[x] copy over required nextflow files (still need to figure out how I want to do organization...a Snakemake folder & a nextflow folder? everything at root?) (#24)
[x] remove eggnog rules and replace with kofamscan in both snakemake and nextflow (#25)
~(maybe) refactor snakemake file to take command line arguments for databases~
~(maybe) include an optional download snakefile/nextflow workflow to download all of the required databases (two files for clustered nr blast database, ~two eggnog database files~ kofamscan files, an hmm profile file)~
[x] update workflow:
[x] improve labels for HGT candidates (#32)
[x] improve logic for labeling contamination (#32)
[x] check and make sure donor diversity index is correct (#27)
[x] add a aggregate/consensus hit score metric (#28)
[x] implement at least one subkingdom BLAST method (#34)
[x] rename tool/repo from 2023-rehgt to prehgt (or preHGT) (#35)
[x] documentation PR (#36)
[x] update README with pub doi
[x] dockerize nextflow (#42)
[x] make sure nextflow pipeline runs on tower (#42)
[x] replace docker container for ncbi-genome-download and conda version (#43)
PR roadmap: