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

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

diff --git a/tools/gridss-annotateVariants.nix b/tools/gridss-annotateVariants.nix
index 4f66c6c..33992c4 100644
--- a/tools/gridss-annotateVariants.nix
+++ b/tools/gridss-annotateVariants.nix
@@ -8,6 +8,7 @@
 , softClipsToSplitReadsAttrs ? {}
 , identifyVariantsAttrs ? {}
 , flags ? null
+, config ? null
 }:
 
 with nixpkgs;
@@ -64,6 +65,7 @@ stdenv.mkDerivation rec {
       INPUT_VCF=input.vcf \
       OUTPUT_VCF=out.vcf \
       WORKING_DIR=$TMPDIR/ \
+      ${optionalString config ("CONFIGURATION_FILE=" + gridssConfig config)} \
       TMP_DIR=$TMPDIR/
 
     mv out.vcf $out
-- 
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