Catching up iss169 to main: New branch to include containerized packages

[wong-nw]

Changes

Created new branch from main rather than trying to pull main into the outdated iss169 branch, and merging the latest changes from branch iss169 into this updated branch. iss169 will be subsequently deleted.

Changes from main:

• Update to use Docker container to control package version (major version release)
• Caching controls
• Schema clean up

Changes from iss169:

• Added seurat_preprocess_init.Rmd to strictly incorporate functions from https://github.com/CCBR/SCOT
  • Will replace seurat_preprocess.Rmd
• Initiated seurat_preprocess_report.Rmd to provide a more polished QC report
• Updated config, schema, params, and nf files to follow inputs used in SCOT
• Updating workflow files to incorporate additional Rmd file

Issues

PR Checklist

(Strikethrough any points that are not applicable.)

• This comment contains a description of changes with justifications, with any relevant issues linked.
• Write tests using nf-test for any new features, bug fixes, or other code changes.
• Update docs if there are any API changes.
• If a new nextflow process is implemented, define the process container and stub.
• Update CHANGELOG.md with a short description of any user-facing changes and reference the PR number. Guidelines: https://keepachangelog.com/en/1.1.0/