Updating nf-core/bactmap Pipeline

[avantonder]

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:

• Updating to current nf-core template: current template is very out of date.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

We welcome contributors of all experience levels.

Goals

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