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diff --git a/README.md b/README.md new file mode 100644 index 0000000..b722356 --- /dev/null +++ b/README.md @@ -0,0 +1,36 @@ +[`pggb`](https://github.com/pangenome/pggb/) builds pangenome variation graphs from a set of input sequences. `pggb.cwl` is a port of `pggb` to the [Common Workflow Language](https://www.commonwl.org/) (CWL). + +# Features + +`pggb.cwl` offers: +- better parallelization, especially of the wfmash all-to-all alignment step and the various visualization steps +- more readable code +- reproducible +- portable across computing environments + +# How to use + +First, compile the [ccwl](https://ccwl.systemreboot.net/) sources to a CWL workflow. +``` +ccwl compile -o pggb.cwl pggb.scm +``` +Now, run the compiled CWL workflow using your preferred CWL implementation. For cwltool, the reference CWL implementation: +``` +cwltool pggb.cwl inputs.yaml +``` +[ravanan](https://forge.systemreboot.net/ravanan/) is a CWL implementation that uses [Guix](https://guix.gnu.org/) to provide robust reproducibility guarantees. To run `pggb.cwl` using ravanan: +``` +ravanan --guix-channels=channels.scm --store=store pggb.cwl inputs.yaml +``` +You may need to pass in more options based on the specifics of your computing environment. + +# Differences + +`pggb.cwl` deviates from `pggb` in the following: +- Number of haplotypes is always required. In contrast, this is optional in `pggb` if sequences follow the [PanSN-spec](https://github.com/pangenome/PanSN-spec). +- External mappers are not supported. +- `--vcf-spec` is not implemented. + +# License + +pggb.cwl is free software released under the terms of the [GNU General Public License](https://www.gnu.org/licenses/gpl.html), either version 3 of the License, or (at your option) any later version. |