Commit 8f59db2c authored by bow's avatar bow
Browse files

Rename VEPNormalizer -> VepNormalizer for consistency

parent ff74a677
...@@ -7,7 +7,7 @@ The Toucan pipeline is a VEP-based annotation pipeline. ...@@ -7,7 +7,7 @@ The Toucan pipeline is a VEP-based annotation pipeline.
Currently, it comprises just two steps: Currently, it comprises just two steps:
* Variant Effect Predictor run * Variant Effect Predictor run
* [VEP Normalizer on the VEP output](../tools/VEPNormalizer.md) * [VEP Normalizer on the VEP output](../tools/VepNormalizer.md)
Example Example
----------- -----------
...@@ -34,7 +34,7 @@ It is wise to set the `cache_version` field as well. ...@@ -34,7 +34,7 @@ It is wise to set the `cache_version` field as well.
Furthermore, the `fork` field will be overwritten by `threads` in case that one exists in the config. Furthermore, the `fork` field will be overwritten by `threads` in case that one exists in the config.
Therefore, it is recommended not to use `fork`, but to rather use `threads`. Therefore, it is recommended not to use `fork`, but to rather use `threads`.
With that in mind, an example configuration using mode `standard` of the VEPNormalizer would thus be: With that in mind, an example configuration using mode `standard` of the VepNormalizer would thus be:
~~~~ ~~~~
{ {
"varianteffectpredictor": { "varianteffectpredictor": {
......
...@@ -24,7 +24,7 @@ Also a impressive list of tools have been added to the updated framework: ...@@ -24,7 +24,7 @@ Also a impressive list of tools have been added to the updated framework:
- MergeTables - MergeTables
- SamplesTsvToJson - SamplesTsvToJson
- Seqstat ( this is a lift over tool based on our previous python implementation of seqstat ) - Seqstat ( this is a lift over tool based on our previous python implementation of seqstat )
- VEPNormalizer ( This normalizer enables a user to parse VEP output VCFs to the exact specs of [VCF 4.1](https://samtools.github.io/hts-specs/VCFv4.1.pdf) ) - VepNormalizer ( This normalizer enables a user to parse VEP output VCFs to the exact specs of [VCF 4.1](https://samtools.github.io/hts-specs/VCFv4.1.pdf) )
- VcfStats - VcfStats
Some tools have a new version for better compatibility with our latest pipelines. The tools that have a changed version are: Some tools have a new version for better compatibility with our latest pipelines. The tools that have a changed version are:
......
VEPNormalizer VepNormalizer
============ ============
Introduction Introduction
...@@ -22,9 +22,9 @@ Example ...@@ -22,9 +22,9 @@ Example
--------- ---------
~~~~bash ~~~~bash
java -jar Biopet-0.3.0.jar tool VEPNormalizer -h java -jar Biopet-0.3.0.jar tool VepNormalizer -h
|VEPNormalizer - Parse VEP-annotated VCF to standard VCF format |VepNormalizer - Parse VEP-annotated VCF to standard VCF format
Usage: VEPNormalizer [options] Usage: VepNormalizer [options]
-l <value> | --log_level <value> -l <value> | --log_level <value>
Log level Log level
......
...@@ -21,7 +21,7 @@ pages: ...@@ -21,7 +21,7 @@ pages:
- ['tools/VcfFilter.md','Tools','VcfFilter'] - ['tools/VcfFilter.md','Tools','VcfFilter']
- ['tools/MpileupToVcf.md', 'Tools', 'MpileupToVcf'] - ['tools/MpileupToVcf.md', 'Tools', 'MpileupToVcf']
- ['tools/sagetools.md', 'Tools', 'Sagetools'] - ['tools/sagetools.md', 'Tools', 'Sagetools']
- ['tools/VEPNormalizer.md', 'Tools', 'VEPNormalizer'] - ['tools/VepNormalizer.md', 'Tools', 'VepNormalizer']
- ['tools/WipeReads.md', 'Tools', 'WipeReads'] - ['tools/WipeReads.md', 'Tools', 'WipeReads']
#- ['developing/Setup.md', 'Developing', 'Setting up your local development environment'] #- ['developing/Setup.md', 'Developing', 'Setting up your local development environment']
- ['about.md', 'About'] - ['about.md', 'About']
......
