25 feature make metadata json path optional analogous to reference flag#26
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marcoreverenna merged 5 commits intoApr 6, 2026
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When metadata is absent the pipeline treats all peptides as a single pool, skips protease splitting, chain filtering, and contaminant removal. All existing behaviour is preserved when metadata is provided.
Documents the optional-flag gating pattern, CSV input assumptions in minimal mode, and the canonical reference for future contributors.
mmseqs2 and clustalo are C binaries not installable via pip/uv; conda (bioconda channel) is the supported environment manager.
Black and isort were left over from before the migration to ruff. Ruff formatter replaces both; removing them eliminates the formatting conflict that was failing the CI.
marcoreverenna
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25-feature-make---metadata-json-path-optional-analogous-to---reference-flag
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