pggb builds pangenome variation graphs from a set of input sequences. pggb.cwl is a port of pggb to the Common Workflow Language (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 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 is a CWL implementation that uses Guix 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. - 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, either version 3 of the License, or (at your option) any later version.