Updating the README and templates

[erinyoung]

UPDATE : THIS PR IS READY TO REVIEW!!!

It's always good to go through the documentation of a repo every once and awhile. Most things are not changed, but I do have some suggestions.

[erinyoung]

And... these files trigger the github actions workflow, so I need to change the file paths.

[kapsakcj]

OK, I'm happy with the way this PR is at this point, but another set of eyes on the rendered markdown & dockerfile templates would be good.

I made some small edits to your changes for clarity & cleaned up some of the links & markdown formatting. I use VSCode to edit Markdown and now I get all kinds of warnings like how bullet points need to be surrounded above and below by empty lines

I also added a template dockerfile with micromamba as the base image

obviously the github actions has failed and I'm fine to override and merge the PR

Apologies that it took me this long to review and do my part!

[kapsakcj]

also forgot to say that the mermaid diagram is awesome, thanks for adding that! Super helpful visual

[erinyoung]

This PR is now ready to review!!!

This is going to fail the GA tests because the Dockerfile template isn't functional - so ignore the GA tests.

This PR is to update and double check the documentation of the StaPH-B/docker-builds repo. This is just to ensure the language and examples are in harmony with current recommended practices.

In the dockerfile-template directory there are three dockerfiles to use for examples:

• Dockerfile (which causes GA to crash)
• Dockerfile_builder - which shows adding an additional stage prior to 'app'
• Dockerfile_mamba - which shows using mamba to install something - thank you @kapsakcj !!!!
• README.md - as a template for a tool-specific readme

In the docker directory there are several files that are used to help those creating Dockerfiles. I only have suggested edits for a subset of docs.

• contribute.md
• get_containers.md * no edits
• make_containers.md * no edits
• run_containers.md
• useful_links.md * no edits

[erinyoung]

I added in a python-centric Dockerfile template for those tools that are installed via pip.

I am not going to add any additional files to his PR because I would like this PR merged before the docker training in October.

[kapsakcj]

Everything looks good, thanks for adding the additional python dockerfile template!