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biopet.biopet
Commits
ccd0ed71
Commit
ccd0ed71
authored
Jan 30, 2015
by
Wai Yi Leung
Browse files
Aligner BWA typo and Mapping clean paths
parent
9d5bc538
Changes
2
Hide whitespace changes
Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
View file @
ccd0ed71
...
...
@@ -6,7 +6,11 @@ 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 sampe wrapper
*
* based on executable verion 0.7.10-r789
*
* @param root Configurable
*/
class
BwaSampe
(
val
root
:
Configurable
)
extends
Bwa
{
@Input
(
doc
=
"Fastq file R1"
,
required
=
true
)
...
...
@@ -39,11 +43,14 @@ class BwaSampe(val root: Configurable) extends Bwa {
var
r
:
String
=
_
def
cmdLine
=
required
(
executable
)
+
required
(
"samse"
)
+
required
(
"sampe"
)
+
optional
(
"-a"
,
a
)
+
optional
(
"-o"
,
o
)
+
optional
(
"-n"
,
n
)
+
optional
(
"-N"
,
N
)
+
optional
(
"-c"
,
c
)
+
optional
(
"-f"
,
output
)
+
optional
(
"-r"
,
r
)
+
optional
(
"-c"
,
c
)
+
conditional
(
P
,
"-P"
)
+
conditional
(
s
,
"-s"
)
+
conditional
(
A
,
"-A"
)
+
...
...
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
ccd0ed71
...
...
@@ -123,7 +123,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
def
biopetScript
()
{
if
(!
skipFlexiprep
)
{
flexiprep
.
outputDir
=
outputDir
+
"flexiprep
/
"
flexiprep
.
outputDir
=
outputDir
+
"flexiprep"
+
File
.
separator
flexiprep
.
input_R1
=
input_R1
if
(
paired
)
flexiprep
.
input_R2
=
input_R2
flexiprep
.
sampleId
=
this
.
sampleId
...
...
@@ -208,7 +208,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
bamFile
=
mergeSamFile
.
output
}
if
(!
skipMetrics
)
addAll
(
BamMetrics
(
this
,
bamFile
,
outputDir
+
"metrics
/
"
).
functions
)
if
(!
skipMetrics
)
addAll
(
BamMetrics
(
this
,
bamFile
,
outputDir
+
"metrics"
+
File
.
separator
).
functions
)
add
(
Ln
(
this
,
swapExt
(
outputDir
,
bamFile
,
".bam"
,
".bai"
),
swapExt
(
outputDir
,
finalBamFile
,
".bam"
,
".bai"
)))
add
(
Ln
(
this
,
bamFile
,
finalBamFile
))
...
...
@@ -357,6 +357,4 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
}
}
object
Mapping
extends
PipelineCommand
{
}
object
Mapping
extends
PipelineCommand
\ No newline at end of file
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