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{nixpkgs ? import <nixpkgs> {}}:
let
bionix = nixpkgs.lib.makeExtensible (self:
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 {};
qsubAttr = qsubAttrs: f: attrs: i: qsub qsubAttrs (f attrs i);
qsubAttrs = attrs: nixpkgs.lib.mapAttrs (_: x: qsubAttr attrs x);
ref = callBionix ./lib/references.nix {};
def = f: defs: attrs: f (defs // attrs);
});
in bionix
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