...@@ -38,7 +38,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable ...@@ -38,7 +38,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
* Created by ahbbollen on 10/27/14. * Created by ahbbollen on 10/27/14.
*/ */
class VEPNormalizer(val root: Configurable) extends BiopetJavaCommandLineFunction { class VepNormalizer(val root: Configurable) extends BiopetJavaCommandLineFunction {
javaMainClass = getClass.getName javaMainClass = getClass.getName
@Input(doc = "Input VCF, may be indexed", shortName = "InputFile", required = true) @Input(doc = "Input VCF, may be indexed", shortName = "InputFile", required = true)
...@@ -60,7 +60,7 @@ class VEPNormalizer(val root: Configurable) extends BiopetJavaCommandLineFunctio ...@@ -60,7 +60,7 @@ class VEPNormalizer(val root: Configurable) extends BiopetJavaCommandLineFunctio
conditional(doNotRemove, "--do-not-remove") conditional(doNotRemove, "--do-not-remove")
} }
object VEPNormalizer extends ToolCommand { object VepNormalizer extends ToolCommand {
def main(args: Array[String]): Unit = { def main(args: Array[String]): Unit = {
val commandArgs: Args = new OptParser() val commandArgs: Args = new OptParser()
......
...@@ -30,8 +30,8 @@ import htsjdk.variant.variantcontext.VariantContext ...@@ -30,8 +30,8 @@ import htsjdk.variant.variantcontext.VariantContext
* This class tests the VEPNormalizer * This class tests the VEPNormalizer
* Created by ahbbollen on 11/24/14. * Created by ahbbollen on 11/24/14.
*/ */
class VEPNormalizerTest extends TestNGSuite with MockitoSugar with Matchers { class VepNormalizerTest extends TestNGSuite with MockitoSugar with Matchers {
import VEPNormalizer._ import VepNormalizer._
private def resourcePath(p: String): String = { private def resourcePath(p: String): String = {
Paths.get(getClass.getResource(p).toURI).toString Paths.get(getClass.getResource(p).toURI).toString
......
...@@ -54,6 +54,6 @@ object BiopetExecutablePublic extends BiopetExecutable { ...@@ -54,6 +54,6 @@ object BiopetExecutablePublic extends BiopetExecutable {
nl.lumc.sasc.biopet.tools.MergeAlleles, nl.lumc.sasc.biopet.tools.MergeAlleles,
nl.lumc.sasc.biopet.tools.SamplesTsvToJson, nl.lumc.sasc.biopet.tools.SamplesTsvToJson,
nl.lumc.sasc.biopet.tools.Seqstat, nl.lumc.sasc.biopet.tools.Seqstat,
nl.lumc.sasc.biopet.tools.VEPNormalizer, nl.lumc.sasc.biopet.tools.VepNormalizer,
nl.lumc.sasc.biopet.tools.AnnotateVcfWithBed) nl.lumc.sasc.biopet.tools.AnnotateVcfWithBed)
} }
...@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.pipelines.toucan ...@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.pipelines.toucan
import nl.lumc.sasc.biopet.core.{ PipelineCommand, BiopetQScript } import nl.lumc.sasc.biopet.core.{ PipelineCommand, BiopetQScript }
import nl.lumc.sasc.biopet.core.config.Configurable import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.extensions.VariantEffectPredictor import nl.lumc.sasc.biopet.extensions.VariantEffectPredictor
import nl.lumc.sasc.biopet.tools.VEPNormalizer import nl.lumc.sasc.biopet.tools.VepNormalizer
import nl.lumc.sasc.biopet.utils.ConfigUtils import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.broadinstitute.gatk.queue.QScript import org.broadinstitute.gatk.queue.QScript
import org.broadinstitute.gatk.utils.commandline.{ Input, Argument } import org.broadinstitute.gatk.utils.commandline.{ Input, Argument }
...@@ -49,7 +49,7 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript { ...@@ -49,7 +49,7 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript {
vep.isIntermediate = true vep.isIntermediate = true
add(vep) add(vep)
val normalizer = new VEPNormalizer(this) val normalizer = new VepNormalizer(this)
normalizer.inputVCF = vep.output normalizer.inputVCF = vep.output
normalizer.outputVCF = swapExt(vep.output, ".vcf", ".normalized.vcf.gz") normalizer.outputVCF = swapExt(vep.output, ".vcf", ".normalized.vcf.gz")
add(normalizer) add(normalizer)
......
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