Commit 748fe576 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Merge remote-tracking branch 'remotes/origin/develop' into fix-gatk_extension_cleanup

parents f2e835df 766d624d
......@@ -156,9 +156,9 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
override def beforeGraph(): Unit = {
super.beforeGraph()
if (!cache && !database) {
Logging.addError("Must supply either cache or database for VariantEffectPredictor")
Logging.addError("Must either set 'cache' or 'database' to true for VariantEffectPredictor")
} else if (cache && dir.isEmpty) {
Logging.addError("Must supply dir to cache for VariantEffectPredictor")
Logging.addError("Must supply 'dir_cache' to cache for VariantEffectPredictor")
}
if (statsText) _summary = new File(output.getAbsolutePath + "_summary.txt")
}
......
......@@ -83,6 +83,25 @@ The following config values are optional:
Annotation queries can be set by the `annotation_queries` config value in the `manwe` config namespace.
By default, a global query is returned.
###Groups
In case you want to add your samples to a specific group in your varda database, you can use the tagging system in your sample config.
Specifically, the `varda_group` tag should be a list of strings pointing to group.
E.g. :
```json
{
"samples": {
"sample1": {
"tags": {
"varda_group": ["group1", "group2"]
}
}
}
}
```
Running the pipeline
---------------
The command to run the pipeline is:
......
......@@ -43,5 +43,17 @@
<artifactId>BiopetToolsExtensions</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.testng</groupId>
<artifactId>testng</artifactId>
<version>6.8</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.scalatest</groupId>
<artifactId>scalatest_2.10</artifactId>
<version>2.2.1</version>
<scope>test</scope>
</dependency>
</dependencies>
</project>
......@@ -40,15 +40,17 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
@Input(doc = "Input GVCF file", shortName = "gvcf", required = false)
var inputGvcf: Option[File] = None
var sampleIds: List[String] = Nil
var outputVcf: Option[File] = None
def sampleInfo: Map[String, Map[String, Any]] = root match {
case m: MultiSampleQScript => m.samples.map { case (sampleId, sample) => sampleId -> sample.sampleTags }
case null => VcfUtils.getSampleIds(inputVCF).map(x => x -> Map[String, Any]()).toMap
case s: SampleLibraryTag => s.sampleId.map(x => x -> Map[String, Any]()).toMap
case _ => throw new IllegalArgumentException("")
}
def init(): Unit = {
inputFiles :+= new InputFile(inputVCF)
sampleIds = root match {
case m: MultiSampleQScript => m.samples.keys.toList
case null => VcfUtils.getSampleIds(inputVCF)
case s: SampleLibraryTag => s.sampleId.toList
case _ => throw new IllegalArgumentException("You don't have any samples")
}
}
override def defaults = Map(
......@@ -79,29 +81,29 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
val gonlVcfFile: Option[File] = config("gonl_vcf")
val exacVcfFile: Option[File] = config("exac_vcf")
var outputFile = normalizer.outputVcf
outputVcf = Some(normalizer.outputVcf)
gonlVcfFile match {
case Some(gonlFile) =>
val vcfWithVcf = new VcfWithVcf(this)
vcfWithVcf.input = outputFile
vcfWithVcf.input = outputVcf.getOrElse(new File(""))
vcfWithVcf.secondaryVcf = gonlFile
vcfWithVcf.output = swapExt(outputDir, normalizer.outputVcf, ".vcf.gz", ".gonl.vcf.gz")
vcfWithVcf.fields ::= ("AF", "AF_gonl", None)
add(vcfWithVcf)
outputFile = vcfWithVcf.output
outputVcf = Some(vcfWithVcf.output)
case _ =>
}
exacVcfFile match {
case Some(exacFile) =>
val vcfWithVcf = new VcfWithVcf(this)
vcfWithVcf.input = outputFile
vcfWithVcf.input = outputVcf.getOrElse(new File(""))
vcfWithVcf.secondaryVcf = exacFile
vcfWithVcf.output = swapExt(outputDir, outputFile, ".vcf.gz", ".exac.vcf.gz")
vcfWithVcf.output = swapExt(outputDir, outputVcf.getOrElse(new File("")), ".vcf.gz", ".exac.vcf.gz")
vcfWithVcf.fields ::= ("AF", "AF_exac", None)
add(vcfWithVcf)
outputFile = vcfWithVcf.output
outputVcf = Some(vcfWithVcf.output)
case _ =>
}
......@@ -116,7 +118,7 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
* @param annotation: ManweDownloadAnnotateVcf object of annotated vcf
* @return
*/
def importAndActivateSample(sampleID: String, inputVcf: File,
def importAndActivateSample(sampleID: String, sampleGroups: List[String], inputVcf: File,
gVCF: File, annotation: ManweAnnotateVcf): ManweActivateAfterAnnotImport = {
val minGQ: Int = config("minimum_genome_quality", default = 20, namespace = "manwe")
......@@ -165,6 +167,7 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
imported.beds = List(bgzippedBed.output)
imported.name = Some(sampleID)
imported.public = isPublic
imported.group = sampleGroups
imported.waitToComplete = false
imported.isIntermediate = true
imported.output = swapExt(outputDir, intersected.output, ".vcf.gz", ".manwe.import")
......@@ -186,7 +189,6 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
def varda(vcf: File, gVcf: File): File = {
val annotationQueries: List[String] = config("annotation_queries", default = List("GLOBAL *"), namespace = "manwe")
//TODO: add groups!!! Need sample-specific group tags for this
val annotate = new ManweAnnotateVcf(this)
annotate.vcf = vcf
......@@ -202,7 +204,14 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
annotatedVcf.output = swapExt(outputDir, annotate.output, ".manwe.annot", "manwe.annot.vcf.gz")
add(annotatedVcf)
val activates = sampleIds map { x => importAndActivateSample(x, vcf, gVcf, annotate) }
val activates = sampleInfo map { x =>
val sampleGroup = x._2.getOrElse("varda_group", Nil) match {
case x: List[String] => x
case Nil => Nil
case _ => throw new IllegalArgumentException("Sample tag 'varda_group' is not a list of strings")
}
importAndActivateSample(x._1, sampleGroup, vcf, gVcf, annotate)
}
val finalLn = new Ln(this)
activates.foreach(x => finalLn.deps :+= x.output)
......
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