Refactor to use bionix tree directly

1 files changed, 14 insertions, 11 deletions

diff --git a/default.nix b/default.nix
index 10d2249..9f96a9d 100644
--- a/default.nix
+++ b/default.nix
@@ -2,18 +2,21 @@
 
 let
   bionix = nixpkgs.lib.makeExtensible (self:
-    let callBionix = file: import file { bionix = self; nixpkgs = nixpkgs; };
-    in with self; {
-      bwa = callBionix ./tools/bwa.nix;
-      crumble = callBionix ./tools/crumble.nix;
-      fastqc = callBionix ./tools/fastqc.nix;
-      gridss = callBionix ./tools/gridss.nix;
-      mosdepth = callBionix ./tools/mosdepth.nix;
-      platypus = callBionix ./tools/platypus.nix;
-      samtools = callBionix ./tools/samtools.nix;
-      strelka = callBionix ./tools/strelka.nix;
+  let callBionix = file: attrs: import file ({ bionix = self; nixpkgs = nixpkgs; } // attrs);
+  in with self; {
+      callBionix = callBionix;
+      id = x: x;
+
+      bwa = callBionix ./tools/bwa.nix {};
+      crumble = callBionix ./tools/crumble.nix {};
+      fastqc = callBionix ./tools/fastqc.nix {};
+      gridss = callBionix ./tools/gridss.nix {};
+      mosdepth = callBionix ./tools/mosdepth.nix {};
+      platypus = callBionix ./tools/platypus.nix {};
+      samtools = callBionix ./tools/samtools.nix {};
+      strelka = callBionix ./tools/strelka.nix {};
 
       qsub = nixpkgs.callPackage ./lib/qsub.nix {};
-      ref = callBionix ./lib/references.nix;
+      ref = callBionix ./lib/references.nix {};
   });
 in bionix