From 3c568bacd397a3ddcb203811f7fa5a1f8af760a3 Mon Sep 17 00:00:00 2001
From: l-d-s <distefano.l@wehi.edu.au>
Date: Thu, 15 Nov 2018 17:25:53 +1100
Subject: Fix up gridss config file.

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

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

diff --git a/tools/gridss-collectGridssMetrics.nix b/tools/gridss-collectGridssMetrics.nix
index 8f87b6f..3babab4 100644
--- a/tools/gridss-collectGridssMetrics.nix
+++ b/tools/gridss-collectGridssMetrics.nix
@@ -26,7 +26,7 @@ stdenv.mkDerivation rec {
     java -Xmx1G -cp ${bionix.gridss.jar} \
 			gridss.analysis.CollectGridssMetrics \
 			${optionalString sorted "ASSUME_SORTED=true"} \
-      ${optionalString (config != null) ("CONFIGURATION_FILE=" + gridssConfig config)} \
+      ${optionalString (config != null) ("CONFIGURATION_FILE=" + bionix.gridss.gridssConfig config)} \
 			I=input.bam \
 			O=$out \
 			THRESHOLD_COVERAGE=${toString thresholdCoverage}
-- 
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