refactor pipeline to remove charcoal decontamination steps, and other cleanup

[taylorreiter]

This pull request:

• removes rules associated with running charcoal, a tool that decontaminates genomes. I had this code included because I was going to decontaminate genomes that go into the pangenomes on the fly, but I have since invested time in decontaminating all of the genomes in the GTDB database, so this no longer needs to take place in this snakefile. Instead, the snakefile downloads the decontaminated genomes and starts from there.
• updates to a new version of GTDB (from rs202 to rs207)
• adds metadata for all bacterial and archaeal RNA seq datasets on the SRA (as well as the code used to generate that metadata)
• adds code to make running on hpc smoother/more efficient, including:
  • adding time parameters for each job that can be used by the slurm cluster for submission
  • removes tmpdir, which was specific to an old cluster I used to use
  • using ancient to respect output files that already exist
  • adding a new folder for the benchmarks to better organize output files
  • adding a .gitignore file
• adds a new database to taxonomic classification; the database contains eukaryotic RNA from common eukaryote genomes, which will enable identification of reads that map to e.g. mouse and other common eukaryotic orgs that might be contaminants
• removes some old comments, and places new TODOs.

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[ben-heil]

Sorry for the slow review, I have no idea how I missed this PR on Thursday and Friday