Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Mirrors
biopet.biopet
Commits
ee949ad1
Commit
ee949ad1
authored
Feb 07, 2017
by
Peter van 't Hof
Browse files
Fixing code warnings
parent
cefa43a5
Changes
2
Hide whitespace changes
Inline
Side-by-side
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
View file @
ee949ad1
...
...
@@ -62,7 +62,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
var
fastqcR1After
:
Fastqc
=
_
var
fastqcR2After
:
Fastqc
=
_
override
def
reportClass
=
{
override
def
reportClass
:
Some
[
FlexiprepReport
]
=
{
val
flexiprepReport
=
new
FlexiprepReport
(
this
)
flexiprepReport
.
outputDir
=
new
File
(
outputDir
,
"report"
)
flexiprepReport
.
summaryFile
=
summaryFile
...
...
@@ -74,6 +74,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
/** Function that's need to be executed before the script is accessed */
def
init
()
{
paired
=
inputR2
.
isDefined
if
(
inputR1
==
null
)
Logging
.
addError
(
"Missing input R1 on flexiprep module"
)
if
(
sampleId
==
null
||
sampleId
.
isEmpty
)
Logging
.
addError
(
"Missing sample ID on flexiprep module"
)
if
(
libId
==
null
||
libId
.
isEmpty
)
Logging
.
addError
(
"Missing library ID on flexiprep module"
)
...
...
@@ -147,10 +148,10 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
}
}
def
fastqR1Qc
=
if
(
paired
)
def
fastqR1Qc
:
File
=
if
(
paired
)
new
File
(
outputDir
,
s
"${sampleId.getOrElse("
x
")}-${libId.getOrElse("
x
")}.R1.qc.sync.fq.gz"
)
else
new
File
(
outputDir
,
s
"${sampleId.getOrElse("
x
")}-${libId.getOrElse("
x
")}.R1.qc.fq.gz"
)
def
fastqR2Qc
=
if
(
paired
)
def
fastqR2Qc
:
Option
[
File
]
=
if
(
paired
)
Some
(
new
File
(
outputDir
,
s
"${sampleId.getOrElse("
x
")}-${libId.getOrElse("
x
")}.R2.qc.sync.fq.gz"
))
else
None
...
...
@@ -225,7 +226,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
/** Must returns stats to store into summary */
def
summaryStats
:
Any
=
Map
()
override
def
summaryDeps
=
qcCmdR1
.
summaryDeps
:::
qcCmdR2
.
summaryDeps
:::
super
.
summaryDeps
override
def
summaryDeps
:
List
[
File
]
=
qcCmdR1
.
summaryDeps
:::
qcCmdR2
.
summaryDeps
:::
super
.
summaryDeps
}
pipe
.
deps
::=
fastqcR1
.
output
...
...
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
ee949ad1
...
...
@@ -31,7 +31,7 @@ import nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
import
nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
import
nl.lumc.sasc.biopet.pipelines.gears.GearsSingle
import
nl.lumc.sasc.biopet.pipelines.mapping.scripts.TophatRecondition
import
nl.lumc.sasc.biopet.utils.
{
Logging
,
textToSize
}
import
nl.lumc.sasc.biopet.utils.textToSize
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.queue.QScript
...
...
@@ -127,7 +127,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
})
/** Settings to add to summary */
def
summarySettings
=
Map
(
def
summarySettings
:
Map
[
String
,
Any
]
=
Map
(
"skip_metrics"
->
skipMetrics
,
"skip_flexiprep"
->
skipFlexiprep
,
"skip_markduplicates"
->
skipMarkduplicates
,
...
...
@@ -137,7 +137,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
"number_of_chunks"
->
(
if
(
chunking
)
numberChunks
.
getOrElse
(
1
)
else
None
)
)
++
(
if
(
root
==
null
)
Map
(
"reference"
->
referenceSummary
)
else
Map
())
override
def
reportClass
=
{
override
def
reportClass
:
Some
[
MappingReport
]
=
{
val
mappingReport
=
new
MappingReport
(
this
)
mappingReport
.
outputDir
=
new
File
(
outputDir
,
"report"
)
mappingReport
.
summaryFile
=
summaryFile
...
...
@@ -295,7 +295,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
addSummaryJobs
()
}
protected
lazy
val
bam2wig
=
if
(
config
(
"generate_wig"
,
default
=
false
))
{
protected
lazy
val
bam2wig
:
Option
[
Bam2Wig
]
=
if
(
config
(
"generate_wig"
,
default
=
false
))
{
Some
(
Bam2Wig
(
this
,
finalBamFile
))
}
else
None
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment