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| author | l-d-s <distefano.l@wehi.edu.au> | 2019-05-21 10:33:13 +1000 |
|---|---|---|
| committer | GitHub <noreply@github.com> | 2019-05-21 10:33:13 +1000 |
| commit | 867e68554307d45e102ba3267f5f469d02fc6a86 (patch) | |
| tree | 02c427934db983d29fd94a12eb004c311de72c84 | |
| parent | 4f41ccacd0370653d406bc623ca14f399b31e7d8 (diff) | |
Update README.md
| -rw-r--r-- | README.md | 4 |
1 files changed, 2 insertions, 2 deletions
@@ -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). |