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authorArun Isaac2026-03-23 23:14:34 +0000
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+[`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.