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biopet.biopet
Commits
1eada82e
Commit
1eada82e
authored
Apr 06, 2015
by
Peter van 't Hof
Browse files
Switch pipeline to reference module
parent
1bdbed83
Changes
20
Hide whitespace changes
Inline
Side-by-side
protected/biopet-gatk-pipelines/src/test/resources/ref.dict
0 → 100644
View file @
1eada82e
@HD VN:1.4 SO:unsorted
@SQ SN:chr1 LN:9 UR:file:/home/pjvan_thof/pipelines/biopet/public/mapping/src/test/resources/ref.fa M5:fe15dbbd0900310caf32827f6da57550
protected/biopet-gatk-pipelines/src/test/resources/ref.fa
0 → 100644
View file @
1eada82e
>chr1
AGTAGTAGT
protected/biopet-gatk-pipelines/src/test/resources/ref.fa.fai
0 → 100644
View file @
1eada82e
chr1 9 6 9 10
protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala
View file @
1eada82e
...
...
@@ -5,6 +5,8 @@
*/
package
nl.lumc.sasc.biopet.pipelines.gatk
import
java.io.
{
FileOutputStream
,
File
}
import
com.google.common.io.Files
import
nl.lumc.sasc.biopet.core.config.Config
import
nl.lumc.sasc.biopet.extensions.bwa.BwaMem
...
...
@@ -90,10 +92,22 @@ class ShivaTest extends TestNGSuite with Matchers {
object
ShivaTest
{
val
outputDir
=
Files
.
createTempDir
()
private
def
copyFile
(
name
:
String
)
:
Unit
=
{
val
is
=
getClass
.
getResourceAsStream
(
"/"
+
name
)
val
os
=
new
FileOutputStream
(
new
File
(
outputDir
,
name
))
org
.
apache
.
commons
.
io
.
IOUtils
.
copy
(
is
,
os
)
os
.
close
()
}
copyFile
(
"ref.fa"
)
copyFile
(
"ref.dict"
)
copyFile
(
"ref.fa.fai"
)
val
config
=
Map
(
"name_prefix"
->
"test"
,
"output_dir"
->
outputDir
,
"reference"
->
"test"
,
"reference"
->
(
outputDir
+
File
.
separator
+
"ref.fa"
),
"referenceFasta"
->
(
outputDir
+
File
.
separator
+
"ref.fa"
),
"gatk_jar"
->
"test"
,
"samtools"
->
Map
(
"exe"
->
"test"
),
"bcftools"
->
Map
(
"exe"
->
"test"
),
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
View file @
1eada82e
...
...
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions.bwa
import
java.io.File
import
nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import
nl.lumc.sasc.biopet.core.
{
Reference
,
BiopetCommandLineFunction
}
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.core.summary.Summarizable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
...
...
@@ -27,7 +27,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
*
* Based on version 0.7.12-r1039
*/
class
BwaMem
(
val
root
:
Configurable
)
extends
Bwa
{
class
BwaMem
(
val
root
:
Configurable
)
extends
Bwa
with
Reference
{
@Input
(
doc
=
"Fastq file R1"
,
shortName
=
"R1"
)
var
R1
:
File
=
_
...
...
@@ -35,7 +35,7 @@ class BwaMem(val root: Configurable) extends Bwa {
var
R2
:
File
=
_
@Input
(
doc
=
"The reference file for the bam files."
,
shortName
=
"R"
)
var
reference
:
File
=
config
(
"
reference
"
)
var
reference
:
File
=
reference
Fasta
(
)
@Output
(
doc
=
"Output file SAM"
,
shortName
=
"output"
)
var
output
:
File
=
_
...
...
public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
View file @
1eada82e
...
...
@@ -35,7 +35,7 @@ import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
* Chip-Seq analysis pipeline
* This pipeline performs QC,mapping and peak calling
*/
class
Carp
(
val
root
:
Configurable
)
extends
QScript
with
MultiSampleQScript
with
SummaryQScript
{
class
Carp
(
val
root
:
Configurable
)
extends
QScript
with
MultiSampleQScript
with
SummaryQScript
with
Reference
{
qscript
=>
def
this
()
=
this
(
null
)
...
...
public/carp/src/test/resources/ref.dict
0 → 100644
View file @
1eada82e
@HD VN:1.4 SO:unsorted
@SQ SN:chr1 LN:9 UR:file:/home/pjvan_thof/pipelines/biopet/public/mapping/src/test/resources/ref.fa M5:fe15dbbd0900310caf32827f6da57550
public/carp/src/test/resources/ref.fa
0 → 100644
View file @
1eada82e
>chr1
AGTAGTAGT
public/carp/src/test/resources/ref.fa.fai
0 → 100644
View file @
1eada82e
chr1 9 6 9 10
public/carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala
View file @
1eada82e
...
