From 99ee99c490cc109b78986181ee1be4ce1cd0c0ed Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Thu, 25 Oct 2018 08:02:20 +1100
Subject: Improve type safety of samtools-merge

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

(limited to 'test-tnpair.nix')

diff --git a/test-tnpair.nix b/test-tnpair.nix
index 7deaf3b..0f6a441 100644
--- a/test-tnpair.nix
+++ b/test-tnpair.nix
@@ -54,6 +54,7 @@ let
       ln -s ${tnpairResult.variants} $out/strelka
       mkdir $out/alignments
       ln -s ${gridss.callVariants {} (with tnpairResult.alignments; [tumour])} $out/gridss
+      ln -s ${samtools.merge {} [tnpairResult.alignments.tumour tnpairResult.alignments.normal]} $out/alignments/merged.bam
       ln -s ${samtools.view { outfmt = types.toCram; } (tnpairResult.alignments.tumour)} $out/alignments/${tnpair.tumour.name}.cram
       ln -s ${samtools.view { outfmt = types.toCram; } (tnpairResult.alignments.normal)} $out/alignments/${tnpair.normal.name}.cram
       ln -s ${flagstat tnpairResult.alignments.tumour} $out/alignments/${tnpair.tumour.name}.flagstat
-- 
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