Commit 79d53026 authored by Peter van 't Hof's avatar Peter van 't Hof

Test with own scatter functions

parent 5f206fa7
......@@ -13,17 +13,23 @@ trait GatkGeneral extends BiopetJavaCommandLineFunction {
override val defaultVmem = "7G"
@Input(required = false)
var intervals: List[File] = config("intervals", submodule = "gatk").getFileList
var intervals: List[File] = Nil
if (config.contains("intervals", submodule = "gatk"))
intervals = config("intervals", submodule = "gatk").getFileList
@Input(required = false)
var excludeIntervals: List[File] = config("exclude_intervals", submodule = "gatk").getFileList
var excludeIntervals: List[File] = Nil
if (config.contains("exclude_intervals", submodule = "gatk"))
excludeIntervals = config("exclude_intervals", submodule = "gatk").getFileList
var reference_sequence: File = config("reference", submodule = "gatk")
var gatkKey: File = config("gatk_key", submodule = "gatk")
@Input(required = false)
var pedigree: List[File] = config("pedigree", submodule = "gatk").getFileList
var pedigree: List[File] = Nil
if (config.contains("pedigree", submodule = "gatk"))
config("pedigree", submodule = "gatk").getFileList
override def commandLine = super.commandLine +
required("--analysis_type", analysis) +
......
......@@ -22,7 +22,7 @@ class HaplotypeCaller(val root: Configurable) extends GatkGeneral with ScatterGa
@Output(required = true)
@Gather(classOf[CatVariantsGatherer])
var output: File = _
var out: File = _
var samplePloidy: Option[Int] = config("ploidy")
......@@ -39,7 +39,7 @@ class HaplotypeCaller(val root: Configurable) extends GatkGeneral with ScatterGa
override def commandLine = super.commandLine +
repeat("-I", input) +
required("-o", output) +
required("-o", out) +
optional("--sample_ploidy", samplePloidy) +
conditional(allSitePLs, "--allSitePLs") +
optional("--stand_call_conf", standCallConf) +
......
......@@ -108,8 +108,8 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
add(genotypeGVCFs)
scriptOutput.hcVcfFile = genotypeGVCFs.out
} else {
val hcGvcf = new HaplotypeCaller(this)
hcGvcf.input_file = scriptOutput.bamFiles
val hcGvcf = new nl.lumc.sasc.biopet.extensions.gatk.own.HaplotypeCaller(this)
hcGvcf.input = scriptOutput.bamFiles
hcGvcf.out = outputDir + outputName + ".hc.discovery.vcf.gz"
add(hcGvcf)
scriptOutput.hcVcfFile = hcGvcf.out
......
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