...
@@ -15,7 +15,7 @@
*/
package
nl.lumc.sasc.biopet.pipelines.carp
import
java.io.File
import
java.io.
{
File
OutputStream
,
File
}
import
com.google.common.io.Files
import
org.apache.commons.io.FileUtils
...
...
@@ -97,8 +97,20 @@ class CarpTest extends TestNGSuite with Matchers {
object
CarpTest
{
val
outputDir
=
Files
.
createTempDir
()
private
def
copyFile
(
name
:
String
)
:
Unit
=
{
val
is
=
getClass
.
getResourceAsStream
(
"/"
+
name
)
val
os
=
new
FileOutputStream
(
new
File
(
outputDir
,
name
))
org
.
apache
.
commons
.
io
.
IOUtils
.
copy
(
is
,
os
)
os
.
close
()
}
copyFile
(
"ref.fa"
)
copyFile
(
"ref.dict"
)
copyFile
(
"ref.fa.fai"
)
val
executables
=
Map
(
"reference"
->
"test"
,
"reference"
->
(
outputDir
+
File
.
separator
+
"ref.fa"
),
"referenceFasta"
->
(
outputDir
+
File
.
separator
+
"ref.fa"
),
"fastqc"
->
Map
(
"exe"
->
"test"
),
"seqtk"
->
Map
(
"exe"
->
"test"
),
"sickle"
->
Map
(
"exe"
->
"test"
),
...
...
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
1eada82e
...
...
@@ -21,10 +21,9 @@ import scala.math._
import
org.broadinstitute.gatk.queue.QScript
import
nl.lumc.sasc.biopet.core.
{
SampleLibraryTag
,
PipelineCommand
}
import
nl.lumc.sasc.biopet.core.
_
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.core.summary.SummaryQScript
import
nl.lumc.sasc.biopet.core.
{
SampleLibraryTag
,
BiopetQScript
,
PipelineCommand
}
import
nl.lumc.sasc.biopet.extensions._
import
nl.lumc.sasc.biopet.extensions.bwa.
{
BwaSamse
,
BwaSampe
,
BwaAln
,
BwaMem
}
import
nl.lumc.sasc.biopet.extensions.
{
Gsnap
,
Tophat
}
...
...
@@ -35,7 +34,7 @@ import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
import
nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
// TODO: documentation
class
Mapping
(
val
root
:
Configurable
)
extends
QScript
with
SummaryQScript
with
SampleLibraryTag
{
class
Mapping
(
val
root
:
Configurable
)
extends
QScript
with
SummaryQScript
with
SampleLibraryTag
with
Reference
{
def
this
()
=
this
(
null
)
...
...
@@ -112,7 +111,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
"aligner"
->
aligner
,
"chunking"
->
chunking
,
"numberChunks"
->
numberChunks
.
getOrElse
(
1
)
)
)
++
(
if
(
root
==
null
)
Map
()
else
Map
(
"reference"
->
referenceSummary
))
/** Will be executed before script */
def
init
()
{
...
...
public/mapping/src/test/resources/ref.dict
0 → 100644
View file @
1eada82e
@HD VN:1.4 SO:unsorted
@SQ SN:chr1 LN:9 UR:file:/home/pjvan_thof/pipelines/biopet/public/mapping/src/test/resources/ref.fa M5:fe15dbbd0900310caf32827f6da57550
public/mapping/src/test/resources/ref.fa
0 → 100644
View file @
1eada82e
>chr1
AGTAGTAGT
public/mapping/src/test/resources/ref.fa.fai
0 → 100644
View file @
1eada82e
chr1 9 6 9 10
public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
View file @
1eada82e
...
...
@@ -15,7 +15,7 @@
*/
package
nl.lumc.sasc.biopet.pipelines.mapping
import
java.io.File
import
java.io.
{
File
OutputStream
,
File
}
import
com.google.common.io.Files
import
nl.lumc.sasc.biopet.extensions._
...
...
@@ -130,8 +130,20 @@ class MappingTest extends TestNGSuite with Matchers {
object
MappingTest
{
val
outputDir
=
Files
.
createTempDir
()
private
def
copyFile
(
name
:
String
)
:
Unit
=
{
val
is
=
getClass
.
getResourceAsStream
(
"/"
+
name
)
val
os
=
new
FileOutputStream
(
new
File
(
outputDir
,
name
))
org
.
apache
.
commons
.
io
.
IOUtils
.
copy
(
is
,
os
)
os
.
close
()
}
copyFile
(
"ref.fa"
)
copyFile
(
"ref.dict"
)
copyFile
(
"ref.fa.fai"
)
val
executables
=
Map
(
"reference"
->
"test"
,
"reference"
->
(
outputDir
+
File
.
separator
+
"ref.fa"
),
"referenceFasta"
->
(
outputDir
+
File
.
separator
+
"ref.fa"
),
"fastqc"
->
Map
(
"exe"
->
"test"
),
"seqtk"
->
Map
(
"exe"
->
"test"
),
"sickle"
->
Map
(
"exe"
->
"test"
),
...
...
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
View file @
1eada82e
...
...
@@ -19,7 +19,7 @@ import java.io.File
import
htsjdk.samtools.SamReaderFactory
import
nl.lumc.sasc.biopet.core.summary.SummaryQScript
import
nl.lumc.sasc.biopet.core.MultiSampleQScript
import
nl.lumc.sasc.biopet.core.
{
Reference
,
MultiSampleQScript
}
import
nl.lumc.sasc.biopet.extensions.Ln
import
nl.lumc.sasc.biopet.extensions.picard.
{
AddOrReplaceReadGroups
,
SamToFastq
,
MarkDuplicates
}
import
nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
...
...
@@ -31,7 +31,7 @@ import scala.collection.JavaConversions._
*
* Created by pjvan_thof on 2/26/15.
*/
trait
ShivaTrait
extends
MultiSampleQScript
with
SummaryQScript
{
trait
ShivaTrait
extends
MultiSampleQScript
with
SummaryQScript
with
Reference
{
qscript
=>
/** Executed before running the script */
...
...
@@ -286,8 +286,8 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
def
summaryFile
=
new
File
(
outputDir
,
"Shiva.summary.json"
)
/** Settings of pipeline for summary */
def
summarySettings
=
Map
()
def
summarySettings
=
Map
(
"reference"
->
referenceSummary
)
/** Files for the summary */
def
summaryFiles
=
Map
()
def
summaryFiles
=
Map
(
"referenceFasta"
->
referenceFasta
()
)
}
public/shiva/src/test/resources/ref.dict
0 → 100644
View file @
1eada82e
@HD VN:1.4 SO:unsorted
@SQ SN:chr1 LN:9 UR:file:/home/pjvan_thof/pipelines/biopet/public/mapping/src/test/resources/ref.fa M5:fe15dbbd0900310caf32827f6da57550
public/shiva/src/test/resources/ref.fa
0 → 100644
View file @
1eada82e
>chr1
AGTAGTAGT
public/shiva/src/test/resources/ref.fa.fai
0 → 100644
View file @
1eada82e
chr1 9 6 9 10
public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
View file @
1eada82e
...
...
@@ -15,6 +15,8 @@
*/
package
nl.lumc.sasc.biopet.pipelines.shiva
import
java.io.
{
File
,
FileOutputStream
}
import
com.google.common.io.Files
import
nl.lumc.sasc.biopet.core.config.Config
import
nl.lumc.sasc.biopet.extensions.bwa.BwaMem
...
...
@@ -85,10 +87,22 @@ class ShivaTest extends TestNGSuite with Matchers {
object
ShivaTest
{
val
outputDir
=
Files
.
createTempDir
()
private
def
copyFile
(
name
:
String
)
:
Unit
=
{
val
is
=
getClass
.
getResourceAsStream
(
"/"
+
name
)
val
os
=
new
FileOutputStream
(
new
File
(
outputDir
,
name
))
org
.
apache
.
commons
.
io
.
IOUtils
.
copy
(
is
,
os
)
os
.
close
()
}
copyFile
(
"ref.fa"
)
copyFile
(
"ref.dict"
)
copyFile
(
"ref.fa.fai"
)
val
config
=
Map
(
"name_prefix"
->
"test"
,
"output_dir"
->
outputDir
,
"reference"
->
"test"
,
"reference"
->
(
outputDir
+
File
.
separator
+
"ref.fa"
),
"referenceFasta"
->
(
outputDir
+
File
.
separator
+
"ref.fa"
),
"gatk_jar"
->
"test"
,
"samtools"
->
Map
(
"exe"
->
"test"
),
"bcftools"
->
Map
(
"exe"
->
"test"
),
...
...
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