large refactor

- use bionix.pkgs instead of nixpkgs
- replace stdenv.mkDerivation with stage

1 files changed, 3 insertions, 4 deletions

diff --git a/tools/gridss.nix b/tools/gridss.nix
index 5bb9484..e8dd304 100644
--- a/tools/gridss.nix
+++ b/tools/gridss.nix
@@ -1,14 +1,13 @@
-{bionix, nixpkgs}:
+{bionix}:
 
-with nixpkgs;
 with bionix;
 
 rec {
-  jar = fetchurl {
+  jar = pkgs.fetchurl {
     url = "https://github.com/PapenfussLab/gridss/releases/download/v2.0.0/gridss-2.0.0-gridss-jar-with-dependencies.jar";
     sha256 = "01srl3qvv060whqg1y1fpxjc5cwga5wscs1bmf1v3z87dignra7k";
   };
-  gridssConfig = callBionixE ./gridss-configFile.nix {};
+  genConfig = callBionixE ./gridss-configFile.nix {};
   callVariants = callBionixE ./gridss-callVariants.nix;
   computeSamTags = callBionixE ./gridss-computeSamTags.nix;
   softClipsToSplitReads = callBionixE ./gridss-softClipsToSplitReads.nix;