Updating nf-core/bactmap Pipeline

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This project aims to update and optimize the nf-core/bactmap pipeline as the last update to the pipeline was June 2021.

We will focus on:

1. Update to current nf-core template: current template is very out of date.
2. Update modules to current versions: many of the tools are old versions.
3. Potentially incorporating long read mapping as an option: would improve pipeline if ONT and PacBio could also be mapped
4. Update documentation: update documentation to reflect updates and improvements to pipeline
5. Identifying additional improvements: as discussed in GitHub issues.

We welcome contributors of all experience levels.

Goals

1. Update pipeline to current nf-core template and standards (intermediate experience).
2. Update all modules (beginner experience)
3. Add support for long-read mapping (intermediate experience).
4. Update documentation (beginner experience)
5. Explore additional enhancements based on community discussions (intermediate experience).