diff --git a/biopet.wdl b/biopet.wdl index 6336e48226e3fa227719c3e93fd7f8a2b57557fa..eaf6664ab9448cb4131467995fa03caab5b4dfd8 100644 --- a/biopet.wdl +++ b/biopet.wdl @@ -482,7 +482,55 @@ task VcfStats { } output { - String resultsDir = outputDir + File? general = outputDir + "/general.tsv" + File? genotype = outputDir + "/genotype.tsv" + File? sampleDistributionAvailableAggregate = outputDir + + "/sample_distributions/Available.aggregate.tsv" + File? sampleDistributionAvailable = outputDir + "/sample_distributions/Available.tsv" + File? sampleDistributionCalledAggregate = outputDir + + "/sample_distributions/Called.aggregate.tsv" + File? sampleDistributionCalled = outputDir + "/sample_distributions/Called.tsv" + File? sampleDistributionFilteredAggregate = outputDir + + "/sample_distributions/Filtered.aggregate.tsv" + File? sampleDistributionFiltered = outputDir + "/sample_distributions/Filtered.tsv" + File? sampleDistributionHetAggregate = outputDir + "/sample_distributions/Het.aggregate.tsv" + File? sampleDistributionHetNoNRefAggregate = outputDir + + "/sample_distributions/HetNonRef.aggregate.tsv" + File? sampleDistributionHetNonRef = outputDir + "/sample_distributions/HetNonRef.tsv" + File? sampleDistributionHet = outputDir + "/sample_distributions/Het.tsv" + File? sampleDistributionHomAggregate = outputDir + "/sample_distributions/Hom.aggregate.tsv" + File? sampleDistributionHomRefAggregate = outputDir + + "/sample_distributions/HomRef.aggregate.tsv" + File? sampleDistributionHomRef = outputDir + "/sample_distributions/HomRef.tsv" + File? sampleDistributionHom = outputDir + "/sample_distributions/Hom.tsv" + File? sampleDistributionHomVarAggregate = outputDir + + "/sample_distributions/HomVar.aggregate.tsv" + File? sampleDistributionHomVar = outputDir + "/sample_distributions/HomVar.tsv" + File? sampleDistributionMixedAggregate = outputDir + + "/sample_distributions/Mixed.aggregate.tsv" + File? sampleDistributionMixed = outputDir + "/sample_distributions/Mixed.tsv" + File? sampleDistributionNoCallAggregate = outputDir + + "/sample_distributions/NoCall.aggregate.tsv" + File? sampleDistributionNoCall = outputDir + "/sample_distributions/NoCall.tsv" + File? sampleDistributionNonInformativeAggregate = outputDir + + "/sample_distributions/NonInformative.aggregate.tsv" + File? sampleDistributionNonInformative = outputDir + + "/sample_distributions/NonInformative.tsv" + File? sampleDistributionToalAggregate = outputDir + + "/sample_distributions/Total.aggregate.tsv" + File? sampleDistributionTotal = outputDir + "/sample_distributions/Total.tsv" + File? sampleDistributionVariantAggregate = outputDir + + "/sample_distributions/Variant.aggregate.tsv" + File? sampleDistributionVariant = outputDir + "/sample_distributions/Variant.tsv" + File? sampleCompareAlleleAbs = outputDir + "/sample_compare/allele.abs.tsv" + File? sampleCompareAlleleNonRefAbs = outputDir + "/sample_compare/allele.non_ref.abs.tsv" + File? sampleCompareAlleleRefAbs = outputDir + "/sample_compare/allele.ref.abs.tsv" + File? sampleCompareAlleleRel = outputDir + "/sample_compare/allele.rel.tsv" + File? sampleCompareGenotypeAbs = outputDir + "/sample_compare/genotype.abs.tsv" + File? sampleCompareGenotypeNonRefAbs = outputDir + + "/sample_compare/genotype.non_ref.abs.tsv" + File? sampleCompareGenotypeRefAbs = outputDir + "/sample_compare/genotype.ref.abs.tsv" + File? sampleCompareGenotypeRel = outputDir + "/sample_compare/genotype.rel.tsv" } runtime {