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 pangenome/pggb#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]

Markdown linting is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks.
To fix this CI test, please run:

• Install markdownlint-cli
  • On Mac: brew install markdownlint-cli
  • Everything else: Install npm then install markdownlint-cli (npm install -g markdownlint-cli)
• Fix the markdown errors
  • Automatically: markdownlint . --config .github/markdownlint.yml --fix
  • Manually resolve anything left from markdownlint . --config .github/markdownlint.yml

Once you push these changes the test should pass, and you can hide this comment 👍

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Thanks again for your contribution!