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biopet.biopet
Commits
c11614e9
Commit
c11614e9
authored
Dec 15, 2016
by
Peter van 't Hof
Browse files
Fixed compile issues
parent
ba8bfc42
Changes
2
Hide whitespace changes
Inline
Side-by-side
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
c11614e9
...
...
@@ -97,19 +97,19 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
protected
var
paired
:
Boolean
=
false
val
flexiprep
=
new
Flexiprep
(
this
)
def
finalBamFile
:
File
=
if
(
skipMarkduplicates
){
def
finalBamFile
:
File
=
if
(
skipMarkduplicates
)
{
new
File
(
outputDir
,
outputName
+
".bam"
)
}
else
new
File
(
outputDir
,
outputName
+
".dedup.bam"
)
/** location of summary file */
def
summaryFile
=
new
File
(
outputDir
,
sampleId
.
getOrElse
(
"x"
)
+
"-"
+
libId
.
getOrElse
(
"x"
)
+
".summary.json"
)
override
def
defaults
=
Map
(
override
def
defaults
:
Map
[
String
,
Any
]
=
Map
(
"gsnap"
->
Map
(
"batch"
->
4
),
"star"
->
Map
(
"outsamunmapped"
->
"Within"
)
)
override
def
fixedValues
=
Map
(
override
def
fixedValues
:
Map
[
String
,
Any
]
=
Map
(
"gsnap"
->
Map
(
"format"
->
"sam"
),
"bowtie"
->
Map
(
"sam"
->
true
)
)
...
...
@@ -276,8 +276,8 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
addSummaryQScript
(
bamMetrics
)
}
// add(Ln(this, swapExt(outputDir, bamFile, ".bam", ".bai"), swapExt(outputDir, new File(outputDir, outputName + ".dedup.bam"), ".bam", ".bai")))
// add(Ln(this, bamFile, new File(outputDir, outputName + ".dedup.bam")))
// add(Ln(this, swapExt(outputDir, bamFile, ".bam", ".bai"), swapExt(outputDir, new File(outputDir, outputName + ".dedup.bam"), ".bam", ".bai")))
// add(Ln(this, bamFile, new File(outputDir, outputName + ".dedup.bam")))
outputFiles
+=
(
"finalBamFile"
->
finalBamFile
)
if
(
config
(
"unmapped_to_gears"
,
default
=
false
).
asBoolean
)
{
...
...
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMapping.scala
View file @
c11614e9
...
...
@@ -83,10 +83,10 @@ trait MultisampleMappingTrait extends MultiSampleQScript
"merge_strategy"
->
mergeStrategy
.
toString
)
def
makeSample
(
id
:
String
)
=
new
Sample
(
id
)
class
Sample
(
sampleId
:
String
)
extends
AbstractSample
(
sampleId
)
{
class
Sample
(
sampleId
:
String
)
extends
AbstractSample
(
sampleId
)
{
sample
=>
def
makeLibrary
(
id
:
String
)
=
new
Library
(
id
)
class
Library
(
libId
:
String
)
extends
AbstractLibrary
(
libId
)
{
class
Library
(
libId
:
String
)
extends
AbstractLibrary
(
libId
)
{
lib
=>
/** By default the bams files are put in the summary, more files can be added here */
def
summaryFiles
:
Map
[
String
,
File
]
=
(
inputR1
.
map
(
"input_R1"
->
_
)
::
inputR2
.
map
(
"input_R2"
->
_
)
::
...
...
@@ -101,11 +101,11 @@ trait MultisampleMappingTrait extends MultiSampleQScript
lazy
val
bamToFastq
:
Boolean
=
config
(
"bam_to_fastq"
,
default
=
false
)
lazy
val
correctReadgroups
:
Boolean
=
config
(
"correct_readgroups"
,
default
=
false
)
lazy
val
mapping
=
if
(
inputR1
.
isDefined
||
(
inputBam
.
isDefined
&&
bamToFastq
))
{
val
m
=
new
Mapping
(
qscript
)
{
lazy
val
mapping
:
Option
[
Mapping
]
=
if
(
inputR1
.
isDefined
||
(
inputBam
.
isDefined
&&
bamToFastq
))
{
val
m
:
Mapping
=
new
Mapping
(
qscript
)
{
override
def
configNamespace
=
"mapping"
override
def
defaults
:
Map
[
String
,
Any
]
=
super
.
defaults
++
Map
(
"keep_final_bamfile"
->
!(
samples
(
sampleId
).
libraries
.
size
>
1
||
Map
(
"keep_final_bamfile"
->
!(
samples
(
lib
.
sampleId
).
libraries
.
size
>
1
||
preProcessBam
.
map
(
_
!=
bamFile
).
getOrElse
(
false
)))
}
m
.
sampleId
=
Some
(
sampleId
)
...
...
@@ -114,14 +114,14 @@ trait MultisampleMappingTrait extends MultiSampleQScript
Some
(
m
)
}
else
None
def
bamFile
=
mapping
match
{
def
bamFile
:
Option
[
File
]
=
mapping
match
{
case
Some
(
m
)
=>
Some
(
m
.
finalBamFile
)
case
_
if
inputBam
.
isDefined
=>
Some
(
new
File
(
libDir
,
s
"$sampleId-$libId.bam"
))
case
_
=>
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
/** This method can be extended to add jobs to the pipeline, to do this the super call of this function must be called by the pipelines */
def
addJobs
()
:
Unit
=
{
...
...
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