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Updated Parameters (markdown)
edit location of config files (bin/config_files), update commands, edit required input files tables
updates to run commands, add user-provided annotations cmd example under Case 2
--virus is now --species virus
update to new submission config file
update new submission config file name
Updated Profile Options & Input Files (markdown)
Updated Outputs (markdown)
Updated Quick Start (markdown)
adds bakta details
Updated Installation (markdown)
Updated Home (markdown)
Updated Get in Touch (markdown)
Updated CDC User Guide (markdown)
Destroyed Submission Guide (markdown)
Destroyed Overview‐2 (markdown)
Destroyed Running the Pipeline (markdown)