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biopet.biopet
Commits
270dfad0
Commit
270dfad0
authored
Jan 25, 2017
by
Peter van 't Hof
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parent
c06191f0
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2
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2 changed files
with
8 additions
and
6 deletions
+8
-6
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
...c/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+1
-1
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMapping.scala
...mc/sasc/biopet/pipelines/mapping/MultisampleMapping.scala
+7
-5
No files found.
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
View file @
270dfad0
...
...
@@ -120,7 +120,7 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
val
className
=
if
(
f
.
getClass
.
isAnonymousClass
)
f
.
getClass
.
getSuperclass
.
getSimpleName
else
f
.
getClass
.
getSimpleName
BiopetQScript
.
safeOutputs
(
f
)
match
{
case
Some
(
o
)
=>
f
.
jobOutputFile
=
new
File
(
o
.
head
.
getAbsoluteFile
.
getParent
,
"."
+
f
.
firstOutput
.
getName
+
"."
+
className
+
".out"
)
case
_
=>
f
.
jobOutputFile
=
new
File
(
"./stdout"
)
// Line is here for test backup
case
_
=>
f
.
jobOutputFile
=
new
File
(
"./stdout"
)
// Line is here for test backup
}
})
...
...
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMapping.scala
View file @
270dfad0
...
...
@@ -35,6 +35,8 @@ import scala.collection.JavaConversions._
/**
* Created by pjvanthof on 18/12/15.
*
* This trait is meant to extend pipelines from that require a alignment step
*/
trait
MultisampleMappingTrait
extends
MultiSampleQScript
with
Reference
{
qscript
:
QScript
=>
...
...
@@ -65,7 +67,7 @@ trait MultisampleMappingTrait extends MultiSampleQScript
Some
(
report
)
}
override
def
defaults
=
super
.
defaults
++
Map
(
"reordersam"
->
Map
(
"allow_incomplete_dict_concordance"
->
true
))
override
def
defaults
:
Map
[
String
,
Any
]
=
super
.
defaults
++
Map
(
"reordersam"
->
Map
(
"allow_incomplete_dict_concordance"
->
true
))
override
def
fixedValues
:
Map
[
String
,
Any
]
=
super
.
fixedValues
++
Map
(
"gearssingle"
->
Map
(
"skip_flexiprep"
->
true
))
...
...
@@ -101,7 +103,7 @@ trait MultisampleMappingTrait extends MultiSampleQScript
lazy
val
bamToFastq
:
Boolean
=
config
(
"bam_to_fastq"
,
default
=
false
)
lazy
val
correctReadgroups
:
Boolean
=
config
(
"correct_readgroups"
,
default
=
false
)
def
keepFinalBamfile
=
samples
(
sampleId
).
libraries
.
size
==
1
def
keepFinalBamfile
:
Boolean
=
samples
(
sampleId
).
libraries
.
size
==
1
lazy
val
mapping
:
Option
[
Mapping
]
=
if
(
inputR1
.
isDefined
||
(
inputBam
.
isDefined
&&
bamToFastq
))
{
val
m
:
Mapping
=
new
Mapping
(
qscript
)
{
...
...
@@ -213,13 +215,13 @@ trait MultisampleMappingTrait extends MultiSampleQScript
def
summaryStats
:
Map
[
String
,
Any
]
=
Map
()
/** This is the merged bam file, None if the merged bam file is NA */
def
bamFile
=
if
(
libraries
.
flatMap
(
_
.
_2
.
bamFile
).
nonEmpty
&&
def
bamFile
:
Option
[
File
]
=
if
(
libraries
.
flatMap
(
_
.
_2
.
bamFile
).
nonEmpty
&&
mergeStrategy
!=
MultisampleMapping
.
MergeStrategy
.
None
)
Some
(
new
File
(
sampleDir
,
s
"$sampleId.bam"
))
else
None
/** By default the preProcessBam is the same as the normal bamFile. A pipeline can extend this is there are preprocess steps */
def
preProcessBam
=
bamFile
def
preProcessBam
:
Option
[
File
]
=
bamFile
/** Default is set to keep the merged files, user can set this in the config. To change the default this method can be overriden */
def
keepMergedFiles
:
Boolean
=
config
(
"keep_merged_files"
,
default
=
true
)
...
...
@@ -278,7 +280,7 @@ trait MultisampleMappingTrait extends MultiSampleQScript
gears
.
outputDir
=
new
File
(
sampleDir
,
"gears"
)
add
(
gears
)
case
"none"
=>
case
x
=>
Logging
.
addError
(
s
"$
{x}
is not a valid value for 'mapping_to_gears'"
)
case
x
=>
Logging
.
addError
(
s
"$
x
is not a valid value for 'mapping_to_gears'"
)
}
}
}
...
...
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