From df004c05e563a3d6e574f9b14c0939f9cd15d802 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Mon, 14 Jan 2019 09:47:18 +1100
Subject: cnvkit: fix annotation bug

---
 tools/cnvkit-batch.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'tools')

diff --git a/tools/cnvkit-batch.nix b/tools/cnvkit-batch.nix
index 67eaac3..6fb97a4 100644
--- a/tools/cnvkit-batch.nix
+++ b/tools/cnvkit-batch.nix
@@ -28,7 +28,7 @@ stage {
     ln -s ${samtools.faidx indexAttrs ref} ref.fa.fai
     cnvkit.py batch ${concatStringsSep " " tumours} \
       ${optionalString (normals != []) ("-n " + concatStringsSep " " normals)} \
-      ${optionalString (annotations != null) annotations} \
+      ${optionalString (annotations != null) "--annotate ${annotations}"} \
       ${if targets != null then "--targets ${targets}" else "-m wgs"} \
       -f ref.fa \
       -p $NIX_BUILD_CORES \
-- 
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