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biopet.biopet
Commits
ee949ad1
Commit
ee949ad1
authored
Feb 07, 2017
by
Peter van 't Hof
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Plain Diff
Fixing code warnings
parent
cefa43a5
Changes
2
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2 changed files
with
9 additions
and
8 deletions
+9
-8
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
...a/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
+5
-4
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
...scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+4
-4
No files found.
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
...
...
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