From 076d8e5296dd390c7b2eed9c6cad80a8c595606a Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Mon, 20 Aug 2018 16:02:53 +0200
Subject: [PATCH] add output files
---
biopet.wdl | 50 +++++++++++++++++++++++++++++++++++++++++++++++++-
1 file changed, 49 insertions(+), 1 deletion(-)
diff --git a/biopet.wdl b/biopet.wdl
index 6336e48..eaf6664 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 {
--
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