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
a10e91cf
Commit
a10e91cf
authored
Dec 03, 2015
by
Peter van 't Hof
Browse files
Rename old Gears to GearsSingle
parent
8e1b1d70
Changes
5
Hide whitespace changes
Inline
Side-by-side
public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/BiopetExecutablePublic.scala
View file @
a10e91cf
...
...
@@ -28,7 +28,7 @@ object BiopetExecutablePublic extends BiopetExecutable {
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
carp
.
Carp
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
toucan
.
Toucan
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
shiva
.
ShivaSvCalling
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
gears
.
Gears
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
gears
.
Gears
Single
)
def
pipelines
:
List
[
MainCommand
]
=
List
(
...
...
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
→
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears
Single
.scala
View file @
a10e91cf
...
...
@@ -28,7 +28,7 @@ import org.broadinstitute.gatk.queue.QScript
/**
* Created by wyleung
*/
class
Gears
(
val
root
:
Configurable
)
extends
QScript
with
SummaryQScript
with
SampleLibraryTag
{
class
Gears
Single
(
val
root
:
Configurable
)
extends
QScript
with
SummaryQScript
with
SampleLibraryTag
{
def
this
()
=
this
(
null
)
@Input
(
doc
=
"R1 reads in FastQ format"
,
shortName
=
"R1"
,
required
=
false
)
...
...
@@ -66,7 +66,7 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript with Sam
}
override
def
reportClass
=
{
val
gears
=
new
GearsReport
(
this
)
val
gears
=
new
Gears
Single
Report
(
this
)
gears
.
outputDir
=
new
File
(
outputDir
,
"report"
)
gears
.
summaryFile
=
summaryFile
sampleId
.
foreach
(
gears
.
args
+=
"sampleId"
->
_
)
...
...
@@ -155,4 +155,4 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript with Sam
}
/** This object give a default main method to the pipelines */
object
Gears
extends
PipelineCommand
\ No newline at end of file
object
GearsSingle
extends
PipelineCommand
\ No newline at end of file
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
→
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears
Single
Report.scala
View file @
a10e91cf
...
...
@@ -18,11 +18,11 @@ package nl.lumc.sasc.biopet.pipelines.gears
import
nl.lumc.sasc.biopet.core.report._
import
nl.lumc.sasc.biopet.utils.config.Configurable
class
GearsReport
(
val
root
:
Configurable
)
extends
ReportBuilderExtension
{
def
builder
=
GearsReport
class
Gears
Single
Report
(
val
root
:
Configurable
)
extends
ReportBuilderExtension
{
def
builder
=
Gears
Single
Report
}
object
GearsReport
extends
ReportBuilder
{
object
Gears
Single
Report
extends
ReportBuilder
{
// TODO: Add dustbin analysis (aggregated)
// TODO: Add alignment stats per sample for the dustbin analysis
...
...
public/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTest.scala
→
public/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears
Single
Test.scala
View file @
a10e91cf
...
...
@@ -31,14 +31,14 @@ import org.scalatest.testng.TestNGSuite
import
org.testng.annotations._
/**
* Test class for [[Gears]]
* Test class for [[Gears
Single
]]
*
* Created by wyleung on 10/22/15.
*/
class
Gears
Pipelin
eTest
(
val
testset
:
String
)
extends
TestNGSuite
with
Matchers
{
def
initPipeline
(
map
:
Map
[
String
,
Any
])
:
Gears
=
{
new
Gears
{
class
Gears
Singl
eTest
(
val
testset
:
String
)
extends
TestNGSuite
with
Matchers
{
def
initPipeline
(
map
:
Map
[
String
,
Any
])
:
Gears
Single
=
{
new
Gears
Single
{
override
def
configName
=
"gears"
override
def
globalConfig
=
new
Config
(
map
)
...
...
@@ -67,16 +67,16 @@ class GearsPipelineTest(val testset: String) extends TestNGSuite with Matchers {
def
testGears
(
testset
:
String
,
fromBam
:
Boolean
,
paired
:
Boolean
,
hasOutputName
:
Boolean
,
hasFileExtension
:
Boolean
)
=
{
val
map
=
ConfigUtils
.
mergeMaps
(
Map
(
"output_dir"
->
GearsTest
.
outputDir
),
Map
(
GearsTest
.
executables
.
toSeq
:
_
*
))
"output_dir"
->
Gears
Single
Test
.
outputDir
),
Map
(
Gears
Single
Test
.
executables
.
toSeq
:
_
*
))
val
gears
:
Gears
=
initPipeline
(
map
)
val
gears
:
Gears
Single
=
initPipeline
(
map
)
if
(
fromBam
)
{
gears
.
bamFile
=
if
(
hasFileExtension
)
Some
(
GearsTest
.
bam
)
else
Some
(
GearsTest
.
bam_noext
)
gears
.
bamFile
=
if
(
hasFileExtension
)
Some
(
Gears
Single
Test
.
bam
)
else
Some
(
Gears
Single
Test
.
bam_noext
)
}
else
{
gears
.
fastqR1
=
if
(
hasFileExtension
)
Some
(
GearsTest
.
r1
)
else
Some
(
GearsTest
.
r1_noext
)
gears
.
fastqR2
=
if
(
paired
)
if
(
hasFileExtension
)
Some
(
GearsTest
.
r2
)
else
Some
(
GearsTest
.
r2_noext
)
else
None
gears
.
fastqR1
=
if
(
hasFileExtension
)
Some
(
Gears
Single
Test
.
r1
)
else
Some
(
Gears
Single
Test
.
r1_noext
)
gears
.
fastqR2
=
if
(
paired
)
if
(
hasFileExtension
)
Some
(
Gears
Single
Test
.
r2
)
else
Some
(
Gears
Single
Test
.
r2_noext
)
else
None
}
if
(
hasOutputName
)
gears
.
outputName
=
"test"
...
...
@@ -106,11 +106,11 @@ class GearsPipelineTest(val testset: String) extends TestNGSuite with Matchers {
// remove temporary run directory all tests in the class have been run
@AfterClass
def
removeTempOutputDir
()
=
{
FileUtils
.
deleteDirectory
(
GearsTest
.
outputDir
)
FileUtils
.
deleteDirectory
(
Gears
Single
Test
.
outputDir
)
}
}
object
GearsTest
{
object
Gears
Single
Test
{
val
outputDir
=
Files
.
createTempDir
()
new
File
(
outputDir
,
"input"
).
mkdirs
()
...
...
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
a10e91cf
...
...
@@ -27,7 +27,7 @@ import nl.lumc.sasc.biopet.extensions.{ Gsnap, Tophat, _ }
import
nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
import
nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
import
nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
import
nl.lumc.sasc.biopet.pipelines.gears.Gears
import
nl.lumc.sasc.biopet.pipelines.gears.Gears
Single
import
nl.lumc.sasc.biopet.pipelines.mapping.scripts.TophatRecondition
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.queue.QScript
...
...
@@ -259,7 +259,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
outputFiles
+=
(
"finalBamFile"
->
finalBamFile
.
getAbsoluteFile
)
if
(
config
(
"unmapped_to_gears"
,
default
=
false
).
asBoolean
)
{
val
gears
=
new
Gears
(
this
)
val
gears
=
new
Gears
Single
(
this
)
gears
.
bamFile
=
Some
(
finalBamFile
)
gears
.
outputDir
=
new
File
(
outputDir
,
"gears"
)
gears
.
init
()
...
...
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