fastify pangenome generation

[subwaystation]

nf-core/pangenome feature request

Hi there!

Describe the solution you'd like

Recently, there has been a major pggb update https://github.com/pangenome/pggb/pull/46. It improves performance significantly. And it changes a little bit the command line API.

• Update Dockerfile
• Update the input parameters
• Update processes to work with the adjusted input parameters
• Update file namings
• Update tests
• Add a new larger test making use of the yeast pangenome

[github-actions[bot]]

Markdown linting is failing

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• Install markdownlint-cli
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• Fix the markdown errors
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  • Manually resolve anything left from markdownlint . --config .github/markdownlint.yml

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