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Add cau-workflow, the skill that routes between the other skills - #12
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Six sibling skills sat at the same level with no entry point, so a user who names a goal rather than a step had nothing to match against. The order of the four commands is a data dependency, and the join keys between their tables are the one thing no per-module skill states, because each correctly describes only itself. It covers no module of its own, so COVERAGE maps it to an empty tuple. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
The skill was written before the tables were renamed, and it lives only on this branch, so the rename could not reach it and the rebase had nothing to conflict with: it would have shipped guides_alignment_metadata.tsv against a tree that no longer writes it. Every argument line in it now matches a per-step skill verbatim. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
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Six sibling skills sat at the same level with no entry point. A user who
names a step gets the right skill today; a user who names a goal -- "I have a
guide library and want to submit it to IGVF" -- has nothing to match against,
because each per-module skill correctly describes only itself.
cau-workflowholds what none of them can: the order of the four commands,which is a data dependency rather than a convention, what flows between them,
and the keys their tables join on. A guide with two sites has two rows, so
guide_idalone is ambiguous and the join needs all five columns -- the kindof thing a user cannot be expected to know.
It also carries the "ask, don't guess" list: the assembly has to match
between reference and annotation, whether the library has an added 5' G, and
that an incomplete element BED inflates
safe_targetingsilently rather thanfailing.
It covers no module of its own, so
COVERAGEmaps it to an empty tuple, witha comment saying that is how a skill declares it routes rather than wraps.
Rebased onto the table rename from #11, and every argument line in it now
matches a per-step skill verbatim.
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