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
This pull request:
ancient
to respect output files that already exist