Add configurable DESeq2 design formula - #20
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DESeq2 was hard-coded to `~ condition`, so within-subject (paired) designs and batch-corrected designs weren't expressible. The design formula is now set in the config YAML via `design_formula` and defaults to `~ condition`, so existing configs are unaffected. Validation happens twice: the Snakefile checks the formula against the design CSV header when the workflow is parsed, so a formula naming a column that doesn't exist (e.g. `~ subject + condition` with no `subject` column) fails before any step runs rather than hours later; deseq2.R repeats the check so the script is safe to run standalone. The formula must also include `condition`, since contrasts are tested on its coefficients. Every variable in the formula is coerced to a factor, so a numeric subject or batch ID is read as a group label rather than a continuous covariate, and a blank value or a single-level variable is reported by name instead of surfacing as a rank-deficient model matrix. The formula is a restricted character set (variable names and R formula operators only), which also keeps it safe to interpolate into the rules' shell commands. Also threads the formula into the generated methods paragraph, which previously claimed a `~condition` design unconditionally. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01VcESmVRNhqwhuw8psAzvkr
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DESeq2 was hard-coded to
~ condition. The design formula is now set in the config YAML viadesign_formulaand defaults to~ condition.