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@@ -26,8 +26,8 @@ BioNix will download or build all of the necessary software and create a soft li
Next, check out the code:
- The pipeline itself is specified in `examples/call.nix` and `examples/default.nix`.
-- The BioNix wrapper for `platypus` is in `tools/platypus-callVariants.nix`.
-- The software package for `platypus` can be found in [nixpkgs](https://github.com/NixOS/nixpkgs/blob/master/pkgs/applications/science/biology/platypus/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).
BioNix pipelines can be easily wrapped in shell scripts: see `examples/ex-tnpair/tnpair` for an example script that accepts a reference fasta, along with paired normal and tumor fastq files, and performs alignment, preprocessing, and variant calling with [`strelka`](https://github.com/Illumina/strelka).