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

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

diff --git a/tools/gridss-collectGridssMetrics.nix b/tools/gridss-collectGridssMetrics.nix
index bb8d2e9..86732b8 100644
--- a/tools/gridss-collectGridssMetrics.nix
+++ b/tools/gridss-collectGridssMetrics.nix
@@ -2,6 +2,7 @@
 , nixpkgs
 , thresholdCoverage ? 10000
 , flags ? null
+, config ? null
 }:
 
 with nixpkgs;
@@ -25,6 +26,7 @@ stdenv.mkDerivation rec {
     java -Xmx1G -cp ${bionix.gridss.jar} \
 			gridss.analysis.CollectGridssMetrics \
 			${optionalString sorted "ASSUME_SORTED=true"} \
+      ${optionalString config ("CONFIGURATION_FILE=" + gridssConfig config)} \
 			I=input.bam \
 			O=$out \
 			THRESHOLD_COVERAGE=${toString thresholdCoverage}
-- 
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