v3.3.1 Cenote-Taker 3: Majestic Gull Attack

Changes from v3.3.0:

1. Added argument --max_dtr_assess. Users can enter a maximum contig length to evaluate DTRs (default 1000000). Practically, long DTR-containing contigs are probably bacterial chromosomes and should be evaluated for prophages and pruned. Since DTR-containing contigs do not get pruned, this was preventing some bacterial chromosome assemblies from getting pruning treatment. #6
2. Fixed hhpred_to_table.py gene_name variable parsing, which previously incorrectly used .strip() function.
3. Fixed location of MMSEQS_outdir in get_ct3_dbs command to avoid error.
4. For read-mapping, --seqtech now effects minimap2 settings

What's Changed

• Update4, to v3.3.1 by @mtisza1 in #7

Full Changelog: v3.3.0...v3.3.1