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-softClipsToSplitReads.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

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

diff --git a/tools/gridss-softClipsToSplitReads.nix b/tools/gridss-softClipsToSplitReads.nix
index 40fa216..47a3abd 100644
--- a/tools/gridss-softClipsToSplitReads.nix
+++ b/tools/gridss-softClipsToSplitReads.nix
@@ -34,7 +34,7 @@ stdenv.mkDerivation rec {
 			I=${input} \
 			O=$out \
       ${optionalString alignerStreaming "ALIGNER_STREAMING=true"} \
-      ${optionalString (config != null) ("CONFIGURATION_FILE=" + gridssConfig config)} \
+      ${optionalString (config != null) ("CONFIGURATION_FILE=" + bionix.gridss.gridssConfig config)} \
 			WORKER_THREADS=$NIX_BUILD_CORES
     '';
   passthru.filetype = filetype.bam { ref = ref; sorting = sort.none {}; };
-- 
cgit v1.2.3