pipeio_rule_list + pipeio_rule_stub — Snakemake rule introspection and generation¶

Goal¶

(promoted from note)

(see source note)

Implement two new pipeio MCP tools:

pipeio_rule_list(pipe, flow) — parse a flow's Snakefile and return structured rule metadata: name, input/output bids patterns, script path, mod membership.
pipeio_rule_stub(pipe, flow, rule_name, inputs, outputs, params, script) — generate a syntactically correct Snakemake rule stub from a contract spec.

Reference captures: 20260325-210858-8941fc, 20260325-210906-92b29c.

Failed in 1800.1s (1 steps, model: opus)

Session: n/a Result note: /storage2/arash/worklog/workflow/captures/20260326-003823-1ae167/note.md

(no output)