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MPUSP / snakemake-assembly-postprocessing Public

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feat: add prokka and bakta for annotation#4

Merged

rabioinf merged 20 commits intomainMPUSP/snakemake-assembly-postprocessing:mainfrom

devMPUSP/snakemake-assembly-postprocessing:devCopy head branch name to clipboard

Dec 10, 2025

Conversation Commits20 (20)Checks Files changed

Merged

feat: add prokka and bakta for annotation#4
rabioinf merged 20 commits intomainfrom
dev

Commits

Commits on Dec 5, 2025

fix: remove option to define output dir in config.
rabioinf
committed
Merge branch 'main' into dev
rabioinf
committed
feat: added prokka for annotation
m-jahn
committed
fix: updated schema
m-jahn
committed
feat: added bakta for annotation
m-jahn
committed
fix: merge commit
m-jahn
committed
fix: use results as standard output dir
m-jahn
committed

Commits on Dec 8, 2025

feat: added quast, allow multiple annotation tools, allow local bakta db
m-jahn
committed
fix: use absolute input paths for pgap helpers
m-jahn
committed

Commits on Dec 9, 2025

fix: use correct input for quast reference, closes #7
m-jahn
committed
fix: update armdfinder db when local db is used. update bakta version.
rabioinf
committed
fix: pipe armfinder_update to log.
rabioinf
committed
fix: correct env names, use relative path for pgap fasta
m-jahn
committed

Commits on Dec 10, 2025

feat: added panaroo as a genome comparison tool, closes #6
m-jahn
committed
fix: validate locus tag for bakta annotation; closes #8
rabioinf
committed
fix: added option to skip pangenome analysis
m-jahn
committed
fix: update readmes
m-jahn
committed
fix: added missing dag.
rabioinf
committed
chore: define parameters in config readme.
rabioinf
committed
chore: update defaults in config readme
rabioinf
committed

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