From 4574deb8e1649eaf63df424585d11645c7cfa7dd Mon Sep 17 00:00:00 2001
From: l-d-s <l@sdf.org>
Date: Mon, 12 Nov 2018 16:54:30 +1100
Subject: Attempt to integrate config file into GRIDSS stage

---
 tools/gridss-extractSVReads.nix | 2 ++
 1 file changed, 2 insertions(+)

(limited to 'tools/gridss-extractSVReads.nix')

diff --git a/tools/gridss-extractSVReads.nix b/tools/gridss-extractSVReads.nix
index a10abf5..e3ed1cc 100644
--- a/tools/gridss-extractSVReads.nix
+++ b/tools/gridss-extractSVReads.nix
@@ -5,6 +5,7 @@
 , flags ? null
 , unmappedReads ? false
 , minClipLength ? 5
+, config ? null
 }:
 
 with nixpkgs;
@@ -35,6 +36,7 @@ stdenv.mkDerivation rec {
       METRICS_OUTPUT=$out/input.sv_metrics \
       INSERT_SIZE_METRICS=$out/input.insert_size_metrics \
       UNMAPPED_READS=${if unmappedReads then "true" else "false"} \
+      ${optionalString config ("CONFIGURATION_FILE=" + gridssConfig config)} \
       MIN_CLIP_LENGTH=${toString minClipLength}
   '';
 }
-- 
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