[jonas-fuchs]

Added CHARMD database and workflows for autofetching!

[github-actions]

respro build QC — charmd

respro build QC

Source: charmd
Status: ⚠️ respro init succeeded with 16 skipped rule(s).
Exit code: 0
Imported single rules: 2660
Imported formula rules: 0
Skipped — reference AA mismatch: 16
Skipped — feature not in GenBank: 0
Skipped — formula member missing: 0

Raw respro init output

[2026-09-17 07:46:11] INFO     respro.db.features — Loaded GenBank data: references +1 (reused 0), features +203 (reused 0)                                     
                      INFO     respro.db.rules_import — Detected 1-based amino acid positions in rules TSV                                                      
                      WARNING  respro.db._rules_features — 16 position(s) with rules have reference AA mismatches and will be skipped:                          
                                 X17403.1 feature 'HCMVUL27' pos 218 (1-based): rule says 'C', feature sequence has 'L' — rule will be skipped                  
                                 X17403.1 feature 'HCMVUL54' pos 267 (1-based): rule says 'N', feature sequence has 'G' — rule will be skipped                  
                                 X17403.1 feature 'HCMVUL54' pos 271 (1-based): rule says 'D', feature sequence has 'T' — rule will be skipped                  
                                 X17403.1 feature 'HCMVUL54' pos 284 (1-based): rule says 'D', feature sequence has 'V' — rule will be skipped                  
                                 X17403.1 feature 'HCMVUL54' pos 651 (1-based): rule says 'S', feature sequence has 'Q' — rule will be skipped                  
                                 X17403.1 feature 'HCMVUL54' pos 722 (1-based): rule says 'I', feature sequence has 'Y' — rule will be skipped                  
                                 X17403.1 feature 'HCMVUL54' pos 954 (1-based): rule says 'R', feature sequence has 'F' — rule will be skipped                  
                                 X17403.1 feature 'HCMVUL54' pos 998 (1-based): rule says 'N', feature sequence has 'V' — rule will be skipped                  
                                 X17403.1 feature 'HCMVUL54' pos 1129 (1-based): rule says 'P', feature sequence has 'D' — rule will be skipped                 
                                 X17403.1 feature 'HCMVUL54' pos 1156 (1-based): rule says 'L', feature sequence has 'K' — rule will be skipped                 
                                 X17403.1 feature 'HCMVUL54' pos 1162 (1-based): rule says 'S', feature sequence has 'P' — rule will be skipped                 
                                 X17403.1 feature 'HCMVUL56' pos 396 (1-based): rule says 'R', feature sequence has 'E' — rule will be skipped                  
                                 X17403.1 feature 'HCMVUL89' pos 663 (1-based): rule says 'A', feature sequence has 'C' — rule will be skipped                  
                                 X17403.1 feature 'HCMVUL97' pos 356 (1-based): rule says 'K', feature sequence has 'V' — rule will be skipped                  
                                 X17403.1 feature 'HCMVUL97' pos 429 (1-based): rule says 'T', feature sequence has 'I' — rule will be skipped                  
                                 X17403.1 feature 'HCMVUL97' pos 669 (1-based): rule says 'A', feature sequence has 'V' — rule will be skipped                  
                      INFO     respro.db.rules_import — Loaded 2660 single resistance rule(s)                                                                   
                      INFO     respro.cli.init — Project initialized: charmd (/tmp/respro_qc_charmd/charmd.db)                                                  
✓ Project initialised: /tmp/respro_qc_charmd/charmd.db

Failed builds must be fixed before merge.

[jonas-fuchs]

@vtilloy This PR add CHARMD. The database builds ;). As soon as this PR is merged, you can download charmd from the CLI directly. Maybe noteworthy. I run monthly workers that check for database updates. So as soon as you update on your side, the database will be updated on my end automatically (i have to check then the PR if everything worked as expected).

have a look at respro build QC in the comment. This reports if rules cannot be imported by respro. Cheers and thanks a lot!