Moving back into the old house!

This github repo (viral-ngs) has been largely defunct since 2020 when it was broken up into more modularized github repos to maintain separate docker images per tool family (see viral-core, viral-assemble, viral-phylo, viral-classify), with each of those separate repos defining their own smaller docker image. Containerized pipelines were moved to viral-pipelines. From 2020-2025, viral-ngs code was maintained in those repositories, with version release tags in the v2.x.x range.

This release re-merges the component docker images back into this monolithic code repo, viral-ngs, with version release tags in the 3.x.x range. In particular, it accomplishes the following:

1. Re-arranges all python code into a pip-installable package
2. Keeps all non-python dependencies defined via conda
3. Maintains modularized (smaller) docker container builds which are more optimal for cloud work. But maintained from a single github repo instead of several. We now add a mega-everything docker image as an option (more ideal for on prem), and we also add multi-arch (arm and x86) docker builds. Different "flavors" of docker image are now also distributed in a single docker repo (quay.io/broadinstitute/viral-ngs) instead of several docker repos--this style is more similar to things like the python or ubuntu docker repos that distribute not just versioned tags, but variations within each version.
4. Optimizes the github actions CI for end to end speed, parallelizing several steps, using native arch runners, sometimes skipping tests where warranted, and optimizing build layer caching. One of the big motivators was to significantly shorten the development cycle as changes need to be made.
5. Updates all the CI machinery to use modern, best practice GH Actions off the shelf (instead of custom invented build scripts ported from Travis).
6. Drops some really old / deprecated tools not well maintained.

Containerized pipelines remain in a separate repo -- this repo encapsulates all our CLI scripts and their dependencies.

Full Changelog: https://github.com/broadinstitute/viral-ngs/compare/v1.25.0...3.0.0