From 7231886ee52379de001ae830ed76a09be556ac57 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Thu, 20 Jun 2019 08:22:32 +1000
Subject: Add CNVkit test

---
 test-tnpair.nix | 7 +++++++
 1 file changed, 7 insertions(+)

(limited to 'test-tnpair.nix')

diff --git a/test-tnpair.nix b/test-tnpair.nix
index 4d6a794..0e13338 100644
--- a/test-tnpair.nix
+++ b/test-tnpair.nix
@@ -47,8 +47,15 @@ let
 
   tnpairResult = processPair tnpair;
 
+  cnvkitResults = rec {
+    cnvs = cnvkit.callCNV {} (with tnpairResult.alignments; { normals = [ normal ]; tumours = [ tumour ];});
+    plot = cnvkit.scatterPlot {} cnvs;
+  };
+
   testNaming = linkDrv [
     (ln (facets.callCNV {} {vcf = tnpairResult.platypusVars; bams = with tnpairResult.alignments; [ normal tumour ];}) "facets")
+    (ln cnvkitResults.cnvs "cnvkit")
+    (ln cnvkitResults.plot "cnvkit.pdf")
     (ln tnpairResult.variants "strelka")
     (ln tnpairResult.glvariants "strelka-gl")
     (ln tnpairResult.variants.indels "strelka.indels.vcf")
-- 
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