v1.3.0

1.3.0 (2026-04-22)

Features

• add RGI for AMR detection (ac2566b)
• added RGI for AMR detection + bug fix (daf2195)

Bug Fixes

• add missing targets to run annotation when tool is specified (7450cce)
• need separate dirs for results because intermediate files do have non-unique names (e028175)
• snakefmt error (45e992c)

v1.2.0

1.2.0 (2026-04-05)

Features

• fix panaroo bug, added fastANI rule, harmonized multi-threading (5d6c810)
• update github CI workflows and config options (df6d610)

Bug Fixes

• adjust threads of prokka run (6f3e4c2)
• introduced general reference parameter in config file. refactored some qc rules. (328c40a)
• new snakefmt directive order (50f20da)
• reference input (7778d93)
• schema and README update (20a6fc9)
• typos (e72502d)
• update CI workflows (fdf4adc)

v1.1.0

1.1.0 (2025-12-10)

Features

• add prokka and bakta for annotation (807df3a)
• added bakta for annotation (4a88b34)
• added panaroo as a genome comparison tool, closes #6 (20e70b2)
• added prokka for annotation (1579c87)
• added quast, allow multiple annotation tools, allow local bakta db (7d9f6cd)

Bug Fixes

• added missing dag. (b1d0d34)
• added option to skip pangenome analysis (0e829f6)
• correct env names, use relative path for pgap fasta (938ac49)
• merge commit (d4cc6c5)
• pipe armfinder_update to log. (a85d20b)
• remove option to define output dir in config. (0454259)
• update armdfinder db when local db is used. update bakta version. (db385f0)
• update readmes (a4a147a)
• updated schema (7e9dfc0)
• use absolute input paths for pgap helpers (f4db893)
• use correct input for quast reference, closes #7 (84c07a6)
• use results as standard output dir (1b6695f)
• validate locus tag for bakta annotation; closes #8 (6048f72)

v1.0.0

1.0.0 (2025-12-03)

Features

• add pgap annotation; closes #2 (2f5d6c8)

Bug Fixes

• snakefmt issue (6eb303b)
• yaml formatting issue (5125d55)