Use DRAM 1.5.0 and trnascan-se 2.0.11

Use hmmer version 3.3.2 with checkv

Use Python 3.12.8 with metaSpades

Define exact package versions in conda environments

Update Dockerfile with full setup included

Lock Python at version 3.12 in conda env for metaSpades

Fix quality threshold customization

Update .gitignore

update to venv location specification

README cosmetics

Remove inspect command and Shiny app - not updated

Clean up README, clarify some options

Avoid termination when instrain profile is not compressed

Enable decompression of instrain output if necessary

Fixed error in function import