Use Snakemake Best Practices

[tsackton]

Although we are getting closer to Snakemake best practices, there are still a number of things that we need to do to be fully in compliance with Snakemake best practice documentation for distribution and reproducibility.

The outstanding issues that I see are:

• [x] Merge all Snakefiles into a single Snakefile for the entire workflow
• [x] Move config files to a config subdir and update code to find them in the right place.
• [x] Set output directories per Snakemake best practices. Note that because of the complexities of the output we can't just dump everything in results, but we probably should get as close as possible.
  • Set the top level directory for output to results
  • Set the top level directory for resources downloaded to resource
• [x] Add additional files requested by WorkflowHub
  • Code of Conduct
  • Contribution instructions
  • Workflow rule graph
  • Workflow documentation
  • Config documentation in the form of a config.md. This should include guidance for the low coverage parameters and the interval creation parameters.
  • Add a YAML file .snakemake-workflow-catalog.yml in the root directory which displays usage instructions. See description here.
• [x] Add testing. Note this is a separate issue, #12
• [x] Add license, #11

If there are other needed tasks, add to this issue. This issue is the main focus of the dev branch right now. Once it is resolved, we'll merge dev into main.

If any of these tasks seem complex enough that they need more discussion we can convert them to their own issues.

[tsackton]

First three tasks closed by #19

[tsackton]

Testing also closed by #19 for now

[tsackton]

License closed by #25 and moving Workflowhub setup to separate issue to deal with later.