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Ship 11 core Nextflow skills and four opt-in packs - #2
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Fold bounded conversion, module, installation and packaging helpers into surviving core skills. Move infrastructure, nf-core analysis/maintenance, plugin authoring and provenance procedures into four optional plugins. Legacy extension migration becomes a plugin-development playbook. Generate all five packages from declarative plans on every import. Keep original resource identity and hashes, ship pack-local provenance, and replace cross-cache file links with namespaced skill handoffs. Optional packs do not silently install core or register another MCP server. Retain core resume/debugging evidence, nf-core-safe editing and explicit publication authority. Expose missing-pack names in core discovery so users receive actionable installation help instead of guessed names. Validate exact inventories, links, versions, full resources, provenance and isolated installation combinations. Prepare version 0.3.0; no release or tag is performed. BREAKING CHANGE: default discovery is reduced from 28 to 11 skills. Specialist entrypoints require explicit installation of optional packs.
Add nine bounded Claude smoke cases and an inspected synthetic conversion execution harness. Keep scope, missing-pack identity, native module advice, output correctness and explicit publication authority as observable checks. Do not require Skill dispatch for a trivial conversion; require working artifacts and an honest verification handoff instead. Compare Snakemake and Nextflow outputs against independent known and holdout values, then prove explicitly selected cached resume. Record the actual runtime release and isolate fixture config from user settings. Document passing installation/routing/execution evidence, synthetic import replay limitations, absent production checks, the unchanged Bash sandbox security refusal and the unavailable edge-runtime plugin dependency. Leave raw account/machine-local reports out of version control.
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odagayev
approved these changes
Oct 9, 2026
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Summary
Follow-up to merged #1: reduce 28 default entrypoints → 11, without deleting specialist knowledge. This implements the approved core/pack plan.
nextflow-platform,nextflow-nf-core,nextflow-plugins,nextflow-provenance. Fold legacy plugin migration into plugin development. All packs enabled: 19 skills, not 11 total capabilities.Verification
See the evidence and limitations.
Limits / review notes
Bash-enabled model evaluation was refused by the SSH-store sandbox safety check; it was not bypassed. Native smoke tests used non-Bash tools, with direct execution of inspected synthetic fixtures separately.
The installed 26.06-edge launcher could not resolve
nf-seqera@1.0.0; this is not execution proof for that edge runtime. No production Platform operations, real registry module execution, private-upstream replay or general scientific-equivalence claim is made.Breaking discovery change: specialist entrypoints now require their named optional pack. README documents installation and human/agent handoffs. Review and merge are deliberately left to the maintainers.