This release provides a major rewrite of the Snakefile to convert fastq_dump and trim into traditional snakemake rules. This allows snakemake to be 100% deterministic in calculating what rules need to be executed and removes runtime <TBD> output files. Additionally, all rules will now automatically rerun with increased memory and time limits if they fail.
By removing checkpoints, the number of rules executed has been reduced by ~25%. Previously, some rules would perform the same action twice to create forward and reverse reads. Now, rules have been split into separate *_paired and *_single rules to prevent this. While this slightly increases code duplication, it provides clearer visibility into the information flow
Additionally, the documentation has been simplified to a single README.md file rather than GitHub Pages. This allows easier transport between various git backends, such as GitHub, GitLab, etc.