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

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

diff --git a/tools/gridss-callVariants.nix b/tools/gridss-callVariants.nix
index 416eb7c..dc978fa 100644
--- a/tools/gridss-callVariants.nix
+++ b/tools/gridss-callVariants.nix
@@ -4,6 +4,7 @@
 , bwaIndexAttrs ? {}
 , faidxAttrs ? {}
 , flags ? null
+, config ? null
 }:
 
 with nixpkgs;
@@ -41,6 +42,7 @@ stdenv.mkDerivation rec {
       WORKER_THREADS=$NIX_BUILD_CORES \
 	    TMP_DIR=. \
 	    WORKING_DIR=. \
+      ${optionalString config ("CONFIGURATION_FILE=" + gridssConfig config)} \
 	    REFERENCE_SEQUENCE="ref.fa" \
       ${concatMapStringsSep " " (i: "INPUT=\"${i}\"") inputs} \
 	    OUTPUT="$out/gridss.vcf" \
-- 
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