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biopet.biopet
Commits
ac61c9dd
Commit
ac61c9dd
authored
Nov 26, 2015
by
Wai Yi Leung
Browse files
Fix bowtie2 readgroup
parent
92bdf700
Changes
2
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public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie2.scala
View file @
ac61c9dd
...
...
@@ -116,7 +116,7 @@ class Bowtie2(val root: Configurable) extends BiopetCommandLineFunction with Ref
var
no_sq
:
Boolean
=
config
(
"no_sq"
,
default
=
false
)
var
rg_id
:
Option
[
String
]
=
config
(
"rg_id"
)
var
rg
:
Option
[
String
]
=
config
(
"rg"
)
var
rg
:
List
[
String
]
=
config
(
"rg"
)
var
omit_sec_seq
:
Boolean
=
config
(
"omit_sec_seq"
,
default
=
false
)
...
...
@@ -202,7 +202,7 @@ class Bowtie2(val root: Configurable) extends BiopetCommandLineFunction with Ref
conditional
(
no_head
,
"--no-head"
)
+
conditional
(
no_sq
,
"--no-sq"
)
+
optional
(
"--rg-id"
,
rg_id
)
+
optional
(
"--rg"
,
rg
)
+
repeat
(
"--rg"
,
rg
)
conditional
(
omit_sec_seq
,
"--omit-sec-seq"
)
+
/* Performance */
optional
(
"--threads"
,
threads
)
+
...
...
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
ac61c9dd
...
...
@@ -441,6 +441,11 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
/** Add bowtie2 jobs **/
def
addBowtie2
(
R1
:
File
,
R2
:
Option
[
File
],
output
:
File
)
:
File
=
{
val
bowtie2
=
new
Bowtie2
(
this
)
bowtie2
.
rg_id
=
Some
(
readgroupId
)
bowtie2
.
rg
+:=
(
"LB:"
+
libId
.
get
)
bowtie2
.
rg
+:=
(
"PL:"
+
platform
)
bowtie2
.
rg
+:=
(
"PU:"
+
platformUnit
)
bowtie2
.
rg
+:=
(
"SM:"
+
sampleId
.
get
)
bowtie2
.
R1
=
R1
if
(
paired
)
bowtie2
.
R2
=
Some
(
R2
.
get
)
val
sortSam
=
new
SortSam
(
this
)
...
...
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