */
def
biopetScript
()
:
Unit
=
{
val
fastqFiles
:
List
[
File
]
=
bamFile
.
map
{
bamfile
=>
// sambamba view -f bam -F "unmapped or mate_is_unmapped" <alnFile> > <extracted.bam>
...
...
@@ -79,7 +84,6 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript with Sam
// start bam to fastq (only on unaligned reads) also extract the matesam
val
samToFastq
=
new
SamToFastq
(
this
)
samToFastq
.
input
=
samFilterUnmapped
.
output
samToFastq
.
stringency
=
Some
(
"LENIENT"
)
samToFastq
.
fastqR1
=
new
File
(
outputDir
,
s
"$outputName.unmapped.R1.fq.gz"
)
samToFastq
.
fastqR2
=
new
File
(
outputDir
,
s
"$outputName.unmapped.R2.fq.gz"
)
samToFastq
.
fastqUnpaired
=
new
File
(
outputDir
,
s
"$outputName.unmapped.singleton.fq.gz"
)
...
...
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