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
0acd0e4b
Commit
0acd0e4b
authored
Nov 22, 2014
by
Peter van 't Hof
Browse files
Added gentrap as artifact
parent
3e431336
Changes
3
Hide whitespace changes
Inline
Side-by-side
public/gentrap/.gitignore
0 → 100644
View file @
0acd0e4b
/target/
\ No newline at end of file
public/gentrap/pom.xml
0 → 100644
View file @
0acd0e4b
<project
xmlns=
"http://maven.apache.org/POM/4.0.0"
xmlns:xsi=
"http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation=
"http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd"
>
<modelVersion>
4.0.0
</modelVersion>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Gentrap
</artifactId>
<version>
0.2.0-DEV
</version>
<packaging>
jar
</packaging>
<inceptionYear>
2014
</inceptionYear>
<name>
Gentrap
</name>
<url>
http://maven.apache.org
</url>
<properties>
<project.build.sourceEncoding>
UTF-8
</project.build.sourceEncoding>
<sting.unpack.phase>
prepare-package
</sting.unpack.phase>
<sting.shade.phase>
package
</sting.shade.phase>
<app.main.class>
nl.lumc.sasc.biopet.core.BiopetExecutable
</app.main.class>
</properties>
<dependencies>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
BiopetFramework
</artifactId>
<version>
0.2.0-DEV
</version>
</dependency>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Mapping
</artifactId>
<version>
0.2.0-DEV
</version>
</dependency>
</dependencies>
<build>
<resources>
<resource>
<directory>
src/main/resources
</directory>
<includes>
<include>
**/*
</include>
</includes>
</resource>
</resources>
<plugins>
<plugin>
<groupId>
org.scala-tools
</groupId>
<artifactId>
maven-scala-plugin
</artifactId>
<version>
2.15.2
</version>
<executions>
<execution>
<id>
scala-compile
</id>
<goals>
<goal>
compile
</goal>
<goal>
testCompile
</goal>
</goals>
<configuration>
<args>
<arg>
-dependencyfile
</arg>
<arg>
${project.build.directory}/.scala_dependencies
</arg>
<arg>
-deprecation
</arg>
<arg>
-feature
</arg>
</args>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>
org.apache.maven.plugins
</groupId>
<artifactId>
maven-jar-plugin
</artifactId>
<version>
2.5
</version>
<configuration>
<archive>
<manifest>
<addDefaultImplementationEntries>
true
</addDefaultImplementationEntries>
<addDefaultSpecificationEntries>
true
</addDefaultSpecificationEntries>
</manifest>
</archive>
</configuration>
</plugin>
<plugin>
<groupId>
org.apache.maven.plugins
</groupId>
<artifactId>
maven-compiler-plugin
</artifactId>
<version>
2.3.2
</version>
<configuration>
<showDeprecation>
true
</showDeprecation>
</configuration>
</plugin>
</plugins>
</build>
</project>
public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
0 → 100644
View file @
0acd0e4b
/**
* Copyright (c) 2014 Leiden University Medical Center
*
* @author Wibowo Arindrarto
*/
package
nl.lumc.sasc.biopet.pipelines.gentrap
import
org.broadinstitute.gatk.queue.QScript
import
org.broadinstitute.gatk.queue.extensions.gatk._
import
org.broadinstitute.gatk.queue.extensions.picard._
import
org.broadinstitute.gatk.queue.function._
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Argument
}
import
nl.lumc.sasc.biopet.core._
import
nl.lumc.sasc.biopet.core.config._
import
nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
import
nl.lumc.sasc.biopet.pipelines.mapping.Mapping
/**
* Gentrap pipeline
* Generic transcriptome analysis pipeline
*/
class
Gentrap
(
val
root
:
Configurable
)
extends
QScript
with
BiopetQScript
{
def
this
()
=
this
(
null
)
/** Read 1 input */
@Input
(
doc
=
"FASTQ file input (single-end or pair 1)"
,
fullName
=
"input_r1"
,
shortName
=
"R1"
,
required
=
true
)
var
inputR1
:
File
=
_
/** Read 2 input (optional) */
@Input
(
doc
=
"FASTQ file input (pair 2)"
,
fullName
=
"input_r2"
,
shortName
=
"R2"
,
required
=
false
)
var
inputR2
:
File
=
_
/** Split aligner to use */
@Argument
(
doc
=
"Split aligner"
,
fullName
=
"aligner"
,
shortName
=
"aln"
,
required
=
true
,
validation
=
"gsnap|tophat|star"
)
var
aligner
:
String
=
_
/** Whether library is strand-specifc (dUTP protocol) or not */
@Argument
(
doc
=
"Whether input data was made using the dUTP strand-specific protocol"
,
fullName
=
"strand_specific"
,
shortName
=
"strandSpec"
,
required
=
true
)
var
strandSpec
:
Boolean
=
_
/** Variant calling */
@Argument
(
doc
=
"Variant caller"
,
fullName
=
"variant_caller"
,
shortName
=
"varCaller"
,
required
=
false
,
validation
=
"varscan|snvmix"
)
var
varcaller
:
String
=
_
/** Cufflinks assembly type */
@Argument
(
doc
=
"Cufflinks assembly type"
,
fullName
=
"transcript_asm"
,
shortName
=
"transAsm"
,
required
=
false
,
validation
=
"none|strict|guided|blind"
)
var
asm
:
List
[
String
]
=
List
(
"none"
)
/** FASTQ trimming */
@Argument
(
doc
=
"Whether to skip trimming input files"
,
fullName
=
"skip_trim_input"
,
shortName
=
"skipTrim"
,
required
=
false
)
var
skipTrim
:
Boolean
=
false
/** FASTQ clipping */
@Argument
(
doc
=
"Whether to skip clipping input files"
,
fullName
=
"skip_clip_input"
,
shortName
=
"skipClip"
,
required
=
false
)
var
skipClip
:
Boolean
=
false
/** Gene-wise read count table output */
@Argument
(
doc
=
"Gene read count table output"
,
fullName
=
"count_gene_read"
,
shortName
=
"cGeneRead"
,
required
=
false
)
var
cGeneRead
:
Boolean
=
_
/** Gene-wise base count table output */
@Argument
(
doc
=
"Gene base count table output"
,
fullName
=
"count_gene_base"
,
shortName
=
"cGeneBase"
,
required
=
false
)
var
cGeneBase
:
Boolean
=
_
/** Exon-wise base count table output */
@Argument
(
doc
=
"Exon base count table output"
,
fullName
=
"count_exon_base"
,
shortName
=
"cExonBase"
,
required
=
false
)
var
cExonBase
:
Boolean
=
_
def
init
()
{
}
def
biopetScript
()
{
}
}
object
Gentrap
extends
PipelineCommand
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