Skip to content
GitLab
Projects
Groups
Snippets
Help
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
B
biopet.biopet
Project overview
Project overview
Details
Activity
Releases
Repository
Repository
Files
Commits
Branches
Tags
Contributors
Graph
Compare
CI / CD
CI / CD
Pipelines
Jobs
Schedules
Operations
Operations
Environments
Analytics
Analytics
CI / CD
Repository
Value Stream
Members
Members
Collapse sidebar
Close sidebar
Activity
Graph
Jobs
Commits
Open sidebar
Mirrors
biopet.biopet
Commits
9869bfcd
Commit
9869bfcd
authored
Feb 09, 2017
by
Sander Bollen
Committed by
GitHub
Feb 09, 2017
Browse files
Options
Browse Files
Download
Plain Diff
Merge pull request #21 from biopet/fix-BIOPET-563
Fixing dependency issue
parents
cdbe8460
2b9de137
Changes
5
Hide whitespace changes
Inline
Side-by-side
Showing
5 changed files
with
20 additions
and
18 deletions
+20
-18
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/DellyCaller.scala
...la/nl/lumc/sasc/biopet/extensions/delly/DellyCaller.scala
+0
-5
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
...a/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
+5
-4
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
...ala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
+2
-2
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
...scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+5
-4
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMapping.scala
...mc/sasc/biopet/pipelines/mapping/MultisampleMapping.scala
+8
-3
No files found.
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/DellyCaller.scala
View file @
9869bfcd
...
...
@@ -41,11 +41,6 @@ class DellyCaller(val root: Configurable) extends BiopetCommandLineFunction with
@Argument
(
doc
=
"What kind of analysis to run: DEL,DUP,INV,TRA"
)
var
analysistype
:
String
=
_
override
def
beforeGraph
()
:
Unit
=
{
super
.
beforeGraph
()
deps
::=
new
File
(
input
.
getParentFile
,
input
.
getName
+
".bai"
)
}
def
cmdLine
=
required
(
executable
)
+
"-t"
+
required
(
analysistype
)
+
"-o"
+
required
(
outputvcf
)
+
...
...
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
View file @
9869bfcd
...
...
@@ -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
...
...
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala
View file @
9869bfcd
...
...
@@ -84,13 +84,13 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
protected
def
executeFlexiprep
(
r1
:
List
[
File
],
r2
:
List
[
File
])
:
(
File
,
Option
[
File
])
=
{
val
read1
:
File
=
if
(
r1
.
size
==
1
)
r1
.
head
else
{
val
outputFile
=
new
File
(
outputDir
,
"merged.R1.fq.gz"
)
Zcat
(
this
,
r1
)
|
new
Gzip
(
this
)
>
outputFile
add
(
Zcat
(
this
,
r1
)
|
new
Gzip
(
this
)
>
outputFile
)
outputFile
}
val
read2
:
Option
[
File
]
=
if
(
r2
.
size
<=
1
)
r2
.
headOption
else
{
val
outputFile
=
new
File
(
outputDir
,
"merged.R2.fq.gz"
)
Zcat
(
this
,
r2
)
|
new
Gzip
(
this
)
>
outputFile
add
(
Zcat
(
this
,
r2
)
|
new
Gzip
(
this
)
>
outputFile
)
Some
(
outputFile
)
}
...
...
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
9869bfcd
...
...
@@ -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
...
...
@@ -178,6 +178,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
}
}
logger
.
debug
(
"Chunks: "
+
numberChunks
.
getOrElse
(
1
))
if
(
numberChunks
.
getOrElse
(
1
)
<=
1
)
chunking
=
false
}
}
...
...
@@ -295,7 +296,7 @@ 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
...
...
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMapping.scala
View file @
9869bfcd
...
...
@@ -67,7 +67,10 @@ trait MultisampleMappingTrait extends MultiSampleQScript
Some
(
report
)
}
override
def
defaults
:
Map
[
String
,
Any
]
=
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
),
"gears"
->
Map
(
"skip_flexiprep"
->
true
)
)
override
def
fixedValues
:
Map
[
String
,
Any
]
=
super
.
fixedValues
++
Map
(
"gearssingle"
->
Map
(
"skip_flexiprep"
->
true
))
...
...
@@ -99,6 +102,8 @@ trait MultisampleMappingTrait extends MultiSampleQScript
lazy
val
inputR1
:
Option
[
File
]
=
MultisampleMapping
.
fileMustBeAbsolute
(
config
(
"R1"
))
lazy
val
inputR2
:
Option
[
File
]
=
MultisampleMapping
.
fileMustBeAbsolute
(
config
(
"R2"
))
lazy
val
qcFastqR1
=
mapping
.
map
(
_
.
flexiprep
.
fastqR1Qc
)
lazy
val
qcFastqR2
=
mapping
.
flatMap
(
_
.
flexiprep
.
fastqR2Qc
)
lazy
val
inputBam
:
Option
[
File
]
=
MultisampleMapping
.
fileMustBeAbsolute
(
if
(
inputR1
.
isEmpty
)
config
(
"bam"
)
else
None
)
lazy
val
bamToFastq
:
Boolean
=
config
(
"bam_to_fastq"
,
default
=
false
)
lazy
val
correctReadgroups
:
Boolean
=
config
(
"correct_readgroups"
,
default
=
false
)
...
...
@@ -274,8 +279,8 @@ trait MultisampleMappingTrait extends MultiSampleQScript
add
(
gears
)
case
"all"
=>
val
gears
=
new
GearsSingle
(
qscript
)
gears
.
fastqR1
=
libraries
.
flatMap
(
_
.
_2
.
input
R1
).
toList
gears
.
fastqR2
=
libraries
.
flatMap
(
_
.
_2
.
input
R2
).
toList
gears
.
fastqR1
=
libraries
.
flatMap
(
_
.
_2
.
qcFastq
R1
).
toList
gears
.
fastqR2
=
libraries
.
flatMap
(
_
.
_2
.
qcFastq
R2
).
toList
gears
.
sampleId
=
Some
(
sampleId
)
gears
.
outputDir
=
new
File
(
sampleDir
,
"gears"
)
add
(
gears
)
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a 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