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biopet.biopet
Commits
0b3c1e25
Commit
0b3c1e25
authored
Apr 21, 2017
by
pjvan_thof
Browse files
Make readgroup_library a config value
parent
74845bd6
Changes
1
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Inline
Side-by-side
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
0b3c1e25
...
...
@@ -86,6 +86,9 @@ class Mapping(val parent: Configurable) extends QScript with SummaryQScript with
/** Readgroup sequencing center */
protected
var
readgroupSequencingCenter
:
Option
[
String
]
=
config
(
"readgroup_sequencing_center"
)
/** Readgroup library */
protected
var
readgroupLibrary
:
Option
[
String
]
=
config
(
"readgroup_library"
)
/** Readgroup description */
protected
var
readgroupDescription
:
Option
[
String
]
=
config
(
"readgroup_description"
)
...
...
@@ -572,7 +575,7 @@ class Mapping(val parent: Configurable) extends QScript with SummaryQScript with
/** Returns readgroup for bwa */
def
getReadGroupBwa
:
String
=
{
var
RG
:
String
=
"@RG\\t"
+
"ID:"
+
readgroupId
+
"\\t"
RG
+=
"LB:"
+
l
ibId
.
get
+
"\\t"
readgroupLibrary
.
foreach
(
lb
=>
RG
+=
"LB:"
+
l
b
+
"\\t"
)
RG
+=
"PL:"
+
platform
+
"\\t"
platformUnit
.
foreach
(
x
=>
RG
+=
"PU:"
+
x
+
"\\t"
)
RG
+=
"SM:"
+
sampleId
.
get
+
"\\t"
...
...
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