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Diffstat (limited to 'README.md')
| -rw-r--r-- | README.md | 10 |
1 files changed, 5 insertions, 5 deletions
@@ -28,7 +28,7 @@ directory and viewing `result/OEBPS/index.html`. Several examples are available in `./examples/`. The main example is presented in `./examples/default.nix` and can be built using `nix build` in `./examples/`. This sample pipeline performs variant calling using -[`platypus`](https://github.com/andyrimmer/Platypus), alignment using +[`octopus`](https://github.com/luntergroup/octopus), alignment using [`bwa mem`](https://github.com/lh3/bwa), and preprocessing using [`samtools`](http://www.htslib.org/). @@ -37,10 +37,10 @@ this pipeline and the other examples. - The pipeline itself is specified in `examples/call.nix` and `examples/default.nix`. -- The BioNix wrapper to run `platypus` is in - `tools/platypus-callVariants.nix`. -- The Nix expression for the `platypus` software itself can be found in - [nixpkgs](https://github.com/NixOS/nixpkgs/blob/master/pkgs/applications/science/biology/platypus/default.nix). +- The BioNix wrapper to run `octopus` is in + `tools/octopus-call.nix`. +- The Nix expression for the `octopus` software itself can be found in + [nixpkgs](https://github.com/NixOS/nixpkgs/blob/master/pkgs/by-name/oc/octopus-caller/package.nix). ## Constructing workflows |