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diff --git a/examples/README.md b/examples/README.md new file mode 100644 index 0000000..66ed04f --- /dev/null +++ b/examples/README.md @@ -0,0 +1,30 @@ +# Bionix examples + +This directory has a few example workflows in bionix along with example data. +A basic workflow is defined in `call.nix`, and an example of applying it to the +sample data is in `default.nix`. To build the `default.nix` workflow, run +``` +nix build +``` +from this directory. + +## NextFlow and WDL translations + +The directories `ex-nextflow` and `ex-wdl` contain translated examples from the +NextFlow and WDL documentation respectively. + +The NextFlow translated example does not come with example data. It can be built with +``` +nix build -f nextflow-example1.nix --arg input /path/to/sample.fa +``` + +The WDL example requires no extra data and can be built with +``` +nix build -f wdl-scatter-gather.nix +``` + +## Example script wrapper + +`ex-tnpair` contains a shell script based example on how a front-end for users +might be constructed. It is a simple tumour-normal somatic calling workflow +using the Strelka variant caller. |