From 9a70a25d6b7771df7ca53fcc34d61f582296e384 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Thu, 10 Jan 2019 12:20:51 +1100
Subject: facets: init

---
 test-tnpair.nix | 2 ++
 1 file changed, 2 insertions(+)

(limited to 'test-tnpair.nix')

diff --git a/test-tnpair.nix b/test-tnpair.nix
index 0851a74..c531a83 100644
--- a/test-tnpair.nix
+++ b/test-tnpair.nix
@@ -35,11 +35,13 @@ let
   processPair = { tumour, normal }: rec {
     alignments = mapAttrs (_: x: markdup (sort (fixmate (alignWithRG x.name x.files)))) { inherit normal tumour; };
     variants = callVariants alignments;
+    platypusVars = platypus.call {} (builtins.attrValues alignments);
   };
 
   tnpairResult = processPair tnpair;
 
   testNaming = linkDrv [
+    (ln (facets.callCNV {} {vcf = tnpairResult.platypusVars; bams = with tnpairResult.alignments; [ normal tumour ];}) "facets")
     (ln tnpairResult.variants "strelka")
     (ln (bowtie.align {inherit ref;} tnpair.normal.files) "alignments/bowtie-normal.bam")
     (ln (gridss.callVariants {} (with tnpairResult.alignments; [normal tumour])) "gridss")
-- 